2 // This file was generated by the Eclipse Implementation of JAXB, v2.3.3
3 // See https://eclipse-ee4j.github.io/jaxb-ri
4 // Any modifications to this file will be lost upon recompilation of the source schema.
5 // Generated on: 2023.11.01 at 07:03:09 PM GMT
8 package jalview.xml.binding.jalview;
10 import java.util.ArrayList;
11 import java.util.List;
12 import javax.xml.bind.annotation.XmlAccessType;
13 import javax.xml.bind.annotation.XmlAccessorType;
14 import javax.xml.bind.annotation.XmlAttribute;
15 import javax.xml.bind.annotation.XmlElement;
16 import javax.xml.bind.annotation.XmlID;
17 import javax.xml.bind.annotation.XmlSchemaType;
18 import javax.xml.bind.annotation.XmlType;
19 import javax.xml.bind.annotation.XmlValue;
20 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
21 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
22 import javax.xml.datatype.XMLGregorianCalendar;
25 * <p>Java class for JalviewModel complex type.
27 * <p>The following schema fragment specifies the expected content
28 * contained within this class.
30 * <pre> &lt;complexType name="JalviewModel"&gt;
31 * &lt;complexContent&gt; &lt;restriction
32 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
33 * &lt;sequence&gt; &lt;element name="creationDate"
34 * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; &lt;element
35 * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
36 * &lt;element name="vamsasModel"
37 * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
38 * &lt;sequence&gt; &lt;element name="JSeq" maxOccurs="unbounded"
39 * minOccurs="0"&gt; &lt;complexType&gt;
40 * &lt;complexContent&gt; &lt;restriction
41 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
42 * &lt;sequence&gt; &lt;element name="features"
43 * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
44 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
45 * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
46 * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
47 * &lt;element name="structureState" maxOccurs="unbounded"
48 * minOccurs="0"&gt; &lt;complexType&gt;
49 * &lt;simpleContent&gt; &lt;extension
50 * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
51 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
52 * &lt;attribute name="visible"
53 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
54 * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
55 * &lt;attribute name="alignwithAlignPanel"
56 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
57 * &lt;attribute name="colourwithAlignPanel"
58 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
59 * &lt;attribute name="colourByJmol"
60 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
61 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
62 * /&gt; &lt;/extension&gt; &lt;/simpleContent&gt;
63 * &lt;/complexType&gt; &lt;/element&gt;
64 * &lt;/sequence&gt; &lt;/extension&gt;
65 * &lt;/complexContent&gt; &lt;/complexType&gt;
66 * &lt;/element&gt; &lt;element name="hiddenSequences"
67 * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
68 * minOccurs="0"/&gt; &lt;element name="rnaViewer" maxOccurs="unbounded"
69 * minOccurs="0"&gt; &lt;complexType&gt;
70 * &lt;complexContent&gt; &lt;restriction
71 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
72 * &lt;sequence&gt; &lt;element name="secondaryStructure"
73 * maxOccurs="unbounded"&gt; &lt;complexType&gt;
74 * &lt;complexContent&gt; &lt;restriction
75 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
76 * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
77 * &lt;attribute name="annotationId" use="required"
78 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
79 * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
80 * &lt;attribute name="viewerState"
81 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
82 * &lt;/restriction&gt; &lt;/complexContent&gt;
83 * &lt;/complexType&gt; &lt;/element&gt;
84 * &lt;/sequence&gt; &lt;attGroup
85 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
86 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
87 * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
88 * &lt;attribute name="dividerLocation"
89 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
90 * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
91 * &lt;/restriction&gt; &lt;/complexContent&gt;
92 * &lt;/complexType&gt; &lt;/element&gt;
93 * &lt;/sequence&gt; &lt;attribute name="colour"
94 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
95 * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
96 * /&gt; &lt;attribute name="end" use="required"
97 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
98 * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
99 * /&gt; &lt;attribute name="hidden"
100 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
101 * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
102 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
103 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
104 * name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
105 * &lt;complexType&gt; &lt;complexContent&gt;
106 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
107 * &lt;sequence&gt; &lt;element name="seq"
108 * type="{http://www.w3.org/2001/XMLSchema}string"
109 * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
110 * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
111 * &lt;/sequence&gt; &lt;attribute name="start"
112 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
113 * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
114 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
115 * /&gt; &lt;attribute name="colour"
116 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
117 * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
118 * &lt;attribute name="pidThreshold"
119 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
120 * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
121 * &lt;attribute name="displayBoxes"
122 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
123 * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
124 * &lt;attribute name="colourText"
125 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
126 * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
127 * &lt;attribute name="textCol2"
128 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
129 * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
130 * /&gt; &lt;attribute name="showUnconserved"
131 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
132 * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
133 * default="true" /&gt; &lt;attribute name="showConsensusHistogram"
134 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
135 * &lt;attribute name="showSequenceLogo"
136 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
137 * &lt;attribute name="normaliseSequenceLogo"
138 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
139 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
140 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
141 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
142 * name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
143 * &lt;complexType&gt; &lt;complexContent&gt;
144 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
145 * &lt;sequence&gt; &lt;element name="AnnotationColours"
146 * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
147 * &lt;element name="hiddenColumns" maxOccurs="unbounded"
148 * minOccurs="0"&gt; &lt;complexType&gt;
149 * &lt;complexContent&gt; &lt;restriction
150 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
151 * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
152 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
153 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
154 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
155 * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
156 * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
157 * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
158 * &lt;attribute name="calcId" use="required"
159 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
160 * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
161 * default="false" /&gt; &lt;attribute name="autoUpdate" use="required"
162 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
163 * &lt;/extension&gt; &lt;/complexContent&gt;
164 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
165 * name="overview" minOccurs="0"&gt; &lt;complexType&gt;
166 * &lt;complexContent&gt; &lt;restriction
167 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
168 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
169 * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
170 * &lt;attribute name="residueColour"
171 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
172 * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
173 * &lt;attribute name="hiddenColour"
174 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
175 * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
176 * &lt;/restriction&gt; &lt;/complexContent&gt;
177 * &lt;/complexType&gt; &lt;/element&gt;
178 * &lt;/sequence&gt; &lt;attGroup
179 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
180 * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
181 * /&gt; &lt;attribute name="pidSelected"
182 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
183 * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
184 * &lt;attribute name="consThreshold"
185 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
186 * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
187 * &lt;attribute name="title"
188 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
189 * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
190 * &lt;attribute name="rightAlignIds"
191 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
192 * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
193 * &lt;attribute name="showColourText"
194 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
195 * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
196 * default="false" /&gt; &lt;attribute name="showBoxes"
197 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
198 * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
199 * /&gt; &lt;attribute name="renderGaps"
200 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
201 * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
202 * /&gt; &lt;attribute name="showNPfeatureTooltip"
203 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
204 * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
205 * /&gt; &lt;attribute name="followHighlight"
206 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
207 * &lt;attribute name="followSelection"
208 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
209 * &lt;attribute name="showAnnotation"
210 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
211 * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
212 * default="false" /&gt; &lt;attribute name="showGroupConservation"
213 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
214 * &lt;attribute name="showGroupConsensus"
215 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
216 * &lt;attribute name="showConsensusHistogram"
217 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
218 * &lt;attribute name="showSequenceLogo"
219 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
220 * &lt;attribute name="normaliseSequenceLogo"
221 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
222 * &lt;attribute name="ignoreGapsinConsensus"
223 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
224 * &lt;attribute name="startRes"
225 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
226 * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
227 * &lt;attribute name="charWidth"
228 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
229 * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
230 * &lt;attribute name="fontName"
231 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
232 * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
233 * &lt;attribute name="fontStyle"
234 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
235 * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
236 * &lt;attribute name="idWidthManuallyAdjusted"
237 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
238 * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
239 * default="true" /&gt; &lt;attribute name="viewName"
240 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
241 * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
242 * /&gt; &lt;attribute name="gatheredViews"
243 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
244 * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
245 * &lt;attribute name="textCol2"
246 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
247 * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
248 * /&gt; &lt;attribute name="id"
249 * type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; &lt;attribute
250 * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
251 * &lt;attribute name="showComplementFeatures"
252 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
253 * &lt;attribute name="showComplementFeaturesOnTop"
254 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
255 * &lt;/restriction&gt; &lt;/complexContent&gt;
256 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
257 * name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
258 * &lt;complexType&gt; &lt;complexContent&gt;
259 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
260 * &lt;sequence&gt; &lt;element name="UserColourScheme"
261 * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
262 * &lt;/sequence&gt; &lt;attribute name="id"
263 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
264 * &lt;/restriction&gt; &lt;/complexContent&gt;
265 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
266 * name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
267 * &lt;complexType&gt; &lt;complexContent&gt;
268 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
269 * &lt;sequence minOccurs="0"&gt; &lt;element name="title"
270 * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
271 * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
272 * &lt;/sequence&gt; &lt;attGroup
273 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="fontName"
274 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
275 * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
276 * &lt;attribute name="fontStyle"
277 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
278 * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
279 * &lt;attribute name="showBootstrap"
280 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
281 * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
282 * /&gt; &lt;attribute name="markUnlinked"
283 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
284 * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
285 * &lt;attribute name="currentTree"
286 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
287 * name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean"
288 * default="false" /&gt; &lt;attribute name="columnReference"
289 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
290 * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
291 * &lt;attribute name="linkToAllViews"
292 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
293 * &lt;/restriction&gt; &lt;/complexContent&gt;
294 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
295 * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
296 * &lt;complexType&gt; &lt;complexContent&gt;
297 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
298 * &lt;sequence&gt; &lt;element name="sequencePoint"
299 * maxOccurs="unbounded"&gt; &lt;complexType&gt;
300 * &lt;complexContent&gt; &lt;restriction
301 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
302 * ref="{www.jalview.org}position"/&gt; &lt;attribute name="sequenceRef"
303 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
304 * &lt;/restriction&gt; &lt;/complexContent&gt;
305 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
306 * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
307 * &lt;complexContent&gt; &lt;restriction
308 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
309 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
310 * &lt;/complexContent&gt; &lt;/complexType&gt;
311 * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
312 * &lt;complexType&gt; &lt;complexContent&gt;
313 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
314 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
315 * &lt;/restriction&gt; &lt;/complexContent&gt;
316 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
317 * name="seqPointMax"&gt; &lt;complexType&gt;
318 * &lt;complexContent&gt; &lt;restriction
319 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
320 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
321 * &lt;/complexContent&gt; &lt;/complexType&gt;
322 * &lt;/element&gt; &lt;element name="pcaData"
323 * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
324 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
325 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
326 * &lt;attribute name="title"
327 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
328 * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
329 * /&gt; &lt;attribute name="xDim"
330 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
331 * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
332 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
333 * /&gt; &lt;attribute name="bgColour"
334 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
335 * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
336 * &lt;attribute name="showLabels"
337 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
338 * name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean"
339 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
340 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
341 * name="FeatureSettings" minOccurs="0"&gt; &lt;complexType&gt;
342 * &lt;complexContent&gt; &lt;restriction
343 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
344 * &lt;sequence&gt; &lt;element name="setting" maxOccurs="unbounded"
345 * minOccurs="0"&gt; &lt;complexType&gt;
346 * &lt;complexContent&gt; &lt;restriction
347 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
348 * &lt;sequence&gt; &lt;element name="attributeName"
349 * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
350 * minOccurs="0"/&gt; &lt;element name="matcherSet"
351 * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
352 * &lt;/sequence&gt; &lt;attribute name="type" use="required"
353 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
354 * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
355 * /&gt; &lt;attribute name="display" use="required"
356 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
357 * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
358 * &lt;attribute name="mincolour"
359 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
360 * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
361 * default="Min" /&gt; &lt;attribute name="threshold"
362 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
363 * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
364 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
365 * /&gt; &lt;attribute name="min"
366 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
367 * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
368 * /&gt; &lt;attribute name="autoScale"
369 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
370 * &lt;/restriction&gt; &lt;/complexContent&gt;
371 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
372 * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
373 * &lt;complexType&gt; &lt;complexContent&gt;
374 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
375 * &lt;attribute name="name" use="required"
376 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
377 * name="display" use="required"
378 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
379 * &lt;/restriction&gt; &lt;/complexContent&gt;
380 * &lt;/complexType&gt; &lt;/element&gt;
381 * &lt;/sequence&gt; &lt;/restriction&gt;
382 * &lt;/complexContent&gt; &lt;/complexType&gt;
383 * &lt;/element&gt; &lt;/sequence&gt; &lt;/sequence&gt;
384 * &lt;/restriction&gt; &lt;/complexContent&gt;
385 * &lt;/complexType&gt; </pre>
389 @XmlAccessorType(XmlAccessType.FIELD)
391 name = "JalviewModel",
392 namespace = "www.jalview.org",
394 { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
395 "userColours", "tree", "pcaViewer", "featureSettings" })
396 public class JalviewModel
399 @XmlElement(required = true)
400 @XmlSchemaType(name = "dateTime")
401 protected XMLGregorianCalendar creationDate;
403 @XmlElement(required = true)
404 protected String version;
406 @XmlElement(required = true)
407 protected VAMSAS vamsasModel;
409 @XmlElement(name = "JSeq")
410 protected List<JalviewModel.JSeq> jSeq;
412 @XmlElement(name = "JGroup")
413 protected List<JalviewModel.JGroup> jGroup;
415 @XmlElement(name = "Viewport")
416 protected List<JalviewModel.Viewport> viewport;
418 @XmlElement(name = "UserColours")
419 protected List<JalviewModel.UserColours> userColours;
421 protected List<JalviewModel.Tree> tree;
423 @XmlElement(name = "PcaViewer")
424 protected List<JalviewModel.PcaViewer> pcaViewer;
426 @XmlElement(name = "FeatureSettings")
427 protected JalviewModel.FeatureSettings featureSettings;
430 * Gets the value of the creationDate property.
432 * @return possible object is {@link XMLGregorianCalendar }
435 public XMLGregorianCalendar getCreationDate()
441 * Sets the value of the creationDate property.
444 * allowed object is {@link XMLGregorianCalendar }
447 public void setCreationDate(XMLGregorianCalendar value)
449 this.creationDate = value;
453 * Gets the value of the version property.
455 * @return possible object is {@link String }
458 public String getVersion()
464 * Sets the value of the version property.
467 * allowed object is {@link String }
470 public void setVersion(String value)
472 this.version = value;
476 * Gets the value of the vamsasModel property.
478 * @return possible object is {@link VAMSAS }
481 public VAMSAS getVamsasModel()
487 * Sets the value of the vamsasModel property.
490 * allowed object is {@link VAMSAS }
493 public void setVamsasModel(VAMSAS value)
495 this.vamsasModel = value;
499 * Gets the value of the jSeq property.
501 * <p> This accessor method returns a reference to the live list, not a
502 * snapshot. Therefore any modification you make to the returned list will be
503 * present inside the JAXB object. This is why there is not a
504 * <CODE>set</CODE> method for the jSeq property.
506 * <p> For example, to add a new item, do as follows: <pre>
507 * getJSeq().add(newItem); </pre>
510 * <p> Objects of the following type(s) are allowed in the list
511 * {@link JalviewModel.JSeq }
515 public List<JalviewModel.JSeq> getJSeq()
519 jSeq = new ArrayList<JalviewModel.JSeq>();
525 * Gets the value of the jGroup property.
