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360c074050cf3acea00ae0aa517341e39decabd9
[jalview.git] / src / jalview / xml / binding / jalview / JalviewModel.java
1 //
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 
6 //
7
8
9 package jalview.xml.binding.jalview;
10
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
24
25
26 /**
27  * <p>Java class for JalviewModel complex type.
28  * 
29  * <p>The following schema fragment specifies the expected content contained within this class.
30  * 
31  * <pre>
32  * <complexType name="JalviewModel">
33  *   <complexContent>
34  *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
35  *       <sequence>
36  *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
37  *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
38  *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
39  *         <sequence>
40  *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
41  *             <complexType>
42  *               <complexContent>
43  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
44  *                   <sequence>
45  *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
46  *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
47  *                       <complexType>
48  *                         <complexContent>
49  *                           <extension base="{www.jalview.org}pdbentry">
50  *                             <sequence>
51  *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
52  *                                 <complexType>
53  *                                   <simpleContent>
54  *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
55  *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
56  *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
57  *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
58  *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
59  *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
60  *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61  *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
62  *                                     </extension>
63  *                                   </simpleContent>
64  *                                 </complexType>
65  *                               </element>
66  *                             </sequence>
67  *                           </extension>
68  *                         </complexContent>
69  *                       </complexType>
70  *                     </element>
71  *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
72  *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
73  *                       <complexType>
74  *                         <complexContent>
75  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
76  *                             <sequence>
77  *                               <element name="secondaryStructure" maxOccurs="unbounded">
78  *                                 <complexType>
79  *                                   <complexContent>
80  *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
81  *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
82  *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
83  *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
84  *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
85  *                                     </restriction>
86  *                                   </complexContent>
87  *                                 </complexType>
88  *                               </element>
89  *                             </sequence>
90  *                             <attGroup ref="{www.jalview.org}swingwindow"/>
91  *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
92  *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
93  *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
94  *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
95  *                           </restriction>
96  *                         </complexContent>
97  *                       </complexType>
98  *                     </element>
99  *                   </sequence>
100  *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
101  *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
102  *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103  *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
104  *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
105  *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
106  *                 </restriction>
107  *               </complexContent>
108  *             </complexType>
109  *           </element>
110  *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
111  *             <complexType>
112  *               <complexContent>
113  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
114  *                   <sequence>
115  *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
116  *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
117  *                   </sequence>
118  *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
119  *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
120  *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
121  *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
122  *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
123  *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124  *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
125  *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
126  *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127  *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128  *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
129  *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
130  *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
131  *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
132  *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
133  *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134  *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
135  *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136  *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
137  *                 </restriction>
138  *               </complexContent>
139  *             </complexType>
140  *           </element>
141  *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
142  *             <complexType>
143  *               <complexContent>
144  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
145  *                   <sequence>
146  *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147  *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
148  *                       <complexType>
149  *                         <complexContent>
150  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
151  *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152  *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
153  *                           </restriction>
154  *                         </complexContent>
155  *                       </complexType>
156  *                     </element>
157  *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
158  *                       <complexType>
159  *                         <complexContent>
160  *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
161  *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
162  *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
163  *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
164  *                           </extension>
165  *                         </complexContent>
166  *                       </complexType>
167  *                     </element>
168  *                     <element name="overview" minOccurs="0">
169  *                       <complexType>
170  *                         <complexContent>
171  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
172  *                             <attGroup ref="{www.jalview.org}swingwindow"/>
173  *                             <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
174  *                             <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
175  *                             <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
176  *                             <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
177  *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
178  *                           </restriction>
179  *                         </complexContent>
180  *                       </complexType>
181  *                     </element>
182  *                   </sequence>
183  *                   <attGroup ref="{www.jalview.org}swingwindow"/>
184  *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185  *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186  *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
187  *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
188  *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
189  *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
190  *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
191  *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
192  *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
193  *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
194  *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
195  *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
196  *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
197  *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
198  *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
199  *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
200  *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
201  *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
202  *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
203  *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
204  *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
205  *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
206  *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
207  *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
208  *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
209  *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
210  *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
211  *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
212  *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
213  *                   <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
214  *                   <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
215  *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
216  *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
217  *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
218  *                   <attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
219  *                   <attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" />
220  *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
221  *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
222  *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
223  *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
224  *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
225  *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
226  *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
227  *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
228  *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
229  *                   <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
230  *                   <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
231  *                 </restriction>
232  *               </complexContent>
233  *             </complexType>
234  *           </element>
235  *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
236  *             <complexType>
237  *               <complexContent>
238  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
239  *                   <sequence>
240  *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
241  *                   </sequence>
242  *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
243  *                 </restriction>
244  *               </complexContent>
245  *             </complexType>
246  *           </element>
247  *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
248  *             <complexType>
249  *               <complexContent>
250  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
251  *                   <sequence minOccurs="0">
252  *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
253  *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
254  *                   </sequence>
255  *                   <attGroup ref="{www.jalview.org}swingwindow"/>
256  *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
257  *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
258  *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
259  *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
260  *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
261  *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
262  *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
263  *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
264  *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
265  *                   <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
266  *                   <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
267  *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
268  *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
269  *                 </restriction>
270  *               </complexContent>
271  *             </complexType>
272  *           </element>
273  *           <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
274  *             <complexType>
275  *               <complexContent>
276  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
277  *                   <sequence>
278  *                     <element name="sequencePoint" maxOccurs="unbounded">
279  *                       <complexType>
280  *                         <complexContent>
281  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
282  *                             <attGroup ref="{www.jalview.org}position"/>
283  *                             <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
284  *                           </restriction>
285  *                         </complexContent>
286  *                       </complexType>
287  *                     </element>
288  *                     <element name="axis" maxOccurs="3" minOccurs="3">
289  *                       <complexType>
290  *                         <complexContent>
291  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
292  *                             <attGroup ref="{www.jalview.org}position"/>
293  *                           </restriction>
294  *                         </complexContent>
295  *                       </complexType>
296  *                     </element>
297  *                     <element name="seqPointMin">
298  *                       <complexType>
299  *                         <complexContent>
300  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
301  *                             <attGroup ref="{www.jalview.org}position"/>
302  *                           </restriction>
303  *                         </complexContent>
304  *                       </complexType>
305  *                     </element>
306  *                     <element name="seqPointMax">
307  *                       <complexType>
308  *                         <complexContent>
309  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
310  *                             <attGroup ref="{www.jalview.org}position"/>
311  *                           </restriction>
312  *                         </complexContent>
313  *                       </complexType>
314  *                     </element>
315  *                     <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
316  *                   </sequence>
317  *                   <attGroup ref="{www.jalview.org}SimilarityParams"/>
318  *                   <attGroup ref="{www.jalview.org}swingwindow"/>
319  *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
320  *                   <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
321  *                   <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
322  *                   <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
323  *                   <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
324  *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
325  *                   <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
326  *                   <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
327  *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
328  *                 </restriction>
329  *               </complexContent>
330  *             </complexType>
331  *           </element>
332  *           <element name="FeatureSettings" minOccurs="0">
333  *             <complexType>
334  *               <complexContent>
335  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
336  *                   <sequence>
337  *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
338  *                       <complexType>
339  *                         <complexContent>
340  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
341  *                             <sequence>
342  *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
343  *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
344  *                             </sequence>
345  *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
346  *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
347  *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
348  *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
349  *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
350  *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
351  *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
352  *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
353  *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
354  *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
355  *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
356  *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
357  *                           </restriction>
358  *                         </complexContent>
359  *                       </complexType>
360  *                     </element>
361  *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
362  *                       <complexType>
363  *                         <complexContent>
364  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
365  *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
366  *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
367  *                           </restriction>
368  *                         </complexContent>
369  *                       </complexType>
370  *                     </element>
371  *                   </sequence>
372  *                 </restriction>
373  *               </complexContent>
374  *             </complexType>
375  *           </element>
376  *         </sequence>
377  *       </sequence>
378  *     </restriction>
379  *   </complexContent>
380  * </complexType>
381  * </pre>
382  * 
383  * 
384  */
385 @XmlAccessorType(XmlAccessType.FIELD)
386 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
387     "creationDate",
388     "version",
389     "vamsasModel",
390     "jSeq",
391     "jGroup",
392     "viewport",
393     "userColours",
394     "tree",
395     "pcaViewer",
396     "featureSettings"
397 })
398 public class JalviewModel {
399
400     @XmlElement(required = true)
401     @XmlSchemaType(name = "dateTime")
402     protected XMLGregorianCalendar creationDate;
403     @XmlElement(required = true)
404     protected String version;
405     @XmlElement(required = true)
406     protected VAMSAS vamsasModel;
407     @XmlElement(name = "JSeq")
408     protected List<JalviewModel.JSeq> jSeq;
409     @XmlElement(name = "JGroup")
410     protected List<JalviewModel.JGroup> jGroup;
411     @XmlElement(name = "Viewport")
412     protected List<JalviewModel.Viewport> viewport;
413     @XmlElement(name = "UserColours")
414     protected List<JalviewModel.UserColours> userColours;
415     protected List<JalviewModel.Tree> tree;
416     @XmlElement(name = "PcaViewer")
417     protected List<JalviewModel.PcaViewer> pcaViewer;
418     @XmlElement(name = "FeatureSettings")
419     protected JalviewModel.FeatureSettings featureSettings;
420
421     /**
422      * Gets the value of the creationDate property.