527 * <p> This accessor method returns a reference to the live list, not a
528 * snapshot. Therefore any modification you make to the returned list will be
529 * present inside the JAXB object. This is why there is not a
530 * <CODE>set</CODE> method for the jGroup property.
532 * <p> For example, to add a new item, do as follows: <pre>
533 * getJGroup().add(newItem); </pre>
536 * <p> Objects of the following type(s) are allowed in the list
537 * {@link JalviewModel.JGroup }
541 public List<JalviewModel.JGroup> getJGroup()
545 jGroup = new ArrayList<JalviewModel.JGroup>();
551 * Gets the value of the viewport property.
553 * <p> This accessor method returns a reference to the live list, not a
554 * snapshot. Therefore any modification you make to the returned list will be
555 * present inside the JAXB object. This is why there is not a
556 * <CODE>set</CODE> method for the viewport property.
558 * <p> For example, to add a new item, do as follows: <pre>
559 * getViewport().add(newItem); </pre>
562 * <p> Objects of the following type(s) are allowed in the list
563 * {@link JalviewModel.Viewport }
567 public List<JalviewModel.Viewport> getViewport()
569 if (viewport == null)
571 viewport = new ArrayList<JalviewModel.Viewport>();
573 return this.viewport;
577 * Gets the value of the userColours property.
579 * <p> This accessor method returns a reference to the live list, not a
580 * snapshot. Therefore any modification you make to the returned list will be
581 * present inside the JAXB object. This is why there is not a
582 * <CODE>set</CODE> method for the userColours property.
584 * <p> For example, to add a new item, do as follows: <pre>
585 * getUserColours().add(newItem); </pre>
588 * <p> Objects of the following type(s) are allowed in the list
589 * {@link JalviewModel.UserColours }
593 public List<JalviewModel.UserColours> getUserColours()
595 if (userColours == null)
597 userColours = new ArrayList<JalviewModel.UserColours>();
599 return this.userColours;
603 * Gets the value of the tree property.
605 * <p> This accessor method returns a reference to the live list, not a
606 * snapshot. Therefore any modification you make to the returned list will be
607 * present inside the JAXB object. This is why there is not a
608 * <CODE>set</CODE> method for the tree property.
610 * <p> For example, to add a new item, do as follows: <pre>
611 * getTree().add(newItem); </pre>
614 * <p> Objects of the following type(s) are allowed in the list
615 * {@link JalviewModel.Tree }
619 public List<JalviewModel.Tree> getTree()
623 tree = new ArrayList<JalviewModel.Tree>();
629 * Gets the value of the pcaViewer property.
631 * <p> This accessor method returns a reference to the live list, not a
632 * snapshot. Therefore any modification you make to the returned list will be
633 * present inside the JAXB object. This is why there is not a
634 * <CODE>set</CODE> method for the pcaViewer property.
636 * <p> For example, to add a new item, do as follows: <pre>
637 * getPcaViewer().add(newItem); </pre>
640 * <p> Objects of the following type(s) are allowed in the list
641 * {@link JalviewModel.PcaViewer }
645 public List<JalviewModel.PcaViewer> getPcaViewer()
647 if (pcaViewer == null)
649 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
651 return this.pcaViewer;
655 * Gets the value of the featureSettings property.
657 * @return possible object is {@link JalviewModel.FeatureSettings }
660 public JalviewModel.FeatureSettings getFeatureSettings()
662 return featureSettings;
666 * Sets the value of the featureSettings property.
669 * allowed object is {@link JalviewModel.FeatureSettings }
672 public void setFeatureSettings(JalviewModel.FeatureSettings value)
674 this.featureSettings = value;
678 * <p>Java class for anonymous complex type.
680 * <p>The following schema fragment specifies the expected content
681 * contained within this class.
683 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
684 * &lt;restriction
685 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
686 * &lt;sequence&gt; &lt;element name="setting"
687 * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
688 * &lt;complexContent&gt; &lt;restriction
689 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
690 * &lt;sequence&gt; &lt;element name="attributeName"
691 * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
692 * minOccurs="0"/&gt; &lt;element name="matcherSet"
693 * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
694 * &lt;/sequence&gt; &lt;attribute name="type" use="required"
695 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
696 * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
697 * /&gt; &lt;attribute name="display" use="required"
698 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
699 * &lt;attribute name="order"
700 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
701 * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
702 * &lt;attribute name="noValueColour"
703 * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
704 * &lt;attribute name="threshold"
705 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
706 * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
707 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
708 * /&gt; &lt;attribute name="min"
709 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
710 * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
711 * /&gt; &lt;attribute name="autoScale"
712 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
713 * &lt;/restriction&gt; &lt;/complexContent&gt;
714 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
715 * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
716 * &lt;complexType&gt; &lt;complexContent&gt;
717 * &lt;restriction
718 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
719 * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
720 * /&gt; &lt;attribute name="display" use="required"
721 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
722 * &lt;/restriction&gt; &lt;/complexContent&gt;
723 * &lt;/complexType&gt; &lt;/element&gt;
724 * &lt;/sequence&gt; &lt;/restriction&gt;
725 * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
729 @XmlAccessorType(XmlAccessType.FIELD)
730 @XmlType(name = "", propOrder = { "setting", "group" })
731 public static class FeatureSettings
734 @XmlElement(namespace = "www.jalview.org")
735 protected List<JalviewModel.FeatureSettings.Setting> setting;
737 @XmlElement(namespace = "www.jalview.org")
738 protected List<JalviewModel.FeatureSettings.Group> group;
741 * Gets the value of the setting property.
743 * <p> This accessor method returns a reference to the live list, not
744 * a snapshot. Therefore any modification you make to the returned list will
745 * be present inside the JAXB object. This is why there is not a
746 * <CODE>set</CODE> method for the setting property.
748 * <p> For example, to add a new item, do as follows: <pre>
749 * getSetting().add(newItem); </pre>
752 * <p> Objects of the following type(s) are allowed in the list
753 * {@link JalviewModel.FeatureSettings.Setting }
757 public List<JalviewModel.FeatureSettings.Setting> getSetting()
761 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
767 * Gets the value of the group property.
769 * <p> This accessor method returns a reference to the live list, not
770 * a snapshot. Therefore any modification you make to the returned list will
771 * be present inside the JAXB object. This is why there is not a
772 * <CODE>set</CODE> method for the group property.
774 * <p> For example, to add a new item, do as follows: <pre>
775 * getGroup().add(newItem); </pre>
778 * <p> Objects of the following type(s) are allowed in the list
779 * {@link JalviewModel.FeatureSettings.Group }
783 public List<JalviewModel.FeatureSettings.Group> getGroup()
787 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
793 * <p>Java class for anonymous complex type.
795 * <p>The following schema fragment specifies the expected content
796 * contained within this class.
798 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
799 * &lt;restriction
800 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
801 * &lt;attribute name="name" use="required"
802 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
803 * &lt;attribute name="display" use="required"
804 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
805 * &lt;/restriction&gt; &lt;/complexContent&gt;
806 * &lt;/complexType&gt; </pre>
810 @XmlAccessorType(XmlAccessType.FIELD)
812 public static class Group
815 @XmlAttribute(name = "name", required = true)
816 protected String name;
818 @XmlAttribute(name = "display", required = true)
819 protected boolean display;
822 * Gets the value of the name property.
824 * @return possible object is {@link String }
827 public String getName()
833 * Sets the value of the name property.
836 * allowed object is {@link String }
839 public void setName(String value)
845 * Gets the value of the display property.
848 public boolean isDisplay()
854 * Sets the value of the display property.
857 public void setDisplay(boolean value)
859 this.display = value;
865 * <p>Java class for anonymous complex type.
867 * <p>The following schema fragment specifies the expected content
868 * contained within this class.
870 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
871 * &lt;restriction
872 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
873 * &lt;sequence&gt; &lt;element name="attributeName"
874 * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
875 * minOccurs="0"/&gt; &lt;element name="matcherSet"
876 * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
877 * &lt;/sequence&gt; &lt;attribute name="type" use="required"
878 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
879 * &lt;attribute name="colour" use="required"
880 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
881 * name="display" use="required"
882 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
883 * &lt;attribute name="order"
884 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
885 * &lt;attribute name="mincolour"
886 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
887 * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
888 * default="Min" /&gt; &lt;attribute name="threshold"
889 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
890 * &lt;attribute name="threshstate"
891 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
892 * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
893 * &lt;attribute name="min"
894 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
895 * &lt;attribute name="colourByLabel"
896 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
897 * &lt;attribute name="autoScale"
898 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
899 * &lt;/restriction&gt; &lt;/complexContent&gt;
900 * &lt;/complexType&gt; </pre>
904 @XmlAccessorType(XmlAccessType.FIELD)
905 @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
906 public static class Setting
909 @XmlElement(namespace = "www.jalview.org")
910 protected List<String> attributeName;
912 @XmlElement(namespace = "www.jalview.org")
913 protected FeatureMatcherSet matcherSet;
915 @XmlAttribute(name = "type", required = true)
916 protected String type;
918 @XmlAttribute(name = "colour", required = true)
919 protected int colour;
921 @XmlAttribute(name = "display", required = true)
922 protected boolean display;
924 @XmlAttribute(name = "order")
925 protected Float order;
927 @XmlAttribute(name = "mincolour")
928 protected Integer mincolour;
930 @XmlAttribute(name = "noValueColour")
931 protected NoValueColour noValueColour;
933 @XmlAttribute(name = "threshold")
934 protected Float threshold;
936 @XmlAttribute(name = "threshstate")
937 protected Integer threshstate;
939 @XmlAttribute(name = "max")
942 @XmlAttribute(name = "min")
945 @XmlAttribute(name = "colourByLabel")
946 protected Boolean colourByLabel;
948 @XmlAttribute(name = "autoScale")
949 protected Boolean autoScale;
952 * Gets the value of the attributeName property.
954 * <p> This accessor method returns a reference to the live list,
955 * not a snapshot. Therefore any modification you make to the returned
956 * list will be present inside the JAXB object. This is why there is not a
957 * <CODE>set</CODE> method for the attributeName property.
959 * <p> For example, to add a new item, do as follows: <pre>
960 * getAttributeName().add(newItem); </pre>
963 * <p> Objects of the following type(s) are allowed in the list
968 public List<String> getAttributeName()
970 if (attributeName == null)
972 attributeName = new ArrayList<String>();
974 return this.attributeName;
978 * Gets the value of the matcherSet property.
980 * @return possible object is {@link FeatureMatcherSet }
983 public FeatureMatcherSet getMatcherSet()
989 * Sets the value of the matcherSet property.
992 * allowed object is {@link FeatureMatcherSet }
995 public void setMatcherSet(FeatureMatcherSet value)
997 this.matcherSet = value;
1001 * Gets the value of the type property.
1003 * @return possible object is {@link String }
1006 public String getType()
1012 * Sets the value of the type property.
1015 * allowed object is {@link String }
1018 public void setType(String value)
1024 * Gets the value of the colour property.
1027 public int getColour()
1033 * Sets the value of the colour property.
1036 public void setColour(int value)
1038 this.colour = value;
1042 * Gets the value of the display property.
1045 public boolean isDisplay()
1051 * Sets the value of the display property.
1054 public void setDisplay(boolean value)
1056 this.display = value;
1060 * Gets the value of the order property.
1062 * @return possible object is {@link Float }
1065 public Float getOrder()
1071 * Sets the value of the order property.
1074 * allowed object is {@link Float }
1077 public void setOrder(Float value)
1083 * Gets the value of the mincolour property.
1085 * @return possible object is {@link Integer }
1088 public Integer getMincolour()
1094 * Sets the value of the mincolour property.
1097 * allowed object is {@link Integer }
1100 public void setMincolour(Integer value)
1102 this.mincolour = value;
1106 * Gets the value of the noValueColour property.
1108 * @return possible object is {@link NoValueColour }
1111 public NoValueColour getNoValueColour()
1113 if (noValueColour == null)
1115 return NoValueColour.MIN;
1119 return noValueColour;
1124 * Sets the value of the noValueColour property.
1127 * allowed object is {@link NoValueColour }
1130 public void setNoValueColour(NoValueColour value)
1132 this.noValueColour = value;
1136 * Gets the value of the threshold property.
1138 * @return possible object is {@link Float }
1141 public Float getThreshold()
1147 * Sets the value of the threshold property.
1150 * allowed object is {@link Float }
1153 public void setThreshold(Float value)
1155 this.threshold = value;
1159 * Gets the value of the threshstate property.
1161 * @return possible object is {@link Integer }
1164 public Integer getThreshstate()
1170 * Sets the value of the threshstate property.
1173 * allowed object is {@link Integer }
1176 public void setThreshstate(Integer value)
1178 this.threshstate = value;
1182 * Gets the value of the max property.
1184 * @return possible object is {@link Float }
1187 public Float getMax()
1193 * Sets the value of the max property.
1196 * allowed object is {@link Float }
1199 public void setMax(Float value)
1205 * Gets the value of the min property.
1207 * @return possible object is {@link Float }
1210 public Float getMin()
1216 * Sets the value of the min property.
1219 * allowed object is {@link Float }
1222 public void setMin(Float value)
1228 * Gets the value of the colourByLabel property.
1230 * @return possible object is {@link Boolean }
1233 public Boolean isColourByLabel()
1235 return colourByLabel;
1239 * Sets the value of the colourByLabel property.
1242 * allowed object is {@link Boolean }
1245 public void setColourByLabel(Boolean value)
1247 this.colourByLabel = value;
1251 * Gets the value of the autoScale property.
1253 * @return possible object is {@link Boolean }
1256 public Boolean isAutoScale()
1262 * Sets the value of the autoScale property.
1265 * allowed object is {@link Boolean }
1268 public void setAutoScale(Boolean value)
1270 this.autoScale = value;
1278 * <p>Java class for anonymous complex type.
1280 * <p>The following schema fragment specifies the expected content
1281 * contained within this class.