423      * 
424      * @return
425      *     possible object is
426      *     {@link XMLGregorianCalendar }
427      *     
428      */
429     public XMLGregorianCalendar getCreationDate() {
430         return creationDate;
431     }
432
433     /**
434      * Sets the value of the creationDate property.
435      * 
436      * @param value
437      *     allowed object is
438      *     {@link XMLGregorianCalendar }
439      *     
440      */
441     public void setCreationDate(XMLGregorianCalendar value) {
442         this.creationDate = value;
443     }
444
445     /**
446      * Gets the value of the version property.
447      * 
448      * @return
449      *     possible object is
450      *     {@link String }
451      *     
452      */
453     public String getVersion() {
454         return version;
455     }
456
457     /**
458      * Sets the value of the version property.
459      * 
460      * @param value
461      *     allowed object is
462      *     {@link String }
463      *     
464      */
465     public void setVersion(String value) {
466         this.version = value;
467     }
468
469     /**
470      * Gets the value of the vamsasModel property.
471      * 
472      * @return
473      *     possible object is
474      *     {@link VAMSAS }
475      *     
476      */
477     public VAMSAS getVamsasModel() {
478         return vamsasModel;
479     }
480
481     /**
482      * Sets the value of the vamsasModel property.
483      * 
484      * @param value
485      *     allowed object is
486      *     {@link VAMSAS }
487      *     
488      */
489     public void setVamsasModel(VAMSAS value) {
490         this.vamsasModel = value;
491     }
492
493     /**
494      * Gets the value of the jSeq property.
495      * 
496      * &lt;p&gt;
497      * This accessor method returns a reference to the live list,
498      * not a snapshot. Therefore any modification you make to the
499      * returned list will be present inside the JAXB object.
500      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
501      * 
502      * &lt;p&gt;
503      * For example, to add a new item, do as follows:
504      * &lt;pre&gt;
505      *    getJSeq().add(newItem);
506      * &lt;/pre&gt;
507      * 
508      * 
509      * &lt;p&gt;
510      * Objects of the following type(s) are allowed in the list
511      * {@link JalviewModel.JSeq }
512      * 
513      * 
514      */
515     public List<JalviewModel.JSeq> getJSeq() {
516         if (jSeq == null) {
517             jSeq = new ArrayList<JalviewModel.JSeq>();
518         }
519         return this.jSeq;
520     }
521
522     /**
523      * Gets the value of the jGroup property.
524      * 
525      * &lt;p&gt;
526      * This accessor method returns a reference to the live list,
527      * not a snapshot. Therefore any modification you make to the
528      * returned list will be present inside the JAXB object.
529      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
530      * 
531      * &lt;p&gt;
532      * For example, to add a new item, do as follows:
533      * &lt;pre&gt;
534      *    getJGroup().add(newItem);
535      * &lt;/pre&gt;
536      * 
537      * 
538      * &lt;p&gt;
539      * Objects of the following type(s) are allowed in the list
540      * {@link JalviewModel.JGroup }
541      * 
542      * 
543      */
544     public List<JalviewModel.JGroup> getJGroup() {
545         if (jGroup == null) {
546             jGroup = new ArrayList<JalviewModel.JGroup>();
547         }
548         return this.jGroup;
549     }
550
551     /**
552      * Gets the value of the viewport property.
553      * 
554      * &lt;p&gt;
555      * This accessor method returns a reference to the live list,
556      * not a snapshot. Therefore any modification you make to the
557      * returned list will be present inside the JAXB object.
558      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
559      * 
560      * &lt;p&gt;
561      * For example, to add a new item, do as follows:
562      * &lt;pre&gt;
563      *    getViewport().add(newItem);
564      * &lt;/pre&gt;
565      * 
566      * 
567      * &lt;p&gt;
568      * Objects of the following type(s) are allowed in the list
569      * {@link JalviewModel.Viewport }
570      * 
571      * 
572      */
573     public List<JalviewModel.Viewport> getViewport() {
574         if (viewport == null) {
575             viewport = new ArrayList<JalviewModel.Viewport>();
576         }
577         return this.viewport;
578     }
579
580     /**
581      * Gets the value of the userColours property.
582      * 
583      * &lt;p&gt;
584      * This accessor method returns a reference to the live list,
585      * not a snapshot. Therefore any modification you make to the
586      * returned list will be present inside the JAXB object.
587      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
588      * 
589      * &lt;p&gt;
590      * For example, to add a new item, do as follows:
591      * &lt;pre&gt;
592      *    getUserColours().add(newItem);
593      * &lt;/pre&gt;
594      * 
595      * 
596      * &lt;p&gt;
597      * Objects of the following type(s) are allowed in the list
598      * {@link JalviewModel.UserColours }
599      * 
600      * 
601      */
602     public List<JalviewModel.UserColours> getUserColours() {
603         if (userColours == null) {
604             userColours = new ArrayList<JalviewModel.UserColours>();
605         }
606         return this.userColours;
607     }
608
609     /**
610      * Gets the value of the tree property.
611      * 
612      * &lt;p&gt;
613      * This accessor method returns a reference to the live list,
614      * not a snapshot. Therefore any modification you make to the
615      * returned list will be present inside the JAXB object.
616      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
617      * 
618      * &lt;p&gt;
619      * For example, to add a new item, do as follows:
620      * &lt;pre&gt;
621      *    getTree().add(newItem);
622      * &lt;/pre&gt;
623      * 
624      * 
625      * &lt;p&gt;
626      * Objects of the following type(s) are allowed in the list
627      * {@link JalviewModel.Tree }
628      * 
629      * 
630      */
631     public List<JalviewModel.Tree> getTree() {
632         if (tree == null) {
633             tree = new ArrayList<JalviewModel.Tree>();
634         }
635         return this.tree;
636     }
637
638     /**
639      * Gets the value of the pcaViewer property.
640      * 
641      * &lt;p&gt;
642      * This accessor method returns a reference to the live list,
643      * not a snapshot. Therefore any modification you make to the
644      * returned list will be present inside the JAXB object.
645      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
646      * 
647      * &lt;p&gt;
648      * For example, to add a new item, do as follows:
649      * &lt;pre&gt;
650      *    getPcaViewer().add(newItem);
651      * &lt;/pre&gt;
652      * 
653      * 
654      * &lt;p&gt;
655      * Objects of the following type(s) are allowed in the list
656      * {@link JalviewModel.PcaViewer }
657      * 
658      * 
659      */
660     public List<JalviewModel.PcaViewer> getPcaViewer() {
661         if (pcaViewer == null) {
662             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
663         }
664         return this.pcaViewer;
665     }
666
667     /**
668      * Gets the value of the featureSettings property.
669      * 
670      * @return
671      *     possible object is
672      *     {@link JalviewModel.FeatureSettings }
673      *     
674      */
675     public JalviewModel.FeatureSettings getFeatureSettings() {
676         return featureSettings;
677     }
678
679     /**
680      * Sets the value of the featureSettings property.
681      * 
682      * @param value
683      *     allowed object is
684      *     {@link JalviewModel.FeatureSettings }
685      *     
686      */
687     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
688         this.featureSettings = value;
689     }
690
691
692     /**
693      * &lt;p&gt;Java class for anonymous complex type.
694      * 
695      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
696      * 
697      * &lt;pre&gt;
698      * &amp;lt;complexType&amp;gt;
699      *   &amp;lt;complexContent&amp;gt;
700      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
701      *       &amp;lt;sequence&amp;gt;
702      *         &amp;lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&amp;gt;
703      *           &amp;lt;complexType&amp;gt;
704      *             &amp;lt;complexContent&amp;gt;
705      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
706      *                 &amp;lt;sequence&amp;gt;
707      *                   &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
708      *                   &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
709      *                 &amp;lt;/sequence&amp;gt;
710      *                 &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
711      *                 &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
712      *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
713      *                 &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
714      *                 &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
715      *                 &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
716      *                 &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
717      *                 &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
718      *                 &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
719      *                 &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
720      *                 &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
721      *                 &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
722      *               &amp;lt;/restriction&amp;gt;
723      *             &amp;lt;/complexContent&amp;gt;
724      *           &amp;lt;/complexType&amp;gt;
725      *         &amp;lt;/element&amp;gt;
726      *         &amp;lt;element name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
727      *           &amp;lt;complexType&amp;gt;
728      *             &amp;lt;complexContent&amp;gt;
729      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
730      *                 &amp;lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
731      *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
732      *               &amp;lt;/restriction&amp;gt;
733      *             &amp;lt;/complexContent&amp;gt;
734      *           &amp;lt;/complexType&amp;gt;
735      *         &amp;lt;/element&amp;gt;
736      *       &amp;lt;/sequence&amp;gt;
737      *     &amp;lt;/restriction&amp;gt;
738      *   &amp;lt;/complexContent&amp;gt;
739      * &amp;lt;/complexType&amp;gt;
740      * &lt;/pre&gt;
741      * 
742      * 
743      */
744     @XmlAccessorType(XmlAccessType.FIELD)
745     @XmlType(name = "", propOrder = {
746         "setting",
747         "group"
748     })
749     public static class FeatureSettings {
750
751         @XmlElement(namespace = "www.jalview.org")
752         protected List<JalviewModel.FeatureSettings.Setting> setting;
753         @XmlElement(namespace = "www.jalview.org")
754         protected List<JalviewModel.FeatureSettings.Group> group;
755
756         /**
757          * Gets the value of the setting property.
758          * 
759          * &lt;p&gt;
760          * This accessor method returns a reference to the live list,
761          * not a snapshot. Therefore any modification you make to the
762          * returned list will be present inside the JAXB object.
763          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
764          * 
765          * &lt;p&gt;
766          * For example, to add a new item, do as follows:
767          * &lt;pre&gt;
768          *    getSetting().add(newItem);
769          * &lt;/pre&gt;
770          * 
771          * 
772          * &lt;p&gt;
773          * Objects of the following type(s) are allowed in the list
774          * {@link JalviewModel.FeatureSettings.Setting }
775          * 
776          * 
777          */
778         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
779             if (setting == null) {
780                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
781             }
782             return this.setting;
783         }
784
785         /**
786          * Gets the value of the group property.
787          * 
788          * &lt;p&gt;
789          * This accessor method returns a reference to the live list,
790          * not a snapshot. Therefore any modification you make to the
791          * returned list will be present inside the JAXB object.
792          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
793          * 
794          * &lt;p&gt;
795          * For example, to add a new item, do as follows:
796          * &lt;pre&gt;
797          *    getGroup().add(newItem);
798          * &lt;/pre&gt;
799          * 
800          * 
801          * &lt;p&gt;
802          * Objects of the following type(s) are allowed in the list
803          * {@link JalviewModel.FeatureSettings.Group }
804          * 
805          * 
806          */
807         public List<JalviewModel.FeatureSettings.Group> getGroup() {
808             if (group == null) {
809                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
810             }
811             return this.group;
812         }
813
814
815         /**
816          * &lt;p&gt;Java class for anonymous complex type.
817          * 
818          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
819          * 
820          * &lt;pre&gt;
821          * &amp;lt;complexType&amp;gt;
822          *   &amp;lt;complexContent&amp;gt;
823          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
824          *       &amp;lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
825          *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
826          *     &amp;lt;/restriction&amp;gt;
827          *   &amp;lt;/complexContent&amp;gt;
828          * &amp;lt;/complexType&amp;gt;
829          * &lt;/pre&gt;
830          * 
831          * 
832          */
833         @XmlAccessorType(XmlAccessType.FIELD)
834         @XmlType(name = "")
835         public static class Group {
836
837             @XmlAttribute(name = "name", required = true)
838             protected String name;
839             @XmlAttribute(name = "display", required = true)
840             protected boolean display;
841
842             /**
843              * Gets the value of the name property.
844              * 
845              * @return
846              *     possible object is
847              *     {@link String }
848              *     
849              */
850             public String getName() {
851                 return name;
852             }
853
854             /**
855              * Sets the value of the name property.
856              * 
857              * @param value
858              *     allowed object is
859              *     {@link String }
860              *     
861              */
862             public void setName(String value) {
863                 this.name = value;
864             }
865
866             /**
867              * Gets the value of the display property.
868              * 
869              */
870             public boolean isDisplay() {
871                 return display;
872             }
873
874             /**
875              * Sets the value of the display property.
876              * 
877              */
878             public void setDisplay(boolean value) {
879                 this.display = value;
880             }
881
882         }
883
884
885         /**
886          * &lt;p&gt;Java class for anonymous complex type.
887          * 
888          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
889          * 
890          * &lt;pre&gt;
891          * &amp;lt;complexType&amp;gt;
892          *   &amp;lt;complexContent&amp;gt;
893          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
894          *       &amp;lt;sequence&amp;gt;
895          *         &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
896          *         &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
897          *       &amp;lt;/sequence&amp;gt;
898          *       &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
899          *       &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
900          *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
901          *       &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
902          *       &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
903          *       &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
904          *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
905          *       &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
906          *       &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
907          *       &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
908          *       &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
909          *       &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
910          *     &amp;lt;/restriction&amp;gt;
911          *   &amp;lt;/complexContent&amp;gt;
912          * &amp;lt;/complexType&amp;gt;
913          * &lt;/pre&gt;
914          * 
915          * 
916          */
917         @XmlAccessorType(XmlAccessType.FIELD)
918         @XmlType(name = "", propOrder = {
919             "attributeName",
920             "matcherSet"
921         })
922         public static class Setting {
923
924             @XmlElement(namespace = "www.jalview.org")
925             protected List<String> attributeName;
926             @XmlElement(namespace = "www.jalview.org")
927             protected FeatureMatcherSet matcherSet;
928             @XmlAttribute(name = "type", required = true)
929             protected String type;
930             @XmlAttribute(name = "colour", required = true)
931             protected int colour;
932             @XmlAttribute(name = "display", required = true)
933             protected boolean display;
934             @XmlAttribute(name = "order")
935             protected Float order;
936             @XmlAttribute(name = "mincolour")
937             protected Integer mincolour;
938             @XmlAttribute(name = "noValueColour")
939             protected NoValueColour noValueColour;
940             @XmlAttribute(name = "threshold")
941             protected Float threshold;
942             @XmlAttribute(name = "threshstate")
943             protected Integer threshstate;
944             @XmlAttribute(name = "max")
945             protected Float max;
946             @XmlAttribute(name = "min")
947             protected Float min;
948             @XmlAttribute(name = "colourByLabel")
949             protected Boolean colourByLabel;
950             @XmlAttribute(name = "autoScale")
951             protected Boolean autoScale;
952
953             /**
954              * Gets the value of the attributeName property.
955              * 
956              * &lt;p&gt;
957              * This accessor method returns a reference to the live list,
958              * not a snapshot. Therefore any modification you make to the
959              * returned list will be present inside the JAXB object.
960              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
961              * 
962              * &lt;p&gt;
963              * For example, to add a new item, do as follows:
964              * &lt;pre&gt;
965              *    getAttributeName().add(newItem);
966              * &lt;/pre&gt;
967              * 
968              * 
969              * &lt;p&gt;
970              * Objects of the following type(s) are allowed in the list
971              * {@link String }
972              * 
973              * 
974              */
975             public List<String> getAttributeName() {
976                 if (attributeName == null) {
977                     attributeName = new ArrayList<String>();
978                 }
979                 return this.attributeName;
980             }
981
982             /**
983              * Gets the value of the matcherSet property.
984              * 
985              * @return
986              *     possible object is
987              *     {@link FeatureMatcherSet }
988              *     
989              */
990             public FeatureMatcherSet getMatcherSet() {
991                 return matcherSet;
992             }
993
994             /**
995              * Sets the value of the matcherSet property.
996              * 
997              * @param value
998              *     allowed object is
999              *     {@link FeatureMatcherSet }
1000              *     
1001              */
1002             public void setMatcherSet(FeatureMatcherSet value) {
1003                 this.matcherSet = value;
1004             }
1005
1006             /**
1007              * Gets the value of the type property.
1008              * 
1009              * @return
1010              *     possible object is
1011              *     {@link String }
1012              *     
1013              */
1014             public String getType() {
1015                 return type;
1016             }
1017
1018             /**
1019              * Sets the value of the type property.
1020              * 
1021              * @param value
1022              *     allowed object is
1023              *     {@link String }
1024              *     
1025              */
1026             public void setType(String value) {
1027                 this.type = value;
1028             }
1029
1030             /**
1031              * Gets the value of the colour property.
1032              * 
1033              */
1034             public int getColour() {
1035                 return colour;
1036             }
1037
1038             /**
1039              * Sets the value of the colour property.
1040              * 
1041              */
1042             public void setColour(int value) {
1043                 this.colour = value;
1044             }
1045
1046             /**
1047              * Gets the value of the display property.
1048              * 
1049              */
1050             public boolean isDisplay() {
1051                 return display;
1052             }
1053
1054             /**
1055              * Sets the value of the display property.
1056              * 
1057              */
1058             public void setDisplay(boolean value) {
1059                 this.display = value;
1060             }
1061
1062             /**
1063              * Gets the value of the order property.
1064              * 
1065              * @return
1066              *     possible object is
1067              *     {@link Float }
1068              *     
1069              */
1070             public Float getOrder() {
1071                 return order;
1072             }
1073
1074             /**
1075              * Sets the value of the order property.
1076              * 
1077              * @param value
1078              *     allowed object is
1079              *     {@link Float }
1080              *     
1081              */
1082             public void setOrder(Float value) {
1083                 this.order = value;
1084             }
1085
1086             /**
1087              * Gets the value of the mincolour property.
1088              * 
1089              * @return
1090              *     possible object is
1091              *     {@link Integer }
1092              *     
1093              */
1094             public Integer getMincolour() {
1095                 return mincolour;
1096             }
1097
1098             /**
1099              * Sets the value of the mincolour property.
1100              * 
1101              * @param value
1102              *     allowed object is
1103              *     {@link Integer }
1104              *     
1105              */
1106             public void setMincolour(Integer value) {
1107                 this.mincolour = value;
1108             }
1109
1110             /**
1111              * Gets the value of the noValueColour property.
1112              * 
1113              * @return
1114              *     possible object is
1115              *     {@link NoValueColour }
1116              *     
1117              */
1118             public NoValueColour getNoValueColour() {
1119                 if (noValueColour == null) {
1120                     return NoValueColour.MIN;
1121                 } else {
1122                     return noValueColour;
1123                 }
1124             }
1125
1126             /**
1127              * Sets the value of the noValueColour property.