1283 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
1284 * &lt;restriction
1285 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1286 * &lt;sequence&gt; &lt;element name="seq"
1287 * type="{http://www.w3.org/2001/XMLSchema}string"
1288 * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
1289 * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
1290 * &lt;/sequence&gt; &lt;attribute name="start"
1291 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1292 * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1293 * &lt;attribute name="name"
1294 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
1295 * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1296 * &lt;attribute name="consThreshold"
1297 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1298 * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1299 * &lt;attribute name="outlineColour"
1300 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1301 * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
1302 * /&gt; &lt;attribute name="displayText"
1303 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1304 * &lt;attribute name="colourText"
1305 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1306 * &lt;attribute name="textCol1"
1307 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1308 * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1309 * &lt;attribute name="textColThreshold"
1310 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1311 * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
1312 * /&gt; &lt;attribute name="ignoreGapsinConsensus"
1313 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1314 * &lt;attribute name="showConsensusHistogram"
1315 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1316 * &lt;attribute name="showSequenceLogo"
1317 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1318 * &lt;attribute name="normaliseSequenceLogo"
1319 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1320 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
1321 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
1322 * &lt;/complexType&gt; </pre>
1326 @XmlAccessorType(XmlAccessType.FIELD)
1327 @XmlType(name = "", propOrder = { "seq", "annotationColours" })
1328 public static class JGroup
1331 @XmlElement(namespace = "www.jalview.org", required = true)
1332 protected List<String> seq;
1334 @XmlElement(namespace = "www.jalview.org")
1335 protected AnnotationColourScheme annotationColours;
1337 @XmlAttribute(name = "start")
1338 protected Integer start;
1340 @XmlAttribute(name = "end")
1341 protected Integer end;
1343 @XmlAttribute(name = "name")
1344 protected String name;
1346 @XmlAttribute(name = "colour")
1347 protected String colour;
1349 @XmlAttribute(name = "consThreshold")
1350 protected Integer consThreshold;
1352 @XmlAttribute(name = "pidThreshold")
1353 protected Integer pidThreshold;
1355 @XmlAttribute(name = "outlineColour")
1356 protected Integer outlineColour;
1358 @XmlAttribute(name = "displayBoxes")
1359 protected Boolean displayBoxes;
1361 @XmlAttribute(name = "displayText")
1362 protected Boolean displayText;
1364 @XmlAttribute(name = "colourText")
1365 protected Boolean colourText;
1367 @XmlAttribute(name = "textCol1")
1368 protected Integer textCol1;
1370 @XmlAttribute(name = "textCol2")
1371 protected Integer textCol2;
1373 @XmlAttribute(name = "textColThreshold")
1374 protected Integer textColThreshold;
1376 @XmlAttribute(name = "showUnconserved")
1377 protected Boolean showUnconserved;
1379 @XmlAttribute(name = "ignoreGapsinConsensus")
1380 protected Boolean ignoreGapsinConsensus;
1382 @XmlAttribute(name = "showConsensusHistogram")
1383 protected Boolean showConsensusHistogram;
1385 @XmlAttribute(name = "showSequenceLogo")
1386 protected Boolean showSequenceLogo;
1388 @XmlAttribute(name = "normaliseSequenceLogo")
1389 protected Boolean normaliseSequenceLogo;
1391 @XmlAttribute(name = "id")
1392 protected String id;
1395 * Gets the value of the seq property.
1397 * <p> This accessor method returns a reference to the live list, not
1398 * a snapshot. Therefore any modification you make to the returned list will
1399 * be present inside the JAXB object. This is why there is not a
1400 * <CODE>set</CODE> method for the seq property.
1402 * <p> For example, to add a new item, do as follows: <pre>
1403 * getSeq().add(newItem); </pre>
1406 * <p> Objects of the following type(s) are allowed in the list
1411 public List<String> getSeq()
1415 seq = new ArrayList<String>();
1421 * Gets the value of the annotationColours property.
1423 * @return possible object is {@link AnnotationColourScheme }
1426 public AnnotationColourScheme getAnnotationColours()
1428 return annotationColours;
1432 * Sets the value of the annotationColours property.
1435 * allowed object is {@link AnnotationColourScheme }
1438 public void setAnnotationColours(AnnotationColourScheme value)
1440 this.annotationColours = value;
1444 * Gets the value of the start property.
1446 * @return possible object is {@link Integer }
1449 public Integer getStart()
1455 * Sets the value of the start property.
1458 * allowed object is {@link Integer }
1461 public void setStart(Integer value)
1467 * Gets the value of the end property.
1469 * @return possible object is {@link Integer }
1472 public Integer getEnd()
1478 * Sets the value of the end property.
1481 * allowed object is {@link Integer }
1484 public void setEnd(Integer value)
1490 * Gets the value of the name property.
1492 * @return possible object is {@link String }
1495 public String getName()
1501 * Sets the value of the name property.
1504 * allowed object is {@link String }
1507 public void setName(String value)
1513 * Gets the value of the colour property.
1515 * @return possible object is {@link String }
1518 public String getColour()
1524 * Sets the value of the colour property.
1527 * allowed object is {@link String }
1530 public void setColour(String value)
1532 this.colour = value;
1536 * Gets the value of the consThreshold property.
1538 * @return possible object is {@link Integer }
1541 public Integer getConsThreshold()
1543 return consThreshold;
1547 * Sets the value of the consThreshold property.
1550 * allowed object is {@link Integer }
1553 public void setConsThreshold(Integer value)
1555 this.consThreshold = value;
1559 * Gets the value of the pidThreshold property.
1561 * @return possible object is {@link Integer }
1564 public Integer getPidThreshold()
1566 return pidThreshold;
1570 * Sets the value of the pidThreshold property.
1573 * allowed object is {@link Integer }
1576 public void setPidThreshold(Integer value)
1578 this.pidThreshold = value;
1582 * Gets the value of the outlineColour property.
1584 * @return possible object is {@link Integer }
1587 public Integer getOutlineColour()
1589 return outlineColour;
1593 * Sets the value of the outlineColour property.
1596 * allowed object is {@link Integer }
1599 public void setOutlineColour(Integer value)
1601 this.outlineColour = value;
1605 * Gets the value of the displayBoxes property.
1607 * @return possible object is {@link Boolean }
1610 public Boolean isDisplayBoxes()
1612 return displayBoxes;
1616 * Sets the value of the displayBoxes property.
1619 * allowed object is {@link Boolean }
1622 public void setDisplayBoxes(Boolean value)
1624 this.displayBoxes = value;
1628 * Gets the value of the displayText property.
1630 * @return possible object is {@link Boolean }
1633 public Boolean isDisplayText()
1639 * Sets the value of the displayText property.
1642 * allowed object is {@link Boolean }
1645 public void setDisplayText(Boolean value)
1647 this.displayText = value;
1651 * Gets the value of the colourText property.
1653 * @return possible object is {@link Boolean }
1656 public Boolean isColourText()
1662 * Sets the value of the colourText property.
1665 * allowed object is {@link Boolean }
1668 public void setColourText(Boolean value)
1670 this.colourText = value;
1674 * Gets the value of the textCol1 property.
1676 * @return possible object is {@link Integer }
1679 public Integer getTextCol1()
1685 * Sets the value of the textCol1 property.
1688 * allowed object is {@link Integer }
1691 public void setTextCol1(Integer value)
1693 this.textCol1 = value;
1697 * Gets the value of the textCol2 property.
1699 * @return possible object is {@link Integer }
1702 public Integer getTextCol2()
1708 * Sets the value of the textCol2 property.
1711 * allowed object is {@link Integer }
1714 public void setTextCol2(Integer value)
1716 this.textCol2 = value;
1720 * Gets the value of the textColThreshold property.
1722 * @return possible object is {@link Integer }
1725 public Integer getTextColThreshold()
1727 return textColThreshold;
1731 * Sets the value of the textColThreshold property.
1734 * allowed object is {@link Integer }
1737 public void setTextColThreshold(Integer value)
1739 this.textColThreshold = value;
1743 * Gets the value of the showUnconserved property.
1745 * @return possible object is {@link Boolean }
1748 public Boolean isShowUnconserved()
1750 return showUnconserved;
1754 * Sets the value of the showUnconserved property.
1757 * allowed object is {@link Boolean }
1760 public void setShowUnconserved(Boolean value)
1762 this.showUnconserved = value;
1766 * Gets the value of the ignoreGapsinConsensus property.
1768 * @return possible object is {@link Boolean }
1771 public boolean isIgnoreGapsinConsensus()
1773 if (ignoreGapsinConsensus == null)
1779 return ignoreGapsinConsensus;
1784 * Sets the value of the ignoreGapsinConsensus property.
1787 * allowed object is {@link Boolean }
1790 public void setIgnoreGapsinConsensus(Boolean value)
1792 this.ignoreGapsinConsensus = value;
1796 * Gets the value of the showConsensusHistogram property.
1798 * @return possible object is {@link Boolean }
1801 public boolean isShowConsensusHistogram()
1803 if (showConsensusHistogram == null)
1809 return showConsensusHistogram;
1814 * Sets the value of the showConsensusHistogram property.
1817 * allowed object is {@link Boolean }
1820 public void setShowConsensusHistogram(Boolean value)
1822 this.showConsensusHistogram = value;
1826 * Gets the value of the showSequenceLogo property.
1828 * @return possible object is {@link Boolean }
1831 public boolean isShowSequenceLogo()
1833 if (showSequenceLogo == null)
1839 return showSequenceLogo;
1844 * Sets the value of the showSequenceLogo property.
1847 * allowed object is {@link Boolean }
1850 public void setShowSequenceLogo(Boolean value)
1852 this.showSequenceLogo = value;
1856 * Gets the value of the normaliseSequenceLogo property.
1858 * @return possible object is {@link Boolean }
1861 public boolean isNormaliseSequenceLogo()
1863 if (normaliseSequenceLogo == null)
1869 return normaliseSequenceLogo;
1874 * Sets the value of the normaliseSequenceLogo property.
1877 * allowed object is {@link Boolean }
1880 public void setNormaliseSequenceLogo(Boolean value)
1882 this.normaliseSequenceLogo = value;
1886 * Gets the value of the id property.
1888 * @return possible object is {@link String }
1891 public String getId()
1897 * Sets the value of the id property.
1900 * allowed object is {@link String }
1903 public void setId(String value)
1911 * <p>Java class for anonymous complex type.
1913 * <p>The following schema fragment specifies the expected content
1914 * contained within this class.
1916 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
1917 * &lt;restriction
1918 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1919 * &lt;sequence&gt; &lt;element name="features"
1920 * type="{www.jalview.org}feature" maxOccurs="unbounded"
1921 * minOccurs="0"/&gt; &lt;element name="pdbids" maxOccurs="unbounded"
1922 * minOccurs="0"&gt; &lt;complexType&gt;
1923 * &lt;complexContent&gt; &lt;extension
1924 * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
1925 * &lt;element name="structureState" maxOccurs="unbounded"
1926 * minOccurs="0"&gt; &lt;complexType&gt;
1927 * &lt;simpleContent&gt; &lt;extension
1928 * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
1929 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1930 * &lt;attribute name="visible"
1931 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1932 * &lt;attribute name="viewId"
1933 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
1934 * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
1935 * default="true" /&gt; &lt;attribute name="colourwithAlignPanel"
1936 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1937 * &lt;attribute name="colourByJmol"
1938 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1939 * &lt;attribute name="type"
1940 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1941 * &lt;/extension&gt; &lt;/simpleContent&gt;
1942 * &lt;/complexType&gt; &lt;/element&gt;
1943 * &lt;/sequence&gt; &lt;/extension&gt;
1944 * &lt;/complexContent&gt; &lt;/complexType&gt;
1945 * &lt;/element&gt; &lt;element name="hiddenSequences"
1946 * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
1947 * minOccurs="0"/&gt; &lt;element name="rnaViewer"
1948 * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
1949 * &lt;complexContent&gt; &lt;restriction
1950 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1951 * &lt;sequence&gt; &lt;element name="secondaryStructure"
1952 * maxOccurs="unbounded"&gt; &lt;complexType&gt;
1953 * &lt;complexContent&gt; &lt;restriction
1954 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
1955 * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1956 * &lt;attribute name="annotationId" use="required"
1957 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
1958 * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1959 * &lt;attribute name="viewerState"
1960 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1961 * &lt;/restriction&gt; &lt;/complexContent&gt;
1962 * &lt;/complexType&gt; &lt;/element&gt;
1963 * &lt;/sequence&gt; &lt;attGroup
1964 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
1965 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
1966 * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1967 * &lt;attribute name="dividerLocation"
1968 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1969 * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1970 * &lt;/restriction&gt; &lt;/complexContent&gt;
1971 * &lt;/complexType&gt; &lt;/element&gt;
1972 * &lt;/sequence&gt; &lt;attribute name="colour"
1973 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1974 * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
1975 * /&gt; &lt;attribute name="end" use="required"
1976 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
1977 * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
1978 * /&gt; &lt;attribute name="hidden"
1979 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1980 * &lt;attribute name="viewreference"
1981 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1982 * &lt;/restriction&gt; &lt;/complexContent&gt;
1983 * &lt;/complexType&gt; </pre>
1987 @XmlAccessorType(XmlAccessType.FIELD)
1991 { "features", "pdbids", "hiddenSequences", "rnaViewer" })
1992 public static class JSeq
1995 @XmlElement(namespace = "www.jalview.org")
1996 protected List<Feature> features;
1998 @XmlElement(namespace = "www.jalview.org")
1999 protected List<JalviewModel.JSeq.Pdbids> pdbids;
2001 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
2002 protected List<Integer> hiddenSequences;
2004 @XmlElement(namespace = "www.jalview.org")
2005 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
2007 @XmlAttribute(name = "colour")
2008 protected Integer colour;
2010 @XmlAttribute(name = "start", required = true)
2011 protected int start;
2013 @XmlAttribute(name = "end", required = true)
2016 @XmlAttribute(name = "id", required = true)
2017 protected String id;
2019 @XmlAttribute(name = "hidden")
2020 protected Boolean hidden;
2022 @XmlAttribute(name = "viewreference")
2023 protected Boolean viewreference;
2026 * Gets the value of the features property.
2028 * <p> This accessor method returns a reference to the live list, not
2029 * a snapshot. Therefore any modification you make to the returned list will
2030 * be present inside the JAXB object. This is why there is not a
2031 * <CODE>set</CODE> method for the features property.
2033 * <p> For example, to add a new item, do as follows: <pre>
2034 * getFeatures().add(newItem); </pre>
2037 * <p> Objects of the following type(s) are allowed in the list
2042 public List<Feature> getFeatures()
2044 if (features == null)
2046 features = new ArrayList<Feature>();
2048 return this.features;
2052 * Gets the value of the pdbids property.
2054 * <p> This accessor method returns a reference to the live list, not
2055 * a snapshot. Therefore any modification you make to the returned list will
2056 * be present inside the JAXB object. This is why there is not a
2057 * <CODE>set</CODE> method for the pdbids property.
2059 * <p> For example, to add a new item, do as follows: <pre>
2060 * getPdbids().add(newItem); </pre>
2063 * <p> Objects of the following type(s) are allowed in the list
2064 * {@link JalviewModel.JSeq.Pdbids }
2068 public List<JalviewModel.JSeq.Pdbids> getPdbids()
2072 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2078 * Gets the value of the hiddenSequences property.
2080 * <p> This accessor method returns a reference to the live list, not
2081 * a snapshot. Therefore any modification you make to the returned list will
2082 * be present inside the JAXB object. This is why there is not a
2083 * <CODE>set</CODE> method for the hiddenSequences property.
2085 * <p> For example, to add a new item, do as follows: <pre>
2086 * getHiddenSequences().add(newItem); </pre>
2089 * <p> Objects of the following type(s) are allowed in the list
2094 public List<Integer> getHiddenSequences()
2096 if (hiddenSequences == null)
2098 hiddenSequences = new ArrayList<Integer>();
2100 return this.hiddenSequences;
2104 * Gets the value of the rnaViewer property.
2106 * <p> This accessor method returns a reference to the live list, not
2107 * a snapshot. Therefore any modification you make to the returned list will
2108 * be present inside the JAXB object. This is why there is not a
2109 * <CODE>set</CODE> method for the rnaViewer property.
2111 * <p> For example, to add a new item, do as follows: <pre>
2112 * getRnaViewer().add(newItem); </pre>
2115 * <p> Objects of the following type(s) are allowed in the list
2116 * {@link JalviewModel.JSeq.RnaViewer }
2120 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
2122 if (rnaViewer == null)
2124 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2126 return this.rnaViewer;
2130 * Gets the value of the colour property.
2132 * @return possible object is {@link Integer }
2135 public Integer getColour()
2141 * Sets the value of the colour property.
2144 * allowed object is {@link Integer }
2147 public void setColour(Integer value)
2149 this.colour = value;
2153 * Gets the value of the start property.
2156 public int getStart()
2162 * Sets the value of the start property.
2165 public void setStart(int value)
2171 * Gets the value of the end property.
2180 * Sets the value of the end property.
2183 public void setEnd(int value)
2189 * Gets the value of the id property.
2191 * @return possible object is {@link String }
2194 public String getId()
2200 * Sets the value of the id property.
2203 * allowed object is {@link String }
2206 public void setId(String value)
2212 * Gets the value of the hidden property.
2214 * @return possible object is {@link Boolean }
2217 public Boolean isHidden()
2223 * Sets the value of the hidden property.
2226 * allowed object is {@link Boolean }
2229 public void setHidden(Boolean value)
2231 this.hidden = value;
2235 * Gets the value of the viewreference property.
2237 * @return possible object is {@link Boolean }
2240 public Boolean isViewreference()
2242 return viewreference;
2246 * Sets the value of the viewreference property.
2249 * allowed object is {@link Boolean }
2252 public void setViewreference(Boolean value)
2254 this.viewreference = value;
2258 * <p>Java class for anonymous complex type.
2260 * <p>The following schema fragment specifies the expected content
2261 * contained within this class.
2263 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
2264 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
2265 * &lt;sequence&gt; &lt;element name="structureState"
2266 * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
2267 * &lt;simpleContent&gt; &lt;extension
2268 * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2269 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2270 * &lt;attribute name="visible"
2271 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2272 * &lt;attribute name="viewId"
2273 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2274 * &lt;attribute name="alignwithAlignPanel"
2275 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2276 * &lt;attribute name="colourwithAlignPanel"
2277 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
2278 * /&gt; &lt;attribute name="colourByJmol"
2279 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2280 * &lt;attribute name="type"
2281 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2282 * &lt;/extension&gt; &lt;/simpleContent&gt;
2283 * &lt;/complexType&gt; &lt;/element&gt;
2284 * &lt;/sequence&gt; &lt;/extension&gt;
2285 * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
2289 @XmlAccessorType(XmlAccessType.FIELD)
2290 @XmlType(name = "", propOrder = { "structureState" })
2291 public static class Pdbids extends Pdbentry
2294 @XmlElement(namespace = "www.jalview.org")
2295 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2298 * Gets the value of the structureState property.
2300 * <p> This accessor method returns a reference to the live list,
2301 * not a snapshot. Therefore any modification you make to the returned
2302 * list will be present inside the JAXB object. This is why there is not a
2303 * <CODE>set</CODE> method for the structureState property.
2305 * <p> For example, to add a new item, do as follows: <pre>
2306 * getStructureState().add(newItem); </pre>
2309 * <p> Objects of the following type(s) are allowed in the list
2310 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2314 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
2316 if (structureState == null)
2318 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2320 return this.structureState;
2324 * <p>Java class for anonymous complex type.
2326 * <p>The following schema fragment specifies the expected content
2327 * contained within this class.
2329 * <pre> &lt;complexType&gt; &lt;simpleContent&gt;
2331 * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2332 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2333 * &lt;attribute name="visible"
2334 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2335 * &lt;attribute name="viewId"
2336 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2337 * &lt;attribute name="alignwithAlignPanel"
2338 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
2339 * /&gt; &lt;attribute name="colourwithAlignPanel"
2340 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
2341 * /&gt; &lt;attribute name="colourByJmol"
2342 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
2343 * /&gt; &lt;attribute name="type"
2344 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2345 * &lt;/extension&gt; &lt;/simpleContent&gt;
2346 * &lt;/complexType&gt; </pre>
2350 @XmlAccessorType(XmlAccessType.FIELD)
2351 @XmlType(name = "", propOrder = { "value" })
2352 public static class StructureState
2356 protected String value;
2358 @XmlAttribute(name = "visible")
2359 protected Boolean visible;
2361 @XmlAttribute(name = "viewId")
2362 protected String viewId;
2364 @XmlAttribute(name = "alignwithAlignPanel")
2365 protected Boolean alignwithAlignPanel;
2367 @XmlAttribute(name = "colourwithAlignPanel")
2368 protected Boolean colourwithAlignPanel;
2370 @XmlAttribute(name = "colourByJmol")
2371 protected Boolean colourByJmol;
2373 @XmlAttribute(name = "type")
2374 protected String type;
2376 @XmlAttribute(name = "width")
2377 protected Integer width;
2379 @XmlAttribute(name = "height")
2380 protected Integer height;
2382 @XmlAttribute(name = "xpos")
2383 protected Integer xpos;
2385 @XmlAttribute(name = "ypos")
2386 protected Integer ypos;
2389 * Gets the value of the value property.
2391 * @return possible object is {@link String }
2394 public String getValue()
2400 * Sets the value of the value property.
2403 * allowed object is {@link String }
2406 public void setValue(String value)
2412 * Gets the value of the visible property.
2414 * @return possible object is {@link Boolean }
2417 public Boolean isVisible()
2423 * Sets the value of the visible property.
2426 * allowed object is {@link Boolean }
2429 public void setVisible(Boolean value)
2431 this.visible = value;
2435 * Gets the value of the viewId property.
2437 * @return possible object is {@link String }
2440 public String getViewId()
2446 * Sets the value of the viewId property.
2449 * allowed object is {@link String }
2452 public void setViewId(String value)
2454 this.viewId = value;
2458 * Gets the value of the alignwithAlignPanel property.
2460 * @return possible object is {@link Boolean }
2463 public boolean isAlignwithAlignPanel()
2465 if (alignwithAlignPanel == null)
2471 return alignwithAlignPanel;
2476 * Sets the value of the alignwithAlignPanel property.
2479 * allowed object is {@link Boolean }
2482 public void setAlignwithAlignPanel(Boolean value)
2484 this.alignwithAlignPanel = value;
2488 * Gets the value of the colourwithAlignPanel property.
2490 * @return possible object is {@link Boolean }
2493 public boolean isColourwithAlignPanel()
2495 if (colourwithAlignPanel == null)
2501 return colourwithAlignPanel;
2506 * Sets the value of the colourwithAlignPanel property.
2509 * allowed object is {@link Boolean }
2512 public void setColourwithAlignPanel(Boolean value)
2514 this.colourwithAlignPanel = value;
2518 * Gets the value of the colourByJmol property.
2520 * @return possible object is {@link Boolean }
2523 public boolean isColourByJmol()
2525 if (colourByJmol == null)
2531 return colourByJmol;
2536 * Sets the value of the colourByJmol property.
2539 * allowed object is {@link Boolean }
2542 public void setColourByJmol(Boolean value)
2544 this.colourByJmol = value;
2548 * Gets the value of the type property.
2550 * @return possible object is {@link String }
2553 public String getType()
2559 * Sets the value of the type property.
2562 * allowed object is {@link String }
2565 public void setType(String value)
2571 * Gets the value of the width property.
2573 * @return possible object is {@link Integer }
2576 public Integer getWidth()
2582 * Sets the value of the width property.
2585 * allowed object is {@link Integer }
2588 public void setWidth(Integer value)
2594 * Gets the value of the height property.
2596 * @return possible object is {@link Integer }
2599 public Integer getHeight()
2605 * Sets the value of the height property.
2608 * allowed object is {@link Integer }
2611 public void setHeight(Integer value)
2613 this.height = value;
2617 * Gets the value of the xpos property.
2619 * @return possible object is {@link Integer }
2622 public Integer getXpos()
2628 * Sets the value of the xpos property.
2631 * allowed object is {@link Integer }
2634 public void setXpos(Integer value)
2640 * Gets the value of the ypos property.
2642 * @return possible object is {@link Integer }
2645 public Integer getYpos()
2651 * Sets the value of the ypos property.
2654 * allowed object is {@link Integer }
2657 public void setYpos(Integer value)
2667 * <p>Java class for anonymous complex type.
2669 * <p>The following schema fragment specifies the expected content
2670 * contained within this class.
2672 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
2673 * &lt;restriction
2674 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2675 * &lt;sequence&gt; &lt;element name="secondaryStructure"
2676 * maxOccurs="unbounded"&gt; &lt;complexType&gt;
2677 * &lt;complexContent&gt; &lt;restriction
2678 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2679 * &lt;attribute name="title"
2680 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2681 * &lt;attribute name="annotationId" use="required"
2682 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2683 * &lt;attribute name="gapped"
2684 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2685 * &lt;attribute name="viewerState"
2686 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2687 * &lt;/restriction&gt; &lt;/complexContent&gt;
2688 * &lt;/complexType&gt; &lt;/element&gt;
2689 * &lt;/sequence&gt; &lt;attGroup
2690 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
2691 * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2692 * &lt;attribute name="viewId"
2693 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2694 * &lt;attribute name="dividerLocation"
2695 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
2696 * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2697 * &lt;/restriction&gt; &lt;/complexContent&gt;
2698 * &lt;/complexType&gt; </pre>
2702 @XmlAccessorType(XmlAccessType.FIELD)
2703 @XmlType(name = "", propOrder = { "secondaryStructure" })
2704 public static class RnaViewer
2707 @XmlElement(namespace = "www.jalview.org", required = true)
2708 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2710 @XmlAttribute(name = "title")
2711 protected String title;
2713 @XmlAttribute(name = "viewId")
2714 protected String viewId;
2716 @XmlAttribute(name = "dividerLocation")
2717 protected Integer dividerLocation;
2719 @XmlAttribute(name = "selectedRna")
2720 protected Integer selectedRna;
2722 @XmlAttribute(name = "width")
2723 protected Integer width;
2725 @XmlAttribute(name = "height")
2726 protected Integer height;
2728 @XmlAttribute(name = "xpos")
2729 protected Integer xpos;
2731 @XmlAttribute(name = "ypos")
2732 protected Integer ypos;
2735 * Gets the value of the secondaryStructure property.
2737 * <p> This accessor method returns a reference to the live list,
2738 * not a snapshot. Therefore any modification you make to the returned
2739 * list will be present inside the JAXB object. This is why there is not a
2740 * <CODE>set</CODE> method for the secondaryStructure
2743 * <p> For example, to add a new item, do as follows: <pre>
2744 * getSecondaryStructure().add(newItem); </pre>
2747 * <p> Objects of the following type(s) are allowed in the list
2748 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2752 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
2754 if (secondaryStructure == null)
2756 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2758 return this.secondaryStructure;
2762 * Gets the value of the title property.
2764 * @return possible object is {@link String }
2767 public String getTitle()
2773 * Sets the value of the title property.
2776 * allowed object is {@link String }
2779 public void setTitle(String value)
2785 * Gets the value of the viewId property.
2787 * @return possible object is {@link String }
2790 public String getViewId()
2796 * Sets the value of the viewId property.
2799 * allowed object is {@link String }
2802 public void setViewId(String value)
2804 this.viewId = value;
2808 * Gets the value of the dividerLocation property.
2810 * @return possible object is {@link Integer }
2813 public Integer getDividerLocation()
2815 return dividerLocation;
2819 * Sets the value of the dividerLocation property.
2822 * allowed object is {@link Integer }
2825 public void setDividerLocation(Integer value)
2827 this.dividerLocation = value;
2831 * Gets the value of the selectedRna property.
2833 * @return possible object is {@link Integer }
2836 public Integer getSelectedRna()
2842 * Sets the value of the selectedRna property.
2845 * allowed object is {@link Integer }
2848 public void setSelectedRna(Integer value)
2850 this.selectedRna = value;
2854 * Gets the value of the width property.
2856 * @return possible object is {@link Integer }
2859 public Integer getWidth()
2865 * Sets the value of the width property.
2868 * allowed object is {@link Integer }
2871 public void setWidth(Integer value)
2877 * Gets the value of the height property.
2879 * @return possible object is {@link Integer }
2882 public Integer getHeight()
2888 * Sets the value of the height property.
2891 * allowed object is {@link Integer }
2894 public void setHeight(Integer value)
2896 this.height = value;
2900 * Gets the value of the xpos property.
2902 * @return possible object is {@link Integer }
2905 public Integer getXpos()
2911 * Sets the value of the xpos property.
2914 * allowed object is {@link Integer }
2917 public void setXpos(Integer value)
2923 * Gets the value of the ypos property.
2925 * @return possible object is {@link Integer }
2928 public Integer getYpos()
2934 * Sets the value of the ypos property.
2937 * allowed object is {@link Integer }
2940 public void setYpos(Integer value)
2946 * <p>Java class for anonymous complex type.
2948 * <p>The following schema fragment specifies the expected content
2949 * contained within this class.
2951 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
2952 * &lt;restriction
2953 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2954 * &lt;attribute name="title"
2955 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2956 * &lt;attribute name="annotationId" use="required"
2957 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2958 * &lt;attribute name="gapped"
2959 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2960 * &lt;attribute name="viewerState"
2961 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2962 * &lt;/restriction&gt; &lt;/complexContent&gt;
2963 * &lt;/complexType&gt; </pre>
2967 @XmlAccessorType(XmlAccessType.FIELD)
2969 public static class SecondaryStructure
2972 @XmlAttribute(name = "title")
2973 protected String title;
2975 @XmlAttribute(name = "annotationId", required = true)
2976 protected String annotationId;
2978 @XmlAttribute(name = "gapped")
2979 protected Boolean gapped;
2981 @XmlAttribute(name = "viewerState")
2982 protected String viewerState;
2985 * Gets the value of the title property.
2987 * @return possible object is {@link String }
2990 public String getTitle()
2996 * Sets the value of the title property.
2999 * allowed object is {@link String }
3002 public void setTitle(String value)
3008 * Gets the value of the annotationId property.
3010 * @return possible object is {@link String }
3013 public String getAnnotationId()
3015 return annotationId;
3019 * Sets the value of the annotationId property.
3022 * allowed object is {@link String }
3025 public void setAnnotationId(String value)
3027 this.annotationId = value;
3031 * Gets the value of the gapped property.
3033 * @return possible object is {@link Boolean }
3036 public Boolean isGapped()
3042 * Sets the value of the gapped property.
3045 * allowed object is {@link Boolean }
3048 public void setGapped(Boolean value)
3050 this.gapped = value;
3054 * Gets the value of the viewerState property.
3056 * @return possible object is {@link String }
3059 public String getViewerState()
3065 * Sets the value of the viewerState property.
3068 * allowed object is {@link String }
3071 public void setViewerState(String value)
3073 this.viewerState = value;
3083 * <p>Java class for anonymous complex type.
3085 * <p>The following schema fragment specifies the expected content
3086 * contained within this class.