1128              * 
1129              * @param value
1130              *     allowed object is
1131              *     {@link NoValueColour }
1132              *     
1133              */
1134             public void setNoValueColour(NoValueColour value) {
1135                 this.noValueColour = value;
1136             }
1137
1138             /**
1139              * Gets the value of the threshold property.
1140              * 
1141              * @return
1142              *     possible object is
1143              *     {@link Float }
1144              *     
1145              */
1146             public Float getThreshold() {
1147                 return threshold;
1148             }
1149
1150             /**
1151              * Sets the value of the threshold property.
1152              * 
1153              * @param value
1154              *     allowed object is
1155              *     {@link Float }
1156              *     
1157              */
1158             public void setThreshold(Float value) {
1159                 this.threshold = value;
1160             }
1161
1162             /**
1163              * Gets the value of the threshstate property.
1164              * 
1165              * @return
1166              *     possible object is
1167              *     {@link Integer }
1168              *     
1169              */
1170             public Integer getThreshstate() {
1171                 return threshstate;
1172             }
1173
1174             /**
1175              * Sets the value of the threshstate property.
1176              * 
1177              * @param value
1178              *     allowed object is
1179              *     {@link Integer }
1180              *     
1181              */
1182             public void setThreshstate(Integer value) {
1183                 this.threshstate = value;
1184             }
1185
1186             /**
1187              * Gets the value of the max property.
1188              * 
1189              * @return
1190              *     possible object is
1191              *     {@link Float }
1192              *     
1193              */
1194             public Float getMax() {
1195                 return max;
1196             }
1197
1198             /**
1199              * Sets the value of the max property.
1200              * 
1201              * @param value
1202              *     allowed object is
1203              *     {@link Float }
1204              *     
1205              */
1206             public void setMax(Float value) {
1207                 this.max = value;
1208             }
1209
1210             /**
1211              * Gets the value of the min property.
1212              * 
1213              * @return
1214              *     possible object is
1215              *     {@link Float }
1216              *     
1217              */
1218             public Float getMin() {
1219                 return min;
1220             }
1221
1222             /**
1223              * Sets the value of the min property.
1224              * 
1225              * @param value
1226              *     allowed object is
1227              *     {@link Float }
1228              *     
1229              */
1230             public void setMin(Float value) {
1231                 this.min = value;
1232             }
1233
1234             /**
1235              * Gets the value of the colourByLabel property.
1236              * 
1237              * @return
1238              *     possible object is
1239              *     {@link Boolean }
1240              *     
1241              */
1242             public Boolean isColourByLabel() {
1243                 return colourByLabel;
1244             }
1245
1246             /**
1247              * Sets the value of the colourByLabel property.
1248              * 
1249              * @param value
1250              *     allowed object is
1251              *     {@link Boolean }
1252              *     
1253              */
1254             public void setColourByLabel(Boolean value) {
1255                 this.colourByLabel = value;
1256             }
1257
1258             /**
1259              * Gets the value of the autoScale property.
1260              * 
1261              * @return
1262              *     possible object is
1263              *     {@link Boolean }
1264              *     
1265              */
1266             public Boolean isAutoScale() {
1267                 return autoScale;
1268             }
1269
1270             /**
1271              * Sets the value of the autoScale property.
1272              * 
1273              * @param value
1274              *     allowed object is
1275              *     {@link Boolean }
1276              *     
1277              */
1278             public void setAutoScale(Boolean value) {
1279                 this.autoScale = value;
1280             }
1281
1282         }
1283
1284     }
1285
1286
1287     /**
1288      * &lt;p&gt;Java class for anonymous complex type.
1289      * 
1290      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
1291      * 
1292      * &lt;pre&gt;
1293      * &amp;lt;complexType&amp;gt;
1294      *   &amp;lt;complexContent&amp;gt;
1295      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1296      *       &amp;lt;sequence&amp;gt;
1297      *         &amp;lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&amp;gt;
1298      *         &amp;lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
1299      *       &amp;lt;/sequence&amp;gt;
1300      *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1301      *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1302      *       &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1303      *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1304      *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1305      *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1306      *       &amp;lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1307      *       &amp;lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1308      *       &amp;lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1309      *       &amp;lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1310      *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1311      *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1312      *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1313      *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1314      *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1315      *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1316      *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1317      *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1318      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1319      *     &amp;lt;/restriction&amp;gt;
1320      *   &amp;lt;/complexContent&amp;gt;
1321      * &amp;lt;/complexType&amp;gt;
1322      * &lt;/pre&gt;
1323      * 
1324      * 
1325      */
1326     @XmlAccessorType(XmlAccessType.FIELD)
1327     @XmlType(name = "", propOrder = {
1328         "seq",
1329         "annotationColours"
1330     })
1331     public static class JGroup {
1332
1333         @XmlElement(namespace = "www.jalview.org", required = true)
1334         protected List<String> seq;
1335         @XmlElement(namespace = "www.jalview.org")
1336         protected AnnotationColourScheme annotationColours;
1337         @XmlAttribute(name = "start")
1338         protected Integer start;
1339         @XmlAttribute(name = "end")
1340         protected Integer end;
1341         @XmlAttribute(name = "name")
1342         protected String name;
1343         @XmlAttribute(name = "colour")
1344         protected String colour;
1345         @XmlAttribute(name = "consThreshold")
1346         protected Integer consThreshold;
1347         @XmlAttribute(name = "pidThreshold")
1348         protected Integer pidThreshold;
1349         @XmlAttribute(name = "outlineColour")
1350         protected Integer outlineColour;
1351         @XmlAttribute(name = "displayBoxes")
1352         protected Boolean displayBoxes;
1353         @XmlAttribute(name = "displayText")
1354         protected Boolean displayText;
1355         @XmlAttribute(name = "colourText")
1356         protected Boolean colourText;
1357         @XmlAttribute(name = "textCol1")
1358         protected Integer textCol1;
1359         @XmlAttribute(name = "textCol2")
1360         protected Integer textCol2;
1361         @XmlAttribute(name = "textColThreshold")
1362         protected Integer textColThreshold;
1363         @XmlAttribute(name = "showUnconserved")
1364         protected Boolean showUnconserved;
1365         @XmlAttribute(name = "ignoreGapsinConsensus")
1366         protected Boolean ignoreGapsinConsensus;
1367         @XmlAttribute(name = "showConsensusHistogram")
1368         protected Boolean showConsensusHistogram;
1369         @XmlAttribute(name = "showSequenceLogo")
1370         protected Boolean showSequenceLogo;
1371         @XmlAttribute(name = "normaliseSequenceLogo")
1372         protected Boolean normaliseSequenceLogo;
1373         @XmlAttribute(name = "id")
1374         protected String id;
1375
1376         /**
1377          * Gets the value of the seq property.
1378          * 
1379          * &lt;p&gt;
1380          * This accessor method returns a reference to the live list,
1381          * not a snapshot. Therefore any modification you make to the
1382          * returned list will be present inside the JAXB object.
1383          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
1384          * 
1385          * &lt;p&gt;
1386          * For example, to add a new item, do as follows:
1387          * &lt;pre&gt;
1388          *    getSeq().add(newItem);
1389          * &lt;/pre&gt;
1390          * 
1391          * 
1392          * &lt;p&gt;
1393          * Objects of the following type(s) are allowed in the list
1394          * {@link String }
1395          * 
1396          * 
1397          */
1398         public List<String> getSeq() {
1399             if (seq == null) {
1400                 seq = new ArrayList<String>();
1401             }
1402             return this.seq;
1403         }
1404
1405         /**
1406          * Gets the value of the annotationColours property.
1407          * 
1408          * @return
1409          *     possible object is
1410          *     {@link AnnotationColourScheme }
1411          *     
1412          */
1413         public AnnotationColourScheme getAnnotationColours() {
1414             return annotationColours;
1415         }
1416
1417         /**
1418          * Sets the value of the annotationColours property.
1419          * 
1420          * @param value
1421          *     allowed object is
1422          *     {@link AnnotationColourScheme }
1423          *     
1424          */
1425         public void setAnnotationColours(AnnotationColourScheme value) {
1426             this.annotationColours = value;
1427         }
1428
1429         /**
1430          * Gets the value of the start property.
1431          * 
1432          * @return
1433          *     possible object is
1434          *     {@link Integer }
1435          *     
1436          */
1437         public Integer getStart() {
1438             return start;
1439         }
1440
1441         /**
1442          * Sets the value of the start property.
1443          * 
1444          * @param value
1445          *     allowed object is
1446          *     {@link Integer }
1447          *     
1448          */
1449         public void setStart(Integer value) {
1450             this.start = value;
1451         }
1452
1453         /**
1454          * Gets the value of the end property.
1455          * 
1456          * @return
1457          *     possible object is
1458          *     {@link Integer }
1459          *     
1460          */
1461         public Integer getEnd() {
1462             return end;
1463         }
1464
1465         /**
1466          * Sets the value of the end property.
1467          * 
1468          * @param value
1469          *     allowed object is
1470          *     {@link Integer }
1471          *     
1472          */
1473         public void setEnd(Integer value) {
1474             this.end = value;
1475         }
1476
1477         /**
1478          * Gets the value of the name property.
1479          * 
1480          * @return
1481          *     possible object is
1482          *     {@link String }
1483          *     
1484          */
1485         public String getName() {
1486             return name;
1487         }
1488
1489         /**
1490          * Sets the value of the name property.
1491          * 
1492          * @param value
1493          *     allowed object is
1494          *     {@link String }
1495          *     
1496          */
1497         public void setName(String value) {
1498             this.name = value;
1499         }
1500
1501         /**
1502          * Gets the value of the colour property.
1503          * 
1504          * @return
1505          *     possible object is
1506          *     {@link String }
1507          *     
1508          */
1509         public String getColour() {
1510             return colour;
1511         }
1512
1513         /**
1514          * Sets the value of the colour property.
1515          * 
1516          * @param value
1517          *     allowed object is
1518          *     {@link String }
1519          *     
1520          */
1521         public void setColour(String value) {
1522             this.colour = value;
1523         }
1524
1525         /**
1526          * Gets the value of the consThreshold property.
1527          * 
1528          * @return
1529          *     possible object is
1530          *     {@link Integer }
1531          *     
1532          */
1533         public Integer getConsThreshold() {
1534             return consThreshold;
1535         }
1536
1537         /**
1538          * Sets the value of the consThreshold property.
1539          * 
1540          * @param value
1541          *     allowed object is
1542          *     {@link Integer }
1543          *     
1544          */
1545         public void setConsThreshold(Integer value) {
1546             this.consThreshold = value;
1547         }
1548
1549         /**
1550          * Gets the value of the pidThreshold property.
1551          * 
1552          * @return
1553          *     possible object is
1554          *     {@link Integer }
1555          *     
1556          */
1557         public Integer getPidThreshold() {
1558             return pidThreshold;
1559         }
1560
1561         /**
1562          * Sets the value of the pidThreshold property.
1563          * 
1564          * @param value
1565          *     allowed object is
1566          *     {@link Integer }
1567          *     
1568          */
1569         public void setPidThreshold(Integer value) {
1570             this.pidThreshold = value;
1571         }
1572
1573         /**
1574          * Gets the value of the outlineColour property.
1575          * 
1576          * @return
1577          *     possible object is
1578          *     {@link Integer }
1579          *     
1580          */
1581         public Integer getOutlineColour() {
1582             return outlineColour;
1583         }
1584
1585         /**
1586          * Sets the value of the outlineColour property.
1587          * 
1588          * @param value
1589          *     allowed object is
1590          *     {@link Integer }
1591          *     
1592          */
1593         public void setOutlineColour(Integer value) {
1594             this.outlineColour = value;
1595         }
1596
1597         /**
1598          * Gets the value of the displayBoxes property.
1599          * 
1600          * @return
1601          *     possible object is
1602          *     {@link Boolean }
1603          *     
1604          */
1605         public Boolean isDisplayBoxes() {
1606             return displayBoxes;
1607         }
1608
1609         /**
1610          * Sets the value of the displayBoxes property.
1611          * 
1612          * @param value
1613          *     allowed object is
1614          *     {@link Boolean }
1615          *     
1616          */
1617         public void setDisplayBoxes(Boolean value) {
1618             this.displayBoxes = value;
1619         }
1620
1621         /**
1622          * Gets the value of the displayText property.
1623          * 
1624          * @return
1625          *     possible object is
1626          *     {@link Boolean }
1627          *     
1628          */
1629         public Boolean isDisplayText() {
1630             return displayText;
1631         }
1632
1633         /**
1634          * Sets the value of the displayText property.
1635          * 
1636          * @param value
1637          *     allowed object is
1638          *     {@link Boolean }
1639          *     
1640          */
1641         public void setDisplayText(Boolean value) {
1642             this.displayText = value;
1643         }
1644
1645         /**
1646          * Gets the value of the colourText property.
1647          * 
1648          * @return
1649          *     possible object is
1650          *     {@link Boolean }
1651          *     
1652          */
1653         public Boolean isColourText() {
1654             return colourText;
1655         }
1656
1657         /**
1658          * Sets the value of the colourText property.
1659          * 
1660          * @param value
1661          *     allowed object is
1662          *     {@link Boolean }
1663          *     
1664          */
1665         public void setColourText(Boolean value) {
1666             this.colourText = value;
1667         }
1668
1669         /**
1670          * Gets the value of the textCol1 property.
1671          * 
1672          * @return
1673          *     possible object is
1674          *     {@link Integer }
1675          *     
1676          */
1677         public Integer getTextCol1() {
1678             return textCol1;
1679         }
1680
1681         /**
1682          * Sets the value of the textCol1 property.
1683          * 
1684          * @param value
1685          *     allowed object is
1686          *     {@link Integer }
1687          *     
1688          */
1689         public void setTextCol1(Integer value) {
1690             this.textCol1 = value;
1691         }
1692
1693         /**
1694          * Gets the value of the textCol2 property.
1695          * 
1696          * @return
1697          *     possible object is
1698          *     {@link Integer }
1699          *     
1700          */
1701         public Integer getTextCol2() {
1702             return textCol2;
1703         }
1704
1705         /**
1706          * Sets the value of the textCol2 property.
1707          * 
1708          * @param value
1709          *     allowed object is
1710          *     {@link Integer }
1711          *     
1712          */
1713         public void setTextCol2(Integer value) {
1714             this.textCol2 = value;
1715         }
1716
1717         /**
1718          * Gets the value of the textColThreshold property.
1719          * 
1720          * @return
1721          *     possible object is
1722          *     {@link Integer }
1723          *     
1724          */
1725         public Integer getTextColThreshold() {
1726             return textColThreshold;
1727         }
1728
1729         /**
1730          * Sets the value of the textColThreshold property.
1731          * 
1732          * @param value
1733          *     allowed object is
1734          *     {@link Integer }
1735          *     
1736          */
1737         public void setTextColThreshold(Integer value) {
1738             this.textColThreshold = value;
1739         }
1740
1741         /**
1742          * Gets the value of the showUnconserved property.
1743          * 
1744          * @return
1745          *     possible object is
1746          *     {@link Boolean }
1747          *     
1748          */
1749         public Boolean isShowUnconserved() {
1750             return showUnconserved;
1751         }
1752
1753         /**
1754          * Sets the value of the showUnconserved property.
1755          * 
1756          * @param value
1757          *     allowed object is
1758          *     {@link Boolean }
1759          *     
1760          */
1761         public void setShowUnconserved(Boolean value) {
1762             this.showUnconserved = value;
1763         }
1764
1765         /**
1766          * Gets the value of the ignoreGapsinConsensus property.
1767          * 
1768          * @return
1769          *     possible object is
1770          *     {@link Boolean }
1771          *     
1772          */
1773         public boolean isIgnoreGapsinConsensus() {
1774             if (ignoreGapsinConsensus == null) {
1775                 return true;
1776             } else {
1777                 return ignoreGapsinConsensus;
1778             }
1779         }
1780
1781         /**
1782          * Sets the value of the ignoreGapsinConsensus property.
1783          * 
1784          * @param value
1785          *     allowed object is
1786          *     {@link Boolean }
1787          *     
1788          */
1789         public void setIgnoreGapsinConsensus(Boolean value) {
1790             this.ignoreGapsinConsensus = value;
1791         }
1792
1793         /**
1794          * Gets the value of the showConsensusHistogram property.
1795          * 
1796          * @return
1797          *     possible object is
1798          *     {@link Boolean }
1799          *     
1800          */
1801         public boolean isShowConsensusHistogram() {
1802             if (showConsensusHistogram == null) {
1803                 return true;
1804             } else {
1805                 return showConsensusHistogram;
1806             }
1807         }
1808
1809         /**
1810          * Sets the value of the showConsensusHistogram property.
1811          * 
1812          * @param value
1813          *     allowed object is
1814          *     {@link Boolean }
1815          *     
1816          */
1817         public void setShowConsensusHistogram(Boolean value) {
1818             this.showConsensusHistogram = value;
1819         }
1820
1821         /**
1822          * Gets the value of the showSequenceLogo property.
1823          * 
1824          * @return
1825          *     possible object is
1826          *     {@link Boolean }
1827          *     
1828          */
1829         public boolean isShowSequenceLogo() {
1830             if (showSequenceLogo == null) {
1831                 return false;
1832             } else {
1833                 return showSequenceLogo;
1834             }
1835         }
1836
1837         /**
1838          * Sets the value of the showSequenceLogo property.
1839          * 
1840          * @param value
1841          *     allowed object is
1842          *     {@link Boolean }
1843          *     
1844          */
1845         public void setShowSequenceLogo(Boolean value) {
1846             this.showSequenceLogo = value;
1847         }
1848
1849         /**
1850          * Gets the value of the normaliseSequenceLogo property.
1851          * 
1852          * @return
1853          *     possible object is
1854          *     {@link Boolean }
1855          *     
1856          */
1857         public boolean isNormaliseSequenceLogo() {
1858             if (normaliseSequenceLogo == null) {
1859                 return false;
1860             } else {
1861                 return normaliseSequenceLogo;
1862             }
1863         }
1864
1865         /**
1866          * Sets the value of the normaliseSequenceLogo property.
1867          * 
1868          * @param value
1869          *     allowed object is
1870          *     {@link Boolean }
1871          *     
1872          */
1873         public void setNormaliseSequenceLogo(Boolean value) {
1874             this.normaliseSequenceLogo = value;
1875         }
1876
1877         /**
1878          * Gets the value of the id property.