3088 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
3089 * &lt;restriction
3090 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3091 * &lt;sequence&gt; &lt;element name="sequencePoint"
3092 * maxOccurs="unbounded"&gt; &lt;complexType&gt;
3093 * &lt;complexContent&gt; &lt;restriction
3094 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
3095 * ref="{www.jalview.org}position"/&gt; &lt;attribute
3096 * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
3097 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
3098 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
3099 * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
3100 * &lt;complexContent&gt; &lt;restriction
3101 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
3102 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
3103 * &lt;/complexContent&gt; &lt;/complexType&gt;
3104 * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
3105 * &lt;complexType&gt; &lt;complexContent&gt;
3106 * &lt;restriction
3107 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
3108 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
3109 * &lt;/complexContent&gt; &lt;/complexType&gt;
3110 * &lt;/element&gt; &lt;element name="seqPointMax"&gt;
3111 * &lt;complexType&gt; &lt;complexContent&gt;
3112 * &lt;restriction
3113 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
3114 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
3115 * &lt;/complexContent&gt; &lt;/complexType&gt;
3116 * &lt;/element&gt; &lt;element name="pcaData"
3117 * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
3118 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
3119 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3120 * &lt;attribute name="title"
3121 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
3122 * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
3123 * /&gt; &lt;attribute name="xDim"
3124 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
3125 * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3126 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
3127 * /&gt; &lt;attribute name="bgColour"
3128 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
3129 * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
3130 * &lt;attribute name="showLabels"
3131 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3132 * &lt;attribute name="linkToAllViews"
3133 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3134 * &lt;/restriction&gt; &lt;/complexContent&gt;
3135 * &lt;/complexType&gt; </pre>
3139 @XmlAccessorType(XmlAccessType.FIELD)
3143 { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
3144 public static class PcaViewer
3147 @XmlElement(namespace = "www.jalview.org", required = true)
3148 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3150 @XmlElement(namespace = "www.jalview.org", required = true)
3151 protected List<JalviewModel.PcaViewer.Axis> axis;
3153 @XmlElement(namespace = "www.jalview.org", required = true)
3154 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3156 @XmlElement(namespace = "www.jalview.org", required = true)
3157 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3159 @XmlElement(namespace = "www.jalview.org", required = true)
3160 protected PcaDataType pcaData;
3162 @XmlAttribute(name = "title")
3163 protected String title;
3165 @XmlAttribute(name = "scoreModelName")
3166 protected String scoreModelName;
3168 @XmlAttribute(name = "xDim")
3169 protected Integer xDim;
3171 @XmlAttribute(name = "yDim")
3172 protected Integer yDim;
3174 @XmlAttribute(name = "zDim")
3175 protected Integer zDim;
3177 @XmlAttribute(name = "bgColour")
3178 protected Integer bgColour;
3180 @XmlAttribute(name = "scaleFactor")
3181 protected Float scaleFactor;
3183 @XmlAttribute(name = "showLabels")
3184 protected Boolean showLabels;
3186 @XmlAttribute(name = "linkToAllViews")
3187 protected Boolean linkToAllViews;
3189 @XmlAttribute(name = "includeGaps")
3190 protected Boolean includeGaps;
3192 @XmlAttribute(name = "matchGaps")
3193 protected Boolean matchGaps;
3195 @XmlAttribute(name = "includeGappedColumns")
3196 protected Boolean includeGappedColumns;
3198 @XmlAttribute(name = "denominateByShortestLength")
3199 protected Boolean denominateByShortestLength;
3201 @XmlAttribute(name = "width")
3202 protected Integer width;
3204 @XmlAttribute(name = "height")
3205 protected Integer height;
3207 @XmlAttribute(name = "xpos")
3208 protected Integer xpos;
3210 @XmlAttribute(name = "ypos")
3211 protected Integer ypos;
3214 * Gets the value of the sequencePoint property.
3216 * <p> This accessor method returns a reference to the live list, not
3217 * a snapshot. Therefore any modification you make to the returned list will
3218 * be present inside the JAXB object. This is why there is not a
3219 * <CODE>set</CODE> method for the sequencePoint property.
3221 * <p> For example, to add a new item, do as follows: <pre>
3222 * getSequencePoint().add(newItem); </pre>
3225 * <p> Objects of the following type(s) are allowed in the list
3226 * {@link JalviewModel.PcaViewer.SequencePoint }
3230 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
3232 if (sequencePoint == null)
3234 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3236 return this.sequencePoint;
3240 * Gets the value of the axis property.
3242 * <p> This accessor method returns a reference to the live list, not
3243 * a snapshot. Therefore any modification you make to the returned list will
3244 * be present inside the JAXB object. This is why there is not a
3245 * <CODE>set</CODE> method for the axis property.
3247 * <p> For example, to add a new item, do as follows: <pre>
3248 * getAxis().add(newItem); </pre>
3251 * <p> Objects of the following type(s) are allowed in the list
3252 * {@link JalviewModel.PcaViewer.Axis }
3256 public List<JalviewModel.PcaViewer.Axis> getAxis()
3260 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3266 * Gets the value of the seqPointMin property.
3268 * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
3271 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
3277 * Sets the value of the seqPointMin property.
3280 * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
3283 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
3285 this.seqPointMin = value;
3289 * Gets the value of the seqPointMax property.
3291 * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
3294 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
3300 * Sets the value of the seqPointMax property.
3303 * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
3306 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
3308 this.seqPointMax = value;
3312 * Gets the value of the pcaData property.
3314 * @return possible object is {@link PcaDataType }
3317 public PcaDataType getPcaData()
3323 * Sets the value of the pcaData property.
3326 * allowed object is {@link PcaDataType }
3329 public void setPcaData(PcaDataType value)
3331 this.pcaData = value;
3335 * Gets the value of the title property.
3337 * @return possible object is {@link String }
3340 public String getTitle()
3346 * Sets the value of the title property.
3349 * allowed object is {@link String }
3352 public void setTitle(String value)
3358 * Gets the value of the scoreModelName property.
3360 * @return possible object is {@link String }
3363 public String getScoreModelName()
3365 return scoreModelName;
3369 * Sets the value of the scoreModelName property.
3372 * allowed object is {@link String }
3375 public void setScoreModelName(String value)
3377 this.scoreModelName = value;
3381 * Gets the value of the xDim property.
3383 * @return possible object is {@link Integer }
3386 public Integer getXDim()
3392 * Sets the value of the xDim property.
3395 * allowed object is {@link Integer }
3398 public void setXDim(Integer value)
3404 * Gets the value of the yDim property.
3406 * @return possible object is {@link Integer }
3409 public Integer getYDim()
3415 * Sets the value of the yDim property.
3418 * allowed object is {@link Integer }
3421 public void setYDim(Integer value)
3427 * Gets the value of the zDim property.
3429 * @return possible object is {@link Integer }
3432 public Integer getZDim()
3438 * Sets the value of the zDim property.
3441 * allowed object is {@link Integer }
3444 public void setZDim(Integer value)
3450 * Gets the value of the bgColour property.
3452 * @return possible object is {@link Integer }
3455 public Integer getBgColour()
3461 * Sets the value of the bgColour property.
3464 * allowed object is {@link Integer }
3467 public void setBgColour(Integer value)
3469 this.bgColour = value;
3473 * Gets the value of the scaleFactor property.
3475 * @return possible object is {@link Float }
3478 public Float getScaleFactor()
3484 * Sets the value of the scaleFactor property.
3487 * allowed object is {@link Float }
3490 public void setScaleFactor(Float value)
3492 this.scaleFactor = value;
3496 * Gets the value of the showLabels property.
3498 * @return possible object is {@link Boolean }
3501 public Boolean isShowLabels()
3507 * Sets the value of the showLabels property.
3510 * allowed object is {@link Boolean }
3513 public void setShowLabels(Boolean value)
3515 this.showLabels = value;
3519 * Gets the value of the linkToAllViews property.
3521 * @return possible object is {@link Boolean }
3524 public Boolean isLinkToAllViews()
3526 return linkToAllViews;
3530 * Sets the value of the linkToAllViews property.
3533 * allowed object is {@link Boolean }
3536 public void setLinkToAllViews(Boolean value)
3538 this.linkToAllViews = value;
3542 * Gets the value of the includeGaps property.
3544 * @return possible object is {@link Boolean }
3547 public Boolean isIncludeGaps()
3553 * Sets the value of the includeGaps property.
3556 * allowed object is {@link Boolean }
3559 public void setIncludeGaps(Boolean value)
3561 this.includeGaps = value;
3565 * Gets the value of the matchGaps property.
3567 * @return possible object is {@link Boolean }
3570 public Boolean isMatchGaps()
3576 * Sets the value of the matchGaps property.
3579 * allowed object is {@link Boolean }
3582 public void setMatchGaps(Boolean value)
3584 this.matchGaps = value;
3588 * Gets the value of the includeGappedColumns property.
3590 * @return possible object is {@link Boolean }
3593 public Boolean isIncludeGappedColumns()
3595 return includeGappedColumns;
3599 * Sets the value of the includeGappedColumns property.
3602 * allowed object is {@link Boolean }
3605 public void setIncludeGappedColumns(Boolean value)
3607 this.includeGappedColumns = value;
3611 * Gets the value of the denominateByShortestLength property.
3613 * @return possible object is {@link Boolean }
3616 public Boolean isDenominateByShortestLength()
3618 return denominateByShortestLength;
3622 * Sets the value of the denominateByShortestLength property.
3625 * allowed object is {@link Boolean }
3628 public void setDenominateByShortestLength(Boolean value)
3630 this.denominateByShortestLength = value;
3634 * Gets the value of the width property.
3636 * @return possible object is {@link Integer }
3639 public Integer getWidth()
3645 * Sets the value of the width property.
3648 * allowed object is {@link Integer }
3651 public void setWidth(Integer value)
3657 * Gets the value of the height property.
3659 * @return possible object is {@link Integer }
3662 public Integer getHeight()
3668 * Sets the value of the height property.
3671 * allowed object is {@link Integer }
3674 public void setHeight(Integer value)
3676 this.height = value;
3680 * Gets the value of the xpos property.
3682 * @return possible object is {@link Integer }
3685 public Integer getXpos()
3691 * Sets the value of the xpos property.
3694 * allowed object is {@link Integer }
3697 public void setXpos(Integer value)
3703 * Gets the value of the ypos property.
3705 * @return possible object is {@link Integer }
3708 public Integer getYpos()
3714 * Sets the value of the ypos property.
3717 * allowed object is {@link Integer }
3720 public void setYpos(Integer value)
3726 * <p>Java class for anonymous complex type.
3728 * <p>The following schema fragment specifies the expected content
3729 * contained within this class.
3731 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
3732 * &lt;restriction
3733 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
3734 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
3735 * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
3739 @XmlAccessorType(XmlAccessType.FIELD)
3741 public static class Axis
3744 @XmlAttribute(name = "xPos")
3745 protected Float xPos;
3747 @XmlAttribute(name = "yPos")
3748 protected Float yPos;
3750 @XmlAttribute(name = "zPos")
3751 protected Float zPos;
3754 * Gets the value of the xPos property.
3756 * @return possible object is {@link Float }
3759 public Float getXPos()
3765 * Sets the value of the xPos property.
3768 * allowed object is {@link Float }
3771 public void setXPos(Float value)
3777 * Gets the value of the yPos property.
3779 * @return possible object is {@link Float }
3782 public Float getYPos()
3788 * Sets the value of the yPos property.
3791 * allowed object is {@link Float }
3794 public void setYPos(Float value)
3800 * Gets the value of the zPos property.
3802 * @return possible object is {@link Float }
3805 public Float getZPos()
3811 * Sets the value of the zPos property.
3814 * allowed object is {@link Float }
3817 public void setZPos(Float value)
3825 * <p>Java class for anonymous complex type.
3827 * <p>The following schema fragment specifies the expected content
3828 * contained within this class.
3830 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
3831 * &lt;restriction
3832 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
3833 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
3834 * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
3838 @XmlAccessorType(XmlAccessType.FIELD)
3840 public static class SeqPointMax
3843 @XmlAttribute(name = "xPos")
3844 protected Float xPos;
3846 @XmlAttribute(name = "yPos")
3847 protected Float yPos;
3849 @XmlAttribute(name = "zPos")
3850 protected Float zPos;
3853 * Gets the value of the xPos property.
3855 * @return possible object is {@link Float }
3858 public Float getXPos()
3864 * Sets the value of the xPos property.
3867 * allowed object is {@link Float }
3870 public void setXPos(Float value)
3876 * Gets the value of the yPos property.
3878 * @return possible object is {@link Float }
3881 public Float getYPos()
3887 * Sets the value of the yPos property.
3890 * allowed object is {@link Float }
3893 public void setYPos(Float value)
3899 * Gets the value of the zPos property.
3901 * @return possible object is {@link Float }
3904 public Float getZPos()
3910 * Sets the value of the zPos property.
3913 * allowed object is {@link Float }
3916 public void setZPos(Float value)
3924 * <p>Java class for anonymous complex type.
3926 * <p>The following schema fragment specifies the expected content
3927 * contained within this class.
3929 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
3930 * &lt;restriction
3931 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
3932 * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
3933 * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
3937 @XmlAccessorType(XmlAccessType.FIELD)
3939 public static class SeqPointMin
3942 @XmlAttribute(name = "xPos")
3943 protected Float xPos;
3945 @XmlAttribute(name = "yPos")
3946 protected Float yPos;
3948 @XmlAttribute(name = "zPos")
3949 protected Float zPos;
3952 * Gets the value of the xPos property.
3954 * @return possible object is {@link Float }
3957 public Float getXPos()
3963 * Sets the value of the xPos property.
3966 * allowed object is {@link Float }
3969 public void setXPos(Float value)
3975 * Gets the value of the yPos property.
3977 * @return possible object is {@link Float }
3980 public Float getYPos()
3986 * Sets the value of the yPos property.
3989 * allowed object is {@link Float }
3992 public void setYPos(Float value)
3998 * Gets the value of the zPos property.
4000 * @return possible object is {@link Float }
4003 public Float getZPos()
4009 * Sets the value of the zPos property.
4012 * allowed object is {@link Float }
4015 public void setZPos(Float value)
4023 * <p>Java class for anonymous complex type.
4025 * <p>The following schema fragment specifies the expected content
4026 * contained within this class.
4028 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
4029 * &lt;restriction
4030 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
4031 * ref="{www.jalview.org}position"/&gt; &lt;attribute
4032 * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
4033 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
4034 * &lt;/complexType&gt; </pre>
4038 @XmlAccessorType(XmlAccessType.FIELD)
4040 public static class SequencePoint
4043 @XmlAttribute(name = "sequenceRef")
4044 protected String sequenceRef;
4046 @XmlAttribute(name = "xPos")
4047 protected Float xPos;
4049 @XmlAttribute(name = "yPos")
4050 protected Float yPos;
4052 @XmlAttribute(name = "zPos")
4053 protected Float zPos;
4056 * Gets the value of the sequenceRef property.
4058 * @return possible object is {@link String }
4061 public String getSequenceRef()
4067 * Sets the value of the sequenceRef property.
4070 * allowed object is {@link String }
4073 public void setSequenceRef(String value)
4075 this.sequenceRef = value;
4079 * Gets the value of the xPos property.
4081 * @return possible object is {@link Float }
4084 public Float getXPos()
4090 * Sets the value of the xPos property.
4093 * allowed object is {@link Float }
4096 public void setXPos(Float value)
4102 * Gets the value of the yPos property.
4104 * @return possible object is {@link Float }
4107 public Float getYPos()
4113 * Sets the value of the yPos property.
4116 * allowed object is {@link Float }
4119 public void setYPos(Float value)
4125 * Gets the value of the zPos property.
4127 * @return possible object is {@link Float }
4130 public Float getZPos()
4136 * Sets the value of the zPos property.
4139 * allowed object is {@link Float }
4142 public void setZPos(Float value)
4152 * <p>Java class for anonymous complex type.
4154 * <p>The following schema fragment specifies the expected content
4155 * contained within this class.
4157 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
4158 * &lt;restriction
4159 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
4160 * minOccurs="0"&gt; &lt;element name="title"
4161 * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
4162 * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4163 * &lt;/sequence&gt; &lt;attGroup
4164 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
4165 * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4166 * &lt;attribute name="fontSize"
4167 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4168 * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4169 * &lt;attribute name="threshold"
4170 * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
4171 * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
4172 * /&gt; &lt;attribute name="showDistances"
4173 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4174 * &lt;attribute name="markUnlinked"
4175 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4176 * &lt;attribute name="fitToWindow"
4177 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4178 * &lt;attribute name="currentTree"
4179 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4180 * &lt;attribute name="columnWise"
4181 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4182 * &lt;attribute name="columnReference"
4183 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
4184 * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4185 * &lt;attribute name="linkToAllViews"
4186 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4187 * &lt;/restriction&gt; &lt;/complexContent&gt;
4188 * &lt;/complexType&gt; </pre>
4192 @XmlAccessorType(XmlAccessType.FIELD)
4193 @XmlType(name = "", propOrder = { "title", "newick" })
4194 public static class Tree
4197 @XmlElement(namespace = "www.jalview.org")
4198 protected String title;
4200 @XmlElement(namespace = "www.jalview.org")
4201 protected String newick;
4203 @XmlAttribute(name = "fontName")
4204 protected String fontName;
4206 @XmlAttribute(name = "fontSize")
4207 protected Integer fontSize;
4209 @XmlAttribute(name = "fontStyle")
4210 protected Integer fontStyle;
4212 @XmlAttribute(name = "threshold")
4213 protected Float threshold;
4215 @XmlAttribute(name = "showBootstrap")
4216 protected Boolean showBootstrap;
4218 @XmlAttribute(name = "showDistances")
4219 protected Boolean showDistances;
4221 @XmlAttribute(name = "markUnlinked")
4222 protected Boolean markUnlinked;
4224 @XmlAttribute(name = "fitToWindow")
4225 protected Boolean fitToWindow;
4227 @XmlAttribute(name = "currentTree")
4228 protected Boolean currentTree;
4230 @XmlAttribute(name = "columnWise")
4231 protected Boolean columnWise;
4233 @XmlAttribute(name = "columnReference")
4234 protected String columnReference;
4236 @XmlAttribute(name = "id")
4237 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4239 @XmlSchemaType(name = "ID")
4240 protected String id;
4242 @XmlAttribute(name = "linkToAllViews")
4243 protected Boolean linkToAllViews;
4245 @XmlAttribute(name = "width")
4246 protected Integer width;
4248 @XmlAttribute(name = "height")
4249 protected Integer height;
4251 @XmlAttribute(name = "xpos")
4252 protected Integer xpos;
4254 @XmlAttribute(name = "ypos")
4255 protected Integer ypos;
4258 * Gets the value of the title property.
4260 * @return possible object is {@link String }
4263 public String getTitle()
4269 * Sets the value of the title property.
4272 * allowed object is {@link String }
4275 public void setTitle(String value)
4281 * Gets the value of the newick property.
4283 * @return possible object is {@link String }
4286 public String getNewick()
4292 * Sets the value of the newick property.
4295 * allowed object is {@link String }
4298 public void setNewick(String value)
4300 this.newick = value;
4304 * Gets the value of the fontName property.
4306 * @return possible object is {@link String }
4309 public String getFontName()
4315 * Sets the value of the fontName property.
4318 * allowed object is {@link String }
4321 public void setFontName(String value)
4323 this.fontName = value;
4327 * Gets the value of the fontSize property.
4329 * @return possible object is {@link Integer }
4332 public Integer getFontSize()
4338 * Sets the value of the fontSize property.
4341 * allowed object is {@link Integer }
4344 public void setFontSize(Integer value)
4346 this.fontSize = value;
4350 * Gets the value of the fontStyle property.
4352 * @return possible object is {@link Integer }
4355 public Integer getFontStyle()
4361 * Sets the value of the fontStyle property.
4364 * allowed object is {@link Integer }
4367 public void setFontStyle(Integer value)
4369 this.fontStyle = value;
4373 * Gets the value of the threshold property.
4375 * @return possible object is {@link Float }
4378 public Float getThreshold()
4384 * Sets the value of the threshold property.
4387 * allowed object is {@link Float }
4390 public void setThreshold(Float value)
4392 this.threshold = value;
4396 * Gets the value of the showBootstrap property.
4398 * @return possible object is {@link Boolean }
4401 public Boolean isShowBootstrap()
4403 return showBootstrap;
4407 * Sets the value of the showBootstrap property.
4410 * allowed object is {@link Boolean }
4413 public void setShowBootstrap(Boolean value)
4415 this.showBootstrap = value;
4419 * Gets the value of the showDistances property.
4421 * @return possible object is {@link Boolean }
4424 public Boolean isShowDistances()
4426 return showDistances;
4430 * Sets the value of the showDistances property.
4433 * allowed object is {@link Boolean }
4436 public void setShowDistances(Boolean value)
4438 this.showDistances = value;
4442 * Gets the value of the markUnlinked property.
4444 * @return possible object is {@link Boolean }
4447 public Boolean isMarkUnlinked()
4449 return markUnlinked;
4453 * Sets the value of the markUnlinked property.
4456 * allowed object is {@link Boolean }
4459 public void setMarkUnlinked(Boolean value)
4461 this.markUnlinked = value;
4465 * Gets the value of the fitToWindow property.
4467 * @return possible object is {@link Boolean }
4470 public Boolean isFitToWindow()
4476 * Sets the value of the fitToWindow property.
4479 * allowed object is {@link Boolean }
4482 public void setFitToWindow(Boolean value)
4484 this.fitToWindow = value;
4488 * Gets the value of the currentTree property.
4490 * @return possible object is {@link Boolean }
4493 public Boolean isCurrentTree()
4499 * Sets the value of the currentTree property.
4502 * allowed object is {@link Boolean }
4505 public void setCurrentTree(Boolean value)
4507 this.currentTree = value;
4511 * Gets the value of the columnWise property.
4513 * @return possible object is {@link Boolean }
4516 public boolean isColumnWise()
4518 if (columnWise == null)
4529 * Sets the value of the columnWise property.
4532 * allowed object is {@link Boolean }
4535 public void setColumnWise(Boolean value)
4537 this.columnWise = value;
4541 * Gets the value of the columnReference property.
4543 * @return possible object is {@link String }
4546 public String getColumnReference()
4548 return columnReference;
4552 * Sets the value of the columnReference property.
4555 * allowed object is {@link String }
4558 public void setColumnReference(String value)
4560 this.columnReference = value;
4564 * Gets the value of the id property.
4566 * @return possible object is {@link String }
4569 public String getId()
4575 * Sets the value of the id property.
4578 * allowed object is {@link String }
4581 public void setId(String value)
4587 * Gets the value of the linkToAllViews property.
4589 * @return possible object is {@link Boolean }
4592 public boolean isLinkToAllViews()
4594 if (linkToAllViews == null)
4600 return linkToAllViews;
4605 * Sets the value of the linkToAllViews property.
4608 * allowed object is {@link Boolean }
4611 public void setLinkToAllViews(Boolean value)
4613 this.linkToAllViews = value;
4617 * Gets the value of the width property.
4619 * @return possible object is {@link Integer }
4622 public Integer getWidth()
4628 * Sets the value of the width property.
4631 * allowed object is {@link Integer }
4634 public void setWidth(Integer value)
4640 * Gets the value of the height property.
4642 * @return possible object is {@link Integer }
4645 public Integer getHeight()
4651 * Sets the value of the height property.
4654 * allowed object is {@link Integer }
4657 public void setHeight(Integer value)
4659 this.height = value;
4663 * Gets the value of the xpos property.
4665 * @return possible object is {@link Integer }
4668 public Integer getXpos()
4674 * Sets the value of the xpos property.
4677 * allowed object is {@link Integer }
4680 public void setXpos(Integer value)
4686 * Gets the value of the ypos property.
4688 * @return possible object is {@link Integer }
4691 public Integer getYpos()
4697 * Sets the value of the ypos property.
4700 * allowed object is {@link Integer }
4703 public void setYpos(Integer value)
4711 * <p>Java class for anonymous complex type.
4713 * <p>The following schema fragment specifies the expected content
4714 * contained within this class.
4716 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
4717 * &lt;restriction
4718 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4719 * &lt;sequence&gt; &lt;element name="UserColourScheme"
4720 * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
4721 * &lt;/sequence&gt; &lt;attribute name="id"
4722 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4723 * &lt;/restriction&gt; &lt;/complexContent&gt;
4724 * &lt;/complexType&gt; </pre>
4728 @XmlAccessorType(XmlAccessType.FIELD)
4729 @XmlType(name = "", propOrder = { "userColourScheme" })
4730 public static class UserColours
4734 name = "UserColourScheme",
4735 namespace = "www.jalview.org",
4737 protected JalviewUserColours userColourScheme;
4739 @XmlAttribute(name = "id")
4740 protected String id;
4743 * Gets the value of the userColourScheme property.
4745 * @return possible object is {@link JalviewUserColours }
4748 public JalviewUserColours getUserColourScheme()
4750 return userColourScheme;
4754 * Sets the value of the userColourScheme property.
4757 * allowed object is {@link JalviewUserColours }
4760 public void setUserColourScheme(JalviewUserColours value)
4762 this.userColourScheme = value;
4766 * Gets the value of the id property.
4768 * @return possible object is {@link String }
4771 public String getId()
4777 * Sets the value of the id property.
4780 * allowed object is {@link String }
4783 public void setId(String value)
4791 * <p>Java class for anonymous complex type.
4793 * <p>The following schema fragment specifies the expected content
4794 * contained within this class.
4796 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
4797 * &lt;restriction
4798 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4799 * &lt;sequence&gt; &lt;element name="AnnotationColours"
4800 * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
4801 * &lt;element name="hiddenColumns" maxOccurs="unbounded"
4802 * minOccurs="0"&gt; &lt;complexType&gt;
4803 * &lt;complexContent&gt; &lt;restriction
4804 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
4805 * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4806 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
4807 * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
4808 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
4809 * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
4810 * &lt;complexType&gt; &lt;complexContent&gt;
4812 * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
4813 * &lt;attribute name="calcId" use="required"
4814 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
4815 * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
4816 * default="false" /&gt; &lt;attribute name="autoUpdate"
4817 * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4818 * &lt;/extension&gt; &lt;/complexContent&gt;
4819 * &lt;/complexType&gt; &lt;/element&gt; &lt;element
4820 * name="overview" minOccurs="0"&gt; &lt;complexType&gt;
4821 * &lt;complexContent&gt; &lt;restriction
4822 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
4823 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
4824 * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
4825 * /&gt; &lt;attribute name="residueColour"
4826 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4827 * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4828 * &lt;attribute name="hiddenColour"
4829 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4830 * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4831 * &lt;/restriction&gt; &lt;/complexContent&gt;
4832 * &lt;/complexType&gt; &lt;/element&gt;
4833 * &lt;/sequence&gt; &lt;attGroup
4834 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
4835 * name="conservationSelected"
4836 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4837 * &lt;attribute name="pidSelected"
4838 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4839 * &lt;attribute name="bgColour"
4840 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
4841 * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4842 * &lt;attribute name="pidThreshold"
4843 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4844 * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4845 * &lt;attribute name="showFullId"
4846 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4847 * &lt;attribute name="rightAlignIds"
4848 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4849 * &lt;attribute name="showText"
4850 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4851 * &lt;attribute name="showColourText"
4852 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4853 * &lt;attribute name="showUnconserved"
4854 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4855 * &lt;attribute name="showBoxes"
4856 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4857 * &lt;attribute name="wrapAlignment"
4858 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4859 * &lt;attribute name="renderGaps"
4860 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4861 * &lt;attribute name="showSequenceFeatures"
4862 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4863 * &lt;attribute name="showNPfeatureTooltip"
4864 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4865 * &lt;attribute name="showDbRefTooltip"
4866 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4867 * &lt;attribute name="followHighlight"
4868 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4869 * &lt;attribute name="followSelection"
4870 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4871 * &lt;attribute name="showAnnotation"
4872 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4873 * &lt;attribute name="centreColumnLabels"
4874 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4875 * &lt;attribute name="showGroupConservation"
4876 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4877 * &lt;attribute name="showGroupConsensus"
4878 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4879 * &lt;attribute name="showConsensusHistogram"
4880 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4881 * &lt;attribute name="showSequenceLogo"
4882 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4883 * &lt;attribute name="normaliseSequenceLogo"
4884 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4885 * &lt;attribute name="ignoreGapsinConsensus"
4886 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4887 * &lt;attribute name="startRes"
4888 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4889 * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4890 * &lt;attribute name="charWidth"
4891 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4892 * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4893 * &lt;attribute name="fontName"
4894 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
4895 * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4896 * &lt;attribute name="fontStyle"
4897 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4898 * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4899 * &lt;attribute name="idWidthManuallyAdjusted"