1879          * 
1880          * @return
1881          *     possible object is
1882          *     {@link String }
1883          *     
1884          */
1885         public String getId() {
1886             return id;
1887         }
1888
1889         /**
1890          * Sets the value of the id property.
1891          * 
1892          * @param value
1893          *     allowed object is
1894          *     {@link String }
1895          *     
1896          */
1897         public void setId(String value) {
1898             this.id = value;
1899         }
1900
1901     }
1902
1903
1904     /**
1905      * &lt;p&gt;Java class for anonymous complex type.
1906      * 
1907      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
1908      * 
1909      * &lt;pre&gt;
1910      * &amp;lt;complexType&amp;gt;
1911      *   &amp;lt;complexContent&amp;gt;
1912      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1913      *       &amp;lt;sequence&amp;gt;
1914      *         &amp;lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
1915      *         &amp;lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&amp;gt;
1916      *           &amp;lt;complexType&amp;gt;
1917      *             &amp;lt;complexContent&amp;gt;
1918      *               &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
1919      *                 &amp;lt;sequence&amp;gt;
1920      *                   &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
1921      *                     &amp;lt;complexType&amp;gt;
1922      *                       &amp;lt;simpleContent&amp;gt;
1923      *                         &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
1924      *                           &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
1925      *                           &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1926      *                           &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1927      *                           &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1928      *                           &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1929      *                           &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1930      *                           &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1931      *                         &amp;lt;/extension&amp;gt;
1932      *                       &amp;lt;/simpleContent&amp;gt;
1933      *                     &amp;lt;/complexType&amp;gt;
1934      *                   &amp;lt;/element&amp;gt;
1935      *                 &amp;lt;/sequence&amp;gt;
1936      *               &amp;lt;/extension&amp;gt;
1937      *             &amp;lt;/complexContent&amp;gt;
1938      *           &amp;lt;/complexType&amp;gt;
1939      *         &amp;lt;/element&amp;gt;
1940      *         &amp;lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
1941      *         &amp;lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&amp;gt;
1942      *           &amp;lt;complexType&amp;gt;
1943      *             &amp;lt;complexContent&amp;gt;
1944      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1945      *                 &amp;lt;sequence&amp;gt;
1946      *                   &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
1947      *                     &amp;lt;complexType&amp;gt;
1948      *                       &amp;lt;complexContent&amp;gt;
1949      *                         &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1950      *                           &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1951      *                           &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1952      *                           &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1953      *                           &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1954      *                         &amp;lt;/restriction&amp;gt;
1955      *                       &amp;lt;/complexContent&amp;gt;
1956      *                     &amp;lt;/complexType&amp;gt;
1957      *                   &amp;lt;/element&amp;gt;
1958      *                 &amp;lt;/sequence&amp;gt;
1959      *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
1960      *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1961      *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1962      *                 &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1963      *                 &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1964      *               &amp;lt;/restriction&amp;gt;
1965      *             &amp;lt;/complexContent&amp;gt;
1966      *           &amp;lt;/complexType&amp;gt;
1967      *         &amp;lt;/element&amp;gt;
1968      *       &amp;lt;/sequence&amp;gt;
1969      *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1970      *       &amp;lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1971      *       &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1972      *       &amp;lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1973      *       &amp;lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1974      *       &amp;lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1975      *     &amp;lt;/restriction&amp;gt;
1976      *   &amp;lt;/complexContent&amp;gt;
1977      * &amp;lt;/complexType&amp;gt;
1978      * &lt;/pre&gt;
1979      * 
1980      * 
1981      */
1982     @XmlAccessorType(XmlAccessType.FIELD)
1983     @XmlType(name = "", propOrder = {
1984         "features",
1985         "pdbids",
1986         "hiddenSequences",
1987         "rnaViewer"
1988     })
1989     public static class JSeq {
1990
1991         @XmlElement(namespace = "www.jalview.org")
1992         protected List<Feature> features;
1993         @XmlElement(namespace = "www.jalview.org")
1994         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1995         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1996         protected List<Integer> hiddenSequences;
1997         @XmlElement(namespace = "www.jalview.org")
1998         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1999         @XmlAttribute(name = "colour")
2000         protected Integer colour;
2001         @XmlAttribute(name = "start", required = true)
2002         protected int start;
2003         @XmlAttribute(name = "end", required = true)
2004         protected int end;
2005         @XmlAttribute(name = "id", required = true)
2006         protected String id;
2007         @XmlAttribute(name = "hidden")
2008         protected Boolean hidden;
2009         @XmlAttribute(name = "viewreference")
2010         protected Boolean viewreference;
2011
2012         /**
2013          * Gets the value of the features property.
2014          * 
2015          * &lt;p&gt;
2016          * This accessor method returns a reference to the live list,
2017          * not a snapshot. Therefore any modification you make to the
2018          * returned list will be present inside the JAXB object.
2019          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
2020          * 
2021          * &lt;p&gt;
2022          * For example, to add a new item, do as follows:
2023          * &lt;pre&gt;
2024          *    getFeatures().add(newItem);
2025          * &lt;/pre&gt;
2026          * 
2027          * 
2028          * &lt;p&gt;
2029          * Objects of the following type(s) are allowed in the list
2030          * {@link Feature }
2031          * 
2032          * 
2033          */
2034         public List<Feature> getFeatures() {
2035             if (features == null) {
2036                 features = new ArrayList<Feature>();
2037             }
2038             return this.features;
2039         }
2040
2041         /**
2042          * Gets the value of the pdbids property.
2043          * 
2044          * &lt;p&gt;
2045          * This accessor method returns a reference to the live list,
2046          * not a snapshot. Therefore any modification you make to the
2047          * returned list will be present inside the JAXB object.
2048          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
2049          * 
2050          * &lt;p&gt;
2051          * For example, to add a new item, do as follows:
2052          * &lt;pre&gt;
2053          *    getPdbids().add(newItem);
2054          * &lt;/pre&gt;
2055          * 
2056          * 
2057          * &lt;p&gt;
2058          * Objects of the following type(s) are allowed in the list
2059          * {@link JalviewModel.JSeq.Pdbids }
2060          * 
2061          * 
2062          */
2063         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2064             if (pdbids == null) {
2065                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2066             }
2067             return this.pdbids;
2068         }
2069
2070         /**
2071          * Gets the value of the hiddenSequences property.
2072          * 
2073          * &lt;p&gt;
2074          * This accessor method returns a reference to the live list,
2075          * not a snapshot. Therefore any modification you make to the
2076          * returned list will be present inside the JAXB object.
2077          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
2078          * 
2079          * &lt;p&gt;
2080          * For example, to add a new item, do as follows:
2081          * &lt;pre&gt;
2082          *    getHiddenSequences().add(newItem);
2083          * &lt;/pre&gt;
2084          * 
2085          * 
2086          * &lt;p&gt;
2087          * Objects of the following type(s) are allowed in the list
2088          * {@link Integer }
2089          * 
2090          * 
2091          */
2092         public List<Integer> getHiddenSequences() {
2093             if (hiddenSequences == null) {
2094                 hiddenSequences = new ArrayList<Integer>();
2095             }
2096             return this.hiddenSequences;
2097         }
2098
2099         /**
2100          * Gets the value of the rnaViewer property.
2101          * 
2102          * &lt;p&gt;
2103          * This accessor method returns a reference to the live list,
2104          * not a snapshot. Therefore any modification you make to the
2105          * returned list will be present inside the JAXB object.
2106          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
2107          * 
2108          * &lt;p&gt;
2109          * For example, to add a new item, do as follows:
2110          * &lt;pre&gt;
2111          *    getRnaViewer().add(newItem);
2112          * &lt;/pre&gt;
2113          * 
2114          * 
2115          * &lt;p&gt;
2116          * Objects of the following type(s) are allowed in the list
2117          * {@link JalviewModel.JSeq.RnaViewer }
2118          * 
2119          * 
2120          */
2121         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2122             if (rnaViewer == null) {
2123                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2124             }
2125             return this.rnaViewer;
2126         }
2127
2128         /**
2129          * Gets the value of the colour property.
2130          * 
2131          * @return
2132          *     possible object is
2133          *     {@link Integer }
2134          *     
2135          */
2136         public Integer getColour() {
2137             return colour;
2138         }
2139
2140         /**
2141          * Sets the value of the colour property.
2142          * 
2143          * @param value
2144          *     allowed object is
2145          *     {@link Integer }
2146          *     
2147          */
2148         public void setColour(Integer value) {
2149             this.colour = value;
2150         }
2151
2152         /**
2153          * Gets the value of the start property.
2154          * 
2155          */
2156         public int getStart() {
2157             return start;
2158         }
2159
2160         /**
2161          * Sets the value of the start property.
2162          * 
2163          */
2164         public void setStart(int value) {
2165             this.start = value;
2166         }
2167
2168         /**
2169          * Gets the value of the end property.
2170          * 
2171          */
2172         public int getEnd() {
2173             return end;
2174         }
2175
2176         /**
2177          * Sets the value of the end property.
2178          * 
2179          */
2180         public void setEnd(int value) {
2181             this.end = value;
2182         }
2183
2184         /**
2185          * Gets the value of the id property.
2186          * 
2187          * @return
2188          *     possible object is
2189          *     {@link String }
2190          *     
2191          */
2192         public String getId() {
2193             return id;
2194         }
2195
2196         /**
2197          * Sets the value of the id property.