4900 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4901 * &lt;attribute name="scaleProteinAsCdna"
4902 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4903 * &lt;attribute name="viewName"
4904 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
4905 * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
4906 * /&gt; &lt;attribute name="gatheredViews"
4907 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4908 * &lt;attribute name="textCol1"
4909 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4910 * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4911 * &lt;attribute name="textColThreshold"
4912 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
4913 * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4914 * &lt;attribute name="complementId"
4915 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
4916 * name="showComplementFeatures"
4917 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4918 * &lt;attribute name="showComplementFeaturesOnTop"
4919 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4920 * &lt;/restriction&gt; &lt;/complexContent&gt;
4921 * &lt;/complexType&gt; </pre>
4925 @XmlAccessorType(XmlAccessType.FIELD)
4929 { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
4930 public static class Viewport
4933 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4934 protected AnnotationColourScheme annotationColours;
4936 @XmlElement(namespace = "www.jalview.org")
4937 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4939 @XmlElement(namespace = "www.jalview.org")
4940 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4942 @XmlElement(namespace = "www.jalview.org")
4943 protected JalviewModel.Viewport.Overview overview;
4945 @XmlAttribute(name = "conservationSelected")
4946 protected Boolean conservationSelected;
4948 @XmlAttribute(name = "pidSelected")
4949 protected Boolean pidSelected;
4951 @XmlAttribute(name = "bgColour")
4952 protected String bgColour;
4954 @XmlAttribute(name = "consThreshold")
4955 protected Integer consThreshold;
4957 @XmlAttribute(name = "pidThreshold")
4958 protected Integer pidThreshold;
4960 @XmlAttribute(name = "title")
4961 protected String title;
4963 @XmlAttribute(name = "showFullId")
4964 protected Boolean showFullId;
4966 @XmlAttribute(name = "rightAlignIds")
4967 protected Boolean rightAlignIds;
4969 @XmlAttribute(name = "showText")
4970 protected Boolean showText;
4972 @XmlAttribute(name = "showColourText")
4973 protected Boolean showColourText;
4975 @XmlAttribute(name = "showUnconserved")
4976 protected Boolean showUnconserved;
4978 @XmlAttribute(name = "showBoxes")
4979 protected Boolean showBoxes;
4981 @XmlAttribute(name = "wrapAlignment")
4982 protected Boolean wrapAlignment;
4984 @XmlAttribute(name = "renderGaps")
4985 protected Boolean renderGaps;
4987 @XmlAttribute(name = "showSequenceFeatures")
4988 protected Boolean showSequenceFeatures;
4990 @XmlAttribute(name = "showNPfeatureTooltip")
4991 protected Boolean showNPfeatureTooltip;
4993 @XmlAttribute(name = "showDbRefTooltip")
4994 protected Boolean showDbRefTooltip;
4996 @XmlAttribute(name = "followHighlight")
4997 protected Boolean followHighlight;
4999 @XmlAttribute(name = "followSelection")
5000 protected Boolean followSelection;
5002 @XmlAttribute(name = "showAnnotation")
5003 protected Boolean showAnnotation;
5005 @XmlAttribute(name = "centreColumnLabels")
5006 protected Boolean centreColumnLabels;
5008 @XmlAttribute(name = "showGroupConservation")
5009 protected Boolean showGroupConservation;
5011 @XmlAttribute(name = "showGroupConsensus")
5012 protected Boolean showGroupConsensus;
5014 @XmlAttribute(name = "showConsensusHistogram")
5015 protected Boolean showConsensusHistogram;
5017 @XmlAttribute(name = "showSequenceLogo")
5018 protected Boolean showSequenceLogo;
5020 @XmlAttribute(name = "normaliseSequenceLogo")
5021 protected Boolean normaliseSequenceLogo;
5023 @XmlAttribute(name = "ignoreGapsinConsensus")
5024 protected Boolean ignoreGapsinConsensus;
5026 @XmlAttribute(name = "startRes")
5027 protected Integer startRes;
5029 @XmlAttribute(name = "startSeq")
5030 protected Integer startSeq;
5032 @XmlAttribute(name = "charWidth")
5033 protected Integer charWidth;
5035 @XmlAttribute(name = "charHeight")
5036 protected Integer charHeight;
5038 @XmlAttribute(name = "fontName")
5039 protected String fontName;
5041 @XmlAttribute(name = "fontSize")
5042 protected Integer fontSize;
5044 @XmlAttribute(name = "fontStyle")
5045 protected Integer fontStyle;
5047 @XmlAttribute(name = "idWidth")
5048 protected Integer idWidth;
5050 @XmlAttribute(name = "idWidthManuallyAdjusted")
5051 protected Boolean idWidthManuallyAdjusted;
5053 @XmlAttribute(name = "scaleProteinAsCdna")
5054 protected Boolean scaleProteinAsCdna;
5056 @XmlAttribute(name = "viewName")
5057 protected String viewName;
5059 @XmlAttribute(name = "sequenceSetId")
5060 protected String sequenceSetId;
5062 @XmlAttribute(name = "gatheredViews")
5063 protected Boolean gatheredViews;
5065 @XmlAttribute(name = "textCol1")
5066 protected Integer textCol1;
5068 @XmlAttribute(name = "textCol2")
5069 protected Integer textCol2;
5071 @XmlAttribute(name = "textColThreshold")
5072 protected Integer textColThreshold;
5074 @XmlAttribute(name = "id")
5075 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5077 @XmlSchemaType(name = "ID")
5078 protected String id;
5080 @XmlAttribute(name = "complementId")
5081 protected String complementId;
5083 @XmlAttribute(name = "showComplementFeatures")
5084 protected Boolean showComplementFeatures;
5086 @XmlAttribute(name = "showComplementFeaturesOnTop")
5087 protected Boolean showComplementFeaturesOnTop;
5089 @XmlAttribute(name = "width")
5090 protected Integer width;
5092 @XmlAttribute(name = "height")
5093 protected Integer height;
5095 @XmlAttribute(name = "xpos")
5096 protected Integer xpos;
5098 @XmlAttribute(name = "ypos")
5099 protected Integer ypos;
5102 * Gets the value of the annotationColours property.
5104 * @return possible object is {@link AnnotationColourScheme }
5107 public AnnotationColourScheme getAnnotationColours()
5109 return annotationColours;
5113 * Sets the value of the annotationColours property.
5116 * allowed object is {@link AnnotationColourScheme }
5119 public void setAnnotationColours(AnnotationColourScheme value)
5121 this.annotationColours = value;
5125 * Gets the value of the hiddenColumns property.
5127 * <p> This accessor method returns a reference to the live list, not
5128 * a snapshot. Therefore any modification you make to the returned list will
5129 * be present inside the JAXB object. This is why there is not a
5130 * <CODE>set</CODE> method for the hiddenColumns property.
5132 * <p> For example, to add a new item, do as follows: <pre>
5133 * getHiddenColumns().add(newItem); </pre>
5136 * <p> Objects of the following type(s) are allowed in the list
5137 * {@link JalviewModel.Viewport.HiddenColumns }
5141 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
5143 if (hiddenColumns == null)
5145 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5147 return this.hiddenColumns;
5151 * Gets the value of the calcIdParam property.
5153 * <p> This accessor method returns a reference to the live list, not
5154 * a snapshot. Therefore any modification you make to the returned list will
5155 * be present inside the JAXB object. This is why there is not a
5156 * <CODE>set</CODE> method for the calcIdParam property.
5158 * <p> For example, to add a new item, do as follows: <pre>
5159 * getCalcIdParam().add(newItem); </pre>
5162 * <p> Objects of the following type(s) are allowed in the list
5163 * {@link JalviewModel.Viewport.CalcIdParam }
5167 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
5169 if (calcIdParam == null)
5171 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5173 return this.calcIdParam;
5177 * Gets the value of the overview property.
5179 * @return possible object is {@link JalviewModel.Viewport.Overview }
5182 public JalviewModel.Viewport.Overview getOverview()
5188 * Sets the value of the overview property.
5191 * allowed object is {@link JalviewModel.Viewport.Overview }
5194 public void setOverview(JalviewModel.Viewport.Overview value)
5196 this.overview = value;
5200 * Gets the value of the conservationSelected property.
5202 * @return possible object is {@link Boolean }
5205 public Boolean isConservationSelected()
5207 return conservationSelected;
5211 * Sets the value of the conservationSelected property.
5214 * allowed object is {@link Boolean }
5217 public void setConservationSelected(Boolean value)
5219 this.conservationSelected = value;
5223 * Gets the value of the pidSelected property.
5225 * @return possible object is {@link Boolean }
5228 public Boolean isPidSelected()
5234 * Sets the value of the pidSelected property.
5237 * allowed object is {@link Boolean }
5240 public void setPidSelected(Boolean value)
5242 this.pidSelected = value;
5246 * Gets the value of the bgColour property.
5248 * @return possible object is {@link String }
5251 public String getBgColour()
5257 * Sets the value of the bgColour property.
5260 * allowed object is {@link String }
5263 public void setBgColour(String value)
5265 this.bgColour = value;
5269 * Gets the value of the consThreshold property.
5271 * @return possible object is {@link Integer }
5274 public Integer getConsThreshold()
5276 return consThreshold;
5280 * Sets the value of the consThreshold property.
5283 * allowed object is {@link Integer }
5286 public void setConsThreshold(Integer value)
5288 this.consThreshold = value;
5292 * Gets the value of the pidThreshold property.
5294 * @return possible object is {@link Integer }
5297 public Integer getPidThreshold()
5299 return pidThreshold;
5303 * Sets the value of the pidThreshold property.
5306 * allowed object is {@link Integer }
5309 public void setPidThreshold(Integer value)
5311 this.pidThreshold = value;
5315 * Gets the value of the title property.
5317 * @return possible object is {@link String }
5320 public String getTitle()
5326 * Sets the value of the title property.
5329 * allowed object is {@link String }
5332 public void setTitle(String value)
5338 * Gets the value of the showFullId property.
5340 * @return possible object is {@link Boolean }
5343 public Boolean isShowFullId()
5349 * Sets the value of the showFullId property.
5352 * allowed object is {@link Boolean }
5355 public void setShowFullId(Boolean value)
5357 this.showFullId = value;
5361 * Gets the value of the rightAlignIds property.
5363 * @return possible object is {@link Boolean }
5366 public Boolean isRightAlignIds()
5368 return rightAlignIds;
5372 * Sets the value of the rightAlignIds property.
5375 * allowed object is {@link Boolean }
5378 public void setRightAlignIds(Boolean value)
5380 this.rightAlignIds = value;
5384 * Gets the value of the showText property.
5386 * @return possible object is {@link Boolean }
5389 public Boolean isShowText()
5395 * Sets the value of the showText property.
5398 * allowed object is {@link Boolean }
5401 public void setShowText(Boolean value)
5403 this.showText = value;
5407 * Gets the value of the showColourText property.
5409 * @return possible object is {@link Boolean }
5412 public Boolean isShowColourText()
5414 return showColourText;
5418 * Sets the value of the showColourText property.
5421 * allowed object is {@link Boolean }
5424 public void setShowColourText(Boolean value)
5426 this.showColourText = value;
5430 * Gets the value of the showUnconserved property.
5432 * @return possible object is {@link Boolean }
5435 public boolean isShowUnconserved()
5437 if (showUnconserved == null)
5443 return showUnconserved;
5448 * Sets the value of the showUnconserved property.
5451 * allowed object is {@link Boolean }
5454 public void setShowUnconserved(Boolean value)
5456 this.showUnconserved = value;
5460 * Gets the value of the showBoxes property.
5462 * @return possible object is {@link Boolean }
5465 public Boolean isShowBoxes()
5471 * Sets the value of the showBoxes property.
5474 * allowed object is {@link Boolean }
5477 public void setShowBoxes(Boolean value)
5479 this.showBoxes = value;
5483 * Gets the value of the wrapAlignment property.
5485 * @return possible object is {@link Boolean }
5488 public Boolean isWrapAlignment()
5490 return wrapAlignment;
5494 * Sets the value of the wrapAlignment property.
5497 * allowed object is {@link Boolean }
5500 public void setWrapAlignment(Boolean value)
5502 this.wrapAlignment = value;
5506 * Gets the value of the renderGaps property.
5508 * @return possible object is {@link Boolean }
5511 public Boolean isRenderGaps()
5517 * Sets the value of the renderGaps property.
5520 * allowed object is {@link Boolean }
5523 public void setRenderGaps(Boolean value)
5525 this.renderGaps = value;
5529 * Gets the value of the showSequenceFeatures property.
5531 * @return possible object is {@link Boolean }
5534 public Boolean isShowSequenceFeatures()
5536 return showSequenceFeatures;
5540 * Sets the value of the showSequenceFeatures property.
5543 * allowed object is {@link Boolean }
5546 public void setShowSequenceFeatures(Boolean value)
5548 this.showSequenceFeatures = value;
5552 * Gets the value of the showNPfeatureTooltip property.
5554 * @return possible object is {@link Boolean }
5557 public Boolean isShowNPfeatureTooltip()
5559 return showNPfeatureTooltip;
5563 * Sets the value of the showNPfeatureTooltip property.
5566 * allowed object is {@link Boolean }
5569 public void setShowNPfeatureTooltip(Boolean value)
5571 this.showNPfeatureTooltip = value;
5575 * Gets the value of the showDbRefTooltip property.
5577 * @return possible object is {@link Boolean }
5580 public Boolean isShowDbRefTooltip()
5582 return showDbRefTooltip;
5586 * Sets the value of the showDbRefTooltip property.
5589 * allowed object is {@link Boolean }
5592 public void setShowDbRefTooltip(Boolean value)
5594 this.showDbRefTooltip = value;
5598 * Gets the value of the followHighlight property.
5600 * @return possible object is {@link Boolean }
5603 public boolean isFollowHighlight()
5605 if (followHighlight == null)
5611 return followHighlight;
5616 * Sets the value of the followHighlight property.
5619 * allowed object is {@link Boolean }
5622 public void setFollowHighlight(Boolean value)
5624 this.followHighlight = value;
5628 * Gets the value of the followSelection property.
5630 * @return possible object is {@link Boolean }
5633 public boolean isFollowSelection()
5635 if (followSelection == null)
5641 return followSelection;
5646 * Sets the value of the followSelection property.
5649 * allowed object is {@link Boolean }
5652 public void setFollowSelection(Boolean value)
5654 this.followSelection = value;
5658 * Gets the value of the showAnnotation property.
5660 * @return possible object is {@link Boolean }
5663 public Boolean isShowAnnotation()
5665 return showAnnotation;
5669 * Sets the value of the showAnnotation property.
5672 * allowed object is {@link Boolean }
5675 public void setShowAnnotation(Boolean value)
5677 this.showAnnotation = value;
5681 * Gets the value of the centreColumnLabels property.
5683 * @return possible object is {@link Boolean }
5686 public boolean isCentreColumnLabels()
5688 if (centreColumnLabels == null)
5694 return centreColumnLabels;
5699 * Sets the value of the centreColumnLabels property.
5702 * allowed object is {@link Boolean }
5705 public void setCentreColumnLabels(Boolean value)
5707 this.centreColumnLabels = value;
5711 * Gets the value of the showGroupConservation property.
5713 * @return possible object is {@link Boolean }
5716 public boolean isShowGroupConservation()
5718 if (showGroupConservation == null)
5724 return showGroupConservation;
5729 * Sets the value of the showGroupConservation property.
5732 * allowed object is {@link Boolean }
5735 public void setShowGroupConservation(Boolean value)
5737 this.showGroupConservation = value;
5741 * Gets the value of the showGroupConsensus property.
5743 * @return possible object is {@link Boolean }
5746 public boolean isShowGroupConsensus()
5748 if (showGroupConsensus == null)
5754 return showGroupConsensus;
5759 * Sets the value of the showGroupConsensus property.
5762 * allowed object is {@link Boolean }
5765 public void setShowGroupConsensus(Boolean value)
5767 this.showGroupConsensus = value;
5771 * Gets the value of the showConsensusHistogram property.
5773 * @return possible object is {@link Boolean }
5776 public boolean isShowConsensusHistogram()
5778 if (showConsensusHistogram == null)
5784 return showConsensusHistogram;
5789 * Sets the value of the showConsensusHistogram property.
5792 * allowed object is {@link Boolean }
5795 public void setShowConsensusHistogram(Boolean value)
5797 this.showConsensusHistogram = value;
5801 * Gets the value of the showSequenceLogo property.
5803 * @return possible object is {@link Boolean }
5806 public boolean isShowSequenceLogo()
5808 if (showSequenceLogo == null)
5814 return showSequenceLogo;
5819 * Sets the value of the showSequenceLogo property.