2198          * 
2199          * @param value
2200          *     allowed object is
2201          *     {@link String }
2202          *     
2203          */
2204         public void setId(String value) {
2205             this.id = value;
2206         }
2207
2208         /**
2209          * Gets the value of the hidden property.
2210          * 
2211          * @return
2212          *     possible object is
2213          *     {@link Boolean }
2214          *     
2215          */
2216         public Boolean isHidden() {
2217             return hidden;
2218         }
2219
2220         /**
2221          * Sets the value of the hidden property.
2222          * 
2223          * @param value
2224          *     allowed object is
2225          *     {@link Boolean }
2226          *     
2227          */
2228         public void setHidden(Boolean value) {
2229             this.hidden = value;
2230         }
2231
2232         /**
2233          * Gets the value of the viewreference property.
2234          * 
2235          * @return
2236          *     possible object is
2237          *     {@link Boolean }
2238          *     
2239          */
2240         public Boolean isViewreference() {
2241             return viewreference;
2242         }
2243
2244         /**
2245          * Sets the value of the viewreference property.
2246          * 
2247          * @param value
2248          *     allowed object is
2249          *     {@link Boolean }
2250          *     
2251          */
2252         public void setViewreference(Boolean value) {
2253             this.viewreference = value;
2254         }
2255
2256
2257         /**
2258          * &lt;p&gt;Java class for anonymous complex type.
2259          * 
2260          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2261          * 
2262          * &lt;pre&gt;
2263          * &amp;lt;complexType&amp;gt;
2264          *   &amp;lt;complexContent&amp;gt;
2265          *     &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
2266          *       &amp;lt;sequence&amp;gt;
2267          *         &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
2268          *           &amp;lt;complexType&amp;gt;
2269          *             &amp;lt;simpleContent&amp;gt;
2270          *               &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2271          *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2272          *                 &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2273          *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2274          *                 &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2275          *                 &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
2276          *                 &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2277          *                 &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2278          *               &amp;lt;/extension&amp;gt;
2279          *             &amp;lt;/simpleContent&amp;gt;
2280          *           &amp;lt;/complexType&amp;gt;
2281          *         &amp;lt;/element&amp;gt;
2282          *       &amp;lt;/sequence&amp;gt;
2283          *     &amp;lt;/extension&amp;gt;
2284          *   &amp;lt;/complexContent&amp;gt;
2285          * &amp;lt;/complexType&amp;gt;
2286          * &lt;/pre&gt;
2287          * 
2288          * 
2289          */
2290         @XmlAccessorType(XmlAccessType.FIELD)
2291         @XmlType(name = "", propOrder = {
2292             "structureState"
2293         })
2294         public static class Pdbids
2295             extends Pdbentry
2296         {
2297
2298             @XmlElement(namespace = "www.jalview.org")
2299             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2300
2301             /**
2302              * Gets the value of the structureState property.
2303              * 
2304              * &lt;p&gt;
2305              * This accessor method returns a reference to the live list,
2306              * not a snapshot. Therefore any modification you make to the
2307              * returned list will be present inside the JAXB object.
2308              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
2309              * 
2310              * &lt;p&gt;
2311              * For example, to add a new item, do as follows:
2312              * &lt;pre&gt;
2313              *    getStructureState().add(newItem);
2314              * &lt;/pre&gt;
2315              * 
2316              * 
2317              * &lt;p&gt;
2318              * Objects of the following type(s) are allowed in the list
2319              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2320              * 
2321              * 
2322              */
2323             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2324                 if (structureState == null) {
2325                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2326                 }
2327                 return this.structureState;
2328             }
2329
2330
2331             /**
2332              * &lt;p&gt;Java class for anonymous complex type.
2333              * 
2334              * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2335              * 
2336              * &lt;pre&gt;
2337              * &amp;lt;complexType&amp;gt;
2338              *   &amp;lt;simpleContent&amp;gt;
2339              *     &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2340              *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2341              *       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2342              *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2343              *       &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2344              *       &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
2345              *       &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2346              *       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2347              *     &amp;lt;/extension&amp;gt;
2348              *   &amp;lt;/simpleContent&amp;gt;
2349              * &amp;lt;/complexType&amp;gt;
2350              * &lt;/pre&gt;
2351              * 
2352              * 
2353              */
2354             @XmlAccessorType(XmlAccessType.FIELD)
2355             @XmlType(name = "", propOrder = {
2356                 "value"
2357             })
2358             public static class StructureState {
2359
2360                 @XmlValue
2361                 protected String value;
2362                 @XmlAttribute(name = "visible")
2363                 protected Boolean visible;
2364                 @XmlAttribute(name = "viewId")
2365                 protected String viewId;
2366                 @XmlAttribute(name = "alignwithAlignPanel")
2367                 protected Boolean alignwithAlignPanel;
2368                 @XmlAttribute(name = "colourwithAlignPanel")
2369                 protected Boolean colourwithAlignPanel;
2370                 @XmlAttribute(name = "colourByJmol")
2371                 protected Boolean colourByJmol;
2372                 @XmlAttribute(name = "type")
2373                 protected String type;
2374                 @XmlAttribute(name = "width")
2375                 protected Integer width;
2376                 @XmlAttribute(name = "height")
2377                 protected Integer height;
2378                 @XmlAttribute(name = "xpos")
2379                 protected Integer xpos;
2380                 @XmlAttribute(name = "ypos")
2381                 protected Integer ypos;
2382
2383                 /**
2384                  * Gets the value of the value property.
2385                  * 
2386                  * @return
2387                  *     possible object is
2388                  *     {@link String }
2389                  *     
2390                  */
2391                 public String getValue() {
2392                     return value;
2393                 }
2394
2395                 /**
2396                  * Sets the value of the value property.
2397                  * 
2398                  * @param value
2399                  *     allowed object is
2400                  *     {@link String }
2401                  *     
2402                  */
2403                 public void setValue(String value) {
2404                     this.value = value;
2405                 }
2406
2407                 /**
2408                  * Gets the value of the visible property.
2409                  * 
2410                  * @return
2411                  *     possible object is
2412                  *     {@link Boolean }
2413                  *     
2414                  */
2415                 public Boolean isVisible() {
2416                     return visible;
2417                 }
2418
2419                 /**
2420                  * Sets the value of the visible property.
2421                  * 
2422                  * @param value
2423                  *     allowed object is
2424                  *     {@link Boolean }
2425                  *     
2426                  */
2427                 public void setVisible(Boolean value) {
2428                     this.visible = value;
2429                 }
2430
2431                 /**
2432                  * Gets the value of the viewId property.
2433                  * 
2434                  * @return
2435                  *     possible object is
2436                  *     {@link String }
2437                  *     
2438                  */
2439                 public String getViewId() {
2440                     return viewId;
2441                 }
2442
2443                 /**
2444                  * Sets the value of the viewId property.
2445                  * 
2446                  * @param value
2447                  *     allowed object is
2448                  *     {@link String }
2449                  *     
2450                  */
2451                 public void setViewId(String value) {
2452                     this.viewId = value;
2453                 }
2454
2455                 /**
2456                  * Gets the value of the alignwithAlignPanel property.
2457                  * 
2458                  * @return
2459                  *     possible object is
2460                  *     {@link Boolean }
2461                  *     
2462                  */
2463                 public boolean isAlignwithAlignPanel() {
2464                     if (alignwithAlignPanel == null) {
2465                         return true;
2466                     } else {
2467                         return alignwithAlignPanel;
2468                     }
2469                 }
2470
2471                 /**
2472                  * Sets the value of the alignwithAlignPanel property.
2473                  * 
2474                  * @param value
2475                  *     allowed object is
2476                  *     {@link Boolean }
2477                  *     
2478                  */
2479                 public void setAlignwithAlignPanel(Boolean value) {
2480                     this.alignwithAlignPanel = value;
2481                 }
2482
2483                 /**
2484                  * Gets the value of the colourwithAlignPanel property.
2485                  * 
2486                  * @return
2487                  *     possible object is
2488                  *     {@link Boolean }
2489                  *     
2490                  */
2491                 public boolean isColourwithAlignPanel() {
2492                     if (colourwithAlignPanel == null) {
2493                         return false;
2494                     } else {
2495                         return colourwithAlignPanel;
2496                     }
2497                 }
2498
2499                 /**
2500                  * Sets the value of the colourwithAlignPanel property.
2501                  * 
2502                  * @param value
2503                  *     allowed object is
2504                  *     {@link Boolean }
2505                  *     
2506                  */
2507                 public void setColourwithAlignPanel(Boolean value) {
2508                     this.colourwithAlignPanel = value;
2509                 }
2510
2511                 /**
2512                  * Gets the value of the colourByJmol property.
2513                  * 
2514                  * @return
2515                  *     possible object is
2516                  *     {@link Boolean }
2517                  *     
2518                  */
2519                 public boolean isColourByJmol() {
2520                     if (colourByJmol == null) {
2521                         return true;
2522                     } else {
2523                         return colourByJmol;
2524                     }
2525                 }
2526
2527                 /**
2528                  * Sets the value of the colourByJmol property.
2529                  * 
2530                  * @param value
2531                  *     allowed object is
2532                  *     {@link Boolean }
2533                  *     
2534                  */
2535                 public void setColourByJmol(Boolean value) {
2536                     this.colourByJmol = value;
2537                 }
2538
2539                 /**
2540                  * Gets the value of the type property.