5822 * allowed object is {@link Boolean }
5825 public void setShowSequenceLogo(Boolean value)
5827 this.showSequenceLogo = value;
5831 * Gets the value of the normaliseSequenceLogo property.
5833 * @return possible object is {@link Boolean }
5836 public boolean isNormaliseSequenceLogo()
5838 if (normaliseSequenceLogo == null)
5844 return normaliseSequenceLogo;
5849 * Sets the value of the normaliseSequenceLogo property.
5852 * allowed object is {@link Boolean }
5855 public void setNormaliseSequenceLogo(Boolean value)
5857 this.normaliseSequenceLogo = value;
5861 * Gets the value of the ignoreGapsinConsensus property.
5863 * @return possible object is {@link Boolean }
5866 public boolean isIgnoreGapsinConsensus()
5868 if (ignoreGapsinConsensus == null)
5874 return ignoreGapsinConsensus;
5879 * Sets the value of the ignoreGapsinConsensus property.
5882 * allowed object is {@link Boolean }
5885 public void setIgnoreGapsinConsensus(Boolean value)
5887 this.ignoreGapsinConsensus = value;
5891 * Gets the value of the startRes property.
5893 * @return possible object is {@link Integer }
5896 public Integer getStartRes()
5902 * Sets the value of the startRes property.
5905 * allowed object is {@link Integer }
5908 public void setStartRes(Integer value)
5910 this.startRes = value;
5914 * Gets the value of the startSeq property.
5916 * @return possible object is {@link Integer }
5919 public Integer getStartSeq()
5925 * Sets the value of the startSeq property.
5928 * allowed object is {@link Integer }
5931 public void setStartSeq(Integer value)
5933 this.startSeq = value;
5937 * Gets the value of the charWidth property.
5939 * @return possible object is {@link Integer }
5942 public Integer getCharWidth()
5948 * Sets the value of the charWidth property.
5951 * allowed object is {@link Integer }
5954 public void setCharWidth(Integer value)
5956 this.charWidth = value;
5960 * Gets the value of the charHeight property.
5962 * @return possible object is {@link Integer }
5965 public Integer getCharHeight()
5971 * Sets the value of the charHeight property.
5974 * allowed object is {@link Integer }
5977 public void setCharHeight(Integer value)
5979 this.charHeight = value;
5983 * Gets the value of the fontName property.
5985 * @return possible object is {@link String }
5988 public String getFontName()
5994 * Sets the value of the fontName property.
5997 * allowed object is {@link String }
6000 public void setFontName(String value)
6002 this.fontName = value;
6006 * Gets the value of the fontSize property.
6008 * @return possible object is {@link Integer }
6011 public Integer getFontSize()
6017 * Sets the value of the fontSize property.
6020 * allowed object is {@link Integer }
6023 public void setFontSize(Integer value)
6025 this.fontSize = value;
6029 * Gets the value of the fontStyle property.
6031 * @return possible object is {@link Integer }
6034 public Integer getFontStyle()
6040 * Sets the value of the fontStyle property.
6043 * allowed object is {@link Integer }
6046 public void setFontStyle(Integer value)
6048 this.fontStyle = value;
6052 * Gets the value of the idWidth property.
6054 * @return possible object is {@link Integer }
6057 public Integer getIdWidth()
6063 * Sets the value of the idWidth property.
6066 * allowed object is {@link Integer }
6069 public void setIdWidth(Integer value)
6071 this.idWidth = value;
6075 * Gets the value of the idWidthManuallyAdjusted property.
6077 * @return possible object is {@link Boolean }
6080 public Boolean isIdWidthManuallyAdjusted()
6082 return idWidthManuallyAdjusted;
6086 * Sets the value of the idWidthManuallyAdjusted property.
6089 * allowed object is {@link Boolean }
6092 public void setIdWidthManuallyAdjusted(Boolean value)
6094 this.idWidthManuallyAdjusted = value;
6098 * Gets the value of the scaleProteinAsCdna property.
6100 * @return possible object is {@link Boolean }
6103 public boolean isScaleProteinAsCdna()
6105 if (scaleProteinAsCdna == null)
6111 return scaleProteinAsCdna;
6116 * Sets the value of the scaleProteinAsCdna property.
6119 * allowed object is {@link Boolean }
6122 public void setScaleProteinAsCdna(Boolean value)
6124 this.scaleProteinAsCdna = value;
6128 * Gets the value of the viewName property.
6130 * @return possible object is {@link String }
6133 public String getViewName()
6139 * Sets the value of the viewName property.
6142 * allowed object is {@link String }
6145 public void setViewName(String value)
6147 this.viewName = value;
6151 * Gets the value of the sequenceSetId property.
6153 * @return possible object is {@link String }
6156 public String getSequenceSetId()
6158 return sequenceSetId;
6162 * Sets the value of the sequenceSetId property.
6165 * allowed object is {@link String }
6168 public void setSequenceSetId(String value)
6170 this.sequenceSetId = value;
6174 * Gets the value of the gatheredViews property.
6176 * @return possible object is {@link Boolean }
6179 public Boolean isGatheredViews()
6181 return gatheredViews;
6185 * Sets the value of the gatheredViews property.
6188 * allowed object is {@link Boolean }
6191 public void setGatheredViews(Boolean value)
6193 this.gatheredViews = value;
6197 * Gets the value of the textCol1 property.
6199 * @return possible object is {@link Integer }
6202 public Integer getTextCol1()
6208 * Sets the value of the textCol1 property.
6211 * allowed object is {@link Integer }
6214 public void setTextCol1(Integer value)
6216 this.textCol1 = value;
6220 * Gets the value of the textCol2 property.
6222 * @return possible object is {@link Integer }
6225 public Integer getTextCol2()
6231 * Sets the value of the textCol2 property.
6234 * allowed object is {@link Integer }
6237 public void setTextCol2(Integer value)
6239 this.textCol2 = value;
6243 * Gets the value of the textColThreshold property.
6245 * @return possible object is {@link Integer }
6248 public Integer getTextColThreshold()
6250 return textColThreshold;
6254 * Sets the value of the textColThreshold property.
6257 * allowed object is {@link Integer }
6260 public void setTextColThreshold(Integer value)
6262 this.textColThreshold = value;
6266 * Gets the value of the id property.
6268 * @return possible object is {@link String }
6271 public String getId()
6277 * Sets the value of the id property.
6280 * allowed object is {@link String }
6283 public void setId(String value)
6289 * Gets the value of the complementId property.
6291 * @return possible object is {@link String }
6294 public String getComplementId()
6296 return complementId;
6300 * Sets the value of the complementId property.
6303 * allowed object is {@link String }
6306 public void setComplementId(String value)
6308 this.complementId = value;
6312 * Gets the value of the showComplementFeatures property.
6314 * @return possible object is {@link Boolean }
6317 public boolean isShowComplementFeatures()
6319 if (showComplementFeatures == null)
6325 return showComplementFeatures;
6330 * Sets the value of the showComplementFeatures property.
6333 * allowed object is {@link Boolean }
6336 public void setShowComplementFeatures(Boolean value)
6338 this.showComplementFeatures = value;
6342 * Gets the value of the showComplementFeaturesOnTop property.
6344 * @return possible object is {@link Boolean }
6347 public boolean isShowComplementFeaturesOnTop()
6349 if (showComplementFeaturesOnTop == null)
6355 return showComplementFeaturesOnTop;
6360 * Sets the value of the showComplementFeaturesOnTop property.
6363 * allowed object is {@link Boolean }
6366 public void setShowComplementFeaturesOnTop(Boolean value)
6368 this.showComplementFeaturesOnTop = value;
6372 * Gets the value of the width property.
6374 * @return possible object is {@link Integer }
6377 public Integer getWidth()
6383 * Sets the value of the width property.
6386 * allowed object is {@link Integer }
6389 public void setWidth(Integer value)
6395 * Gets the value of the height property.
6397 * @return possible object is {@link Integer }
6400 public Integer getHeight()
6406 * Sets the value of the height property.
6409 * allowed object is {@link Integer }
6412 public void setHeight(Integer value)
6414 this.height = value;
6418 * Gets the value of the xpos property.
6420 * @return possible object is {@link Integer }
6423 public Integer getXpos()
6429 * Sets the value of the xpos property.
6432 * allowed object is {@link Integer }
6435 public void setXpos(Integer value)
6441 * Gets the value of the ypos property.
6443 * @return possible object is {@link Integer }
6446 public Integer getYpos()
6452 * Sets the value of the ypos property.
6455 * allowed object is {@link Integer }
6458 public void setYpos(Integer value)
6464 * <p>Java class for anonymous complex type.
6466 * <p>The following schema fragment specifies the expected content
6467 * contained within this class.
6469 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
6471 * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
6472 * &lt;attribute name="calcId" use="required"
6473 * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6474 * &lt;attribute name="needsUpdate"
6475 * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
6476 * /&gt; &lt;attribute name="autoUpdate" use="required"
6477 * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6478 * &lt;/extension&gt; &lt;/complexContent&gt;
6479 * &lt;/complexType&gt; </pre>
6483 @XmlAccessorType(XmlAccessType.FIELD)
6485 public static class CalcIdParam extends WebServiceParameterSet
6488 @XmlAttribute(name = "calcId", required = true)
6489 protected String calcId;
6491 @XmlAttribute(name = "needsUpdate")
6492 protected Boolean needsUpdate;
6494 @XmlAttribute(name = "autoUpdate", required = true)
6495 protected boolean autoUpdate;
6498 * Gets the value of the calcId property.
6500 * @return possible object is {@link String }
6503 public String getCalcId()
6509 * Sets the value of the calcId property.
6512 * allowed object is {@link String }
6515 public void setCalcId(String value)
6517 this.calcId = value;
6521 * Gets the value of the needsUpdate property.
6523 * @return possible object is {@link Boolean }
6526 public boolean isNeedsUpdate()
6528 if (needsUpdate == null)
6539 * Sets the value of the needsUpdate property.
6542 * allowed object is {@link Boolean }
6545 public void setNeedsUpdate(Boolean value)
6547 this.needsUpdate = value;
6551 * Gets the value of the autoUpdate property.
6554 public boolean isAutoUpdate()
6560 * Sets the value of the autoUpdate property.
6563 public void setAutoUpdate(boolean value)
6565 this.autoUpdate = value;
6571 * <p>Java class for anonymous complex type.
6573 * <p>The following schema fragment specifies the expected content
6574 * contained within this class.
6576 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
6577 * &lt;restriction
6578 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6579 * &lt;attribute name="start"
6580 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
6581 * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6582 * &lt;/restriction&gt; &lt;/complexContent&gt;
6583 * &lt;/complexType&gt; </pre>
6587 @XmlAccessorType(XmlAccessType.FIELD)
6589 public static class HiddenColumns
6592 @XmlAttribute(name = "start")
6593 protected Integer start;
6595 @XmlAttribute(name = "end")
6596 protected Integer end;
6599 * Gets the value of the start property.
6601 * @return possible object is {@link Integer }
6604 public Integer getStart()
6610 * Sets the value of the start property.
6613 * allowed object is {@link Integer }
6616 public void setStart(Integer value)
6622 * Gets the value of the end property.
6624 * @return possible object is {@link Integer }
6627 public Integer getEnd()
6633 * Sets the value of the end property.
6636 * allowed object is {@link Integer }
6639 public void setEnd(Integer value)
6647 * <p>Java class for anonymous complex type.
6649 * <p>The following schema fragment specifies the expected content
6650 * contained within this class.
6652 * <pre> &lt;complexType&gt; &lt;complexContent&gt;
6653 * &lt;restriction
6654 * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
6655 * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
6656 * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
6657 * /&gt; &lt;attribute name="residueColour"
6658 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
6659 * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6660 * &lt;attribute name="hiddenColour"
6661 * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
6662 * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6663 * &lt;/restriction&gt; &lt;/complexContent&gt;
6664 * &lt;/complexType&gt; </pre>
6668 @XmlAccessorType(XmlAccessType.FIELD)
6670 public static class Overview
6673 @XmlAttribute(name = "showHidden")
6674 protected Boolean showHidden;
6676 @XmlAttribute(name = "residueColour")
6677 protected Integer residueColour;
6679 @XmlAttribute(name = "gapColour")
6680 protected Integer gapColour;
6682 @XmlAttribute(name = "hiddenColour")
6683 protected Integer hiddenColour;
6685 @XmlAttribute(name = "title")
6686 protected String title;
6688 @XmlAttribute(name = "width")
6689 protected Integer width;
6691 @XmlAttribute(name = "height")
6692 protected Integer height;
6694 @XmlAttribute(name = "xpos")
6695 protected Integer xpos;
6697 @XmlAttribute(name = "ypos")
6698 protected Integer ypos;
6701 * Gets the value of the showHidden property.
6703 * @return possible object is {@link Boolean }
6706 public Boolean isShowHidden()
6712 * Sets the value of the showHidden property.
6715 * allowed object is {@link Boolean }
6718 public void setShowHidden(Boolean value)
6720 this.showHidden = value;
6724 * Gets the value of the residueColour property.
6726 * @return possible object is {@link Integer }
6729 public Integer getResidueColour()
6731 return residueColour;
6735 * Sets the value of the residueColour property.
6738 * allowed object is {@link Integer }
6741 public void setResidueColour(Integer value)
6743 this.residueColour = value;
6747 * Gets the value of the gapColour property.
6749 * @return possible object is {@link Integer }
6752 public Integer getGapColour()
6758 * Sets the value of the gapColour property.
6761 * allowed object is {@link Integer }
6764 public void setGapColour(Integer value)
6766 this.gapColour = value;
6770 * Gets the value of the hiddenColour property.
6772 * @return possible object is {@link Integer }
6775 public Integer getHiddenColour()
6777 return hiddenColour;
6781 * Sets the value of the hiddenColour property.
6784 * allowed object is {@link Integer }
6787 public void setHiddenColour(Integer value)
6789 this.hiddenColour = value;
6793 * Gets the value of the title property.
6795 * @return possible object is {@link String }
6798 public String getTitle()
6804 * Sets the value of the title property.
6807 * allowed object is {@link String }
6810 public void setTitle(String value)
6816 * Gets the value of the width property.
6818 * @return possible object is {@link Integer }
6821 public Integer getWidth()
6827 * Sets the value of the width property.
6830 * allowed object is {@link Integer }
6833 public void setWidth(Integer value)
6839 * Gets the value of the height property.
6841 * @return possible object is {@link Integer }
6844 public Integer getHeight()
6850 * Sets the value of the height property.
6853 * allowed object is {@link Integer }
6856 public void setHeight(Integer value)
6858 this.height = value;
6862 * Gets the value of the xpos property.
6864 * @return possible object is {@link Integer }
6867 public Integer getXpos()
6873 * Sets the value of the xpos property.
6876 * allowed object is {@link Integer }
6879 public void setXpos(Integer value)
6885 * Gets the value of the ypos property.
6887 * @return possible object is {@link Integer }
6890 public Integer getYpos()
6896 * Sets the value of the ypos property.
6899 * allowed object is {@link Integer }
6902 public void setYpos(Integer value)