2541                  * 
2542                  * @return
2543                  *     possible object is
2544                  *     {@link String }
2545                  *     
2546                  */
2547                 public String getType() {
2548                     return type;
2549                 }
2550
2551                 /**
2552                  * Sets the value of the type property.
2553                  * 
2554                  * @param value
2555                  *     allowed object is
2556                  *     {@link String }
2557                  *     
2558                  */
2559                 public void setType(String value) {
2560                     this.type = value;
2561                 }
2562
2563                 /**
2564                  * Gets the value of the width property.
2565                  * 
2566                  * @return
2567                  *     possible object is
2568                  *     {@link Integer }
2569                  *     
2570                  */
2571                 public Integer getWidth() {
2572                     return width;
2573                 }
2574
2575                 /**
2576                  * Sets the value of the width property.
2577                  * 
2578                  * @param value
2579                  *     allowed object is
2580                  *     {@link Integer }
2581                  *     
2582                  */
2583                 public void setWidth(Integer value) {
2584                     this.width = value;
2585                 }
2586
2587                 /**
2588                  * Gets the value of the height property.
2589                  * 
2590                  * @return
2591                  *     possible object is
2592                  *     {@link Integer }
2593                  *     
2594                  */
2595                 public Integer getHeight() {
2596                     return height;
2597                 }
2598
2599                 /**
2600                  * Sets the value of the height property.
2601                  * 
2602                  * @param value
2603                  *     allowed object is
2604                  *     {@link Integer }
2605                  *     
2606                  */
2607                 public void setHeight(Integer value) {
2608                     this.height = value;
2609                 }
2610
2611                 /**
2612                  * Gets the value of the xpos property.
2613                  * 
2614                  * @return
2615                  *     possible object is
2616                  *     {@link Integer }
2617                  *     
2618                  */
2619                 public Integer getXpos() {
2620                     return xpos;
2621                 }
2622
2623                 /**
2624                  * Sets the value of the xpos property.
2625                  * 
2626                  * @param value
2627                  *     allowed object is
2628                  *     {@link Integer }
2629                  *     
2630                  */
2631                 public void setXpos(Integer value) {
2632                     this.xpos = value;
2633                 }
2634
2635                 /**
2636                  * Gets the value of the ypos property.
2637                  * 
2638                  * @return
2639                  *     possible object is
2640                  *     {@link Integer }
2641                  *     
2642                  */
2643                 public Integer getYpos() {
2644                     return ypos;
2645                 }
2646
2647                 /**
2648                  * Sets the value of the ypos property.
2649                  * 
2650                  * @param value
2651                  *     allowed object is
2652                  *     {@link Integer }
2653                  *     
2654                  */
2655                 public void setYpos(Integer value) {
2656                     this.ypos = value;
2657                 }
2658
2659             }
2660
2661         }
2662
2663
2664         /**
2665          * &lt;p&gt;Java class for anonymous complex type.
2666          * 
2667          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2668          * 
2669          * &lt;pre&gt;
2670          * &amp;lt;complexType&amp;gt;
2671          *   &amp;lt;complexContent&amp;gt;
2672          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2673          *       &amp;lt;sequence&amp;gt;
2674          *         &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
2675          *           &amp;lt;complexType&amp;gt;
2676          *             &amp;lt;complexContent&amp;gt;
2677          *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2678          *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2679          *                 &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2680          *                 &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2681          *                 &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2682          *               &amp;lt;/restriction&amp;gt;
2683          *             &amp;lt;/complexContent&amp;gt;
2684          *           &amp;lt;/complexType&amp;gt;
2685          *         &amp;lt;/element&amp;gt;
2686          *       &amp;lt;/sequence&amp;gt;
2687          *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2688          *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2689          *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2690          *       &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2691          *       &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2692          *     &amp;lt;/restriction&amp;gt;
2693          *   &amp;lt;/complexContent&amp;gt;
2694          * &amp;lt;/complexType&amp;gt;
2695          * &lt;/pre&gt;
2696          * 
2697          * 
2698          */
2699         @XmlAccessorType(XmlAccessType.FIELD)
2700         @XmlType(name = "", propOrder = {
2701             "secondaryStructure"
2702         })
2703         public static class RnaViewer {
2704
2705             @XmlElement(namespace = "www.jalview.org", required = true)
2706             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2707             @XmlAttribute(name = "title")
2708             protected String title;
2709             @XmlAttribute(name = "viewId")
2710             protected String viewId;
2711             @XmlAttribute(name = "dividerLocation")
2712             protected Integer dividerLocation;
2713             @XmlAttribute(name = "selectedRna")
2714             protected Integer selectedRna;
2715             @XmlAttribute(name = "width")
2716             protected Integer width;
2717             @XmlAttribute(name = "height")
2718             protected Integer height;
2719             @XmlAttribute(name = "xpos")
2720             protected Integer xpos;
2721             @XmlAttribute(name = "ypos")
2722             protected Integer ypos;
2723
2724             /**
2725              * Gets the value of the secondaryStructure property.
2726              * 
2727              * &lt;p&gt;
2728              * This accessor method returns a reference to the live list,
2729              * not a snapshot. Therefore any modification you make to the
2730              * returned list will be present inside the JAXB object.
2731              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure property.
2732              * 
2733              * &lt;p&gt;
2734              * For example, to add a new item, do as follows:
2735              * &lt;pre&gt;
2736              *    getSecondaryStructure().add(newItem);
2737              * &lt;/pre&gt;
2738              * 
2739              * 
2740              * &lt;p&gt;
2741              * Objects of the following type(s) are allowed in the list
2742              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2743              * 
2744              * 
2745              */
2746             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2747                 if (secondaryStructure == null) {
2748                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2749                 }
2750                 return this.secondaryStructure;
2751             }
2752
2753             /**
2754              * Gets the value of the title property.
2755              * 
2756              * @return
2757              *     possible object is
2758              *     {@link String }
2759              *     
2760              */
2761             public String getTitle() {
2762                 return title;
2763             }
2764
2765             /**
2766              * Sets the value of the title property.
2767              * 
2768              * @param value
2769              *     allowed object is
2770              *     {@link String }
2771              *     
2772              */
2773             public void setTitle(String value) {
2774                 this.title = value;
2775             }
2776
2777             /**
2778              * Gets the value of the viewId property.
2779              * 
2780              * @return
2781              *     possible object is
2782              *     {@link String }
2783              *     
2784              */
2785             public String getViewId() {
2786                 return viewId;
2787             }
2788
2789             /**
2790              * Sets the value of the viewId property.
2791              * 
2792              * @param value
2793              *     allowed object is
2794              *     {@link String }
2795              *     
2796              */
2797             public void setViewId(String value) {
2798                 this.viewId = value;
2799             }
2800
2801             /**
2802              * Gets the value of the dividerLocation property.
2803              * 
2804              * @return
2805              *     possible object is
2806              *     {@link Integer }
2807              *     
2808              */
2809             public Integer getDividerLocation() {
2810                 return dividerLocation;
2811             }
2812
2813             /**
2814              * Sets the value of the dividerLocation property.
2815              * 
2816              * @param value
2817              *     allowed object is
2818              *     {@link Integer }
2819              *     
2820              */
2821             public void setDividerLocation(Integer value) {
2822                 this.dividerLocation = value;
2823             }
2824
2825             /**
2826              * Gets the value of the selectedRna property.
2827              * 
2828              * @return
2829              *     possible object is
2830              *     {@link Integer }
2831              *     
2832              */
2833             public Integer getSelectedRna() {
2834                 return selectedRna;
2835             }
2836
2837             /**
2838              * Sets the value of the selectedRna property.
2839              * 
2840              * @param value
2841              *     allowed object is
2842              *     {@link Integer }
2843              *     
2844              */
2845             public void setSelectedRna(Integer value) {
2846                 this.selectedRna = value;
2847             }
2848
2849             /**
2850              * Gets the value of the width property.
2851              * 
2852              * @return
2853              *     possible object is
2854              *     {@link Integer }
2855              *     
2856              */
2857             public Integer getWidth() {
2858                 return width;
2859             }
2860
2861             /**
2862              * Sets the value of the width property.
2863              * 
2864              * @param value
2865              *     allowed object is
2866              *     {@link Integer }
2867              *     
2868              */
2869             public void setWidth(Integer value) {
2870                 this.width = value;
2871             }
2872
2873             /**
2874              * Gets the value of the height property.
2875              * 
2876              * @return
2877              *     possible object is
2878              *     {@link Integer }
2879              *     
2880              */
2881             public Integer getHeight() {
2882                 return height;
2883             }
2884
2885             /**
2886              * Sets the value of the height property.
2887              * 
2888              * @param value
2889              *     allowed object is
2890              *     {@link Integer }
2891              *     
2892              */
2893             public void setHeight(Integer value) {
2894                 this.height = value;
2895             }
2896
2897             /**
2898              * Gets the value of the xpos property.
2899              * 
2900              * @return
2901              *     possible object is
2902              *     {@link Integer }
2903              *     
2904              */
2905             public Integer getXpos() {
2906                 return xpos;
2907             }
2908
2909             /**
2910              * Sets the value of the xpos property.
2911              * 
2912              * @param value
2913              *     allowed object is
2914              *     {@link Integer }
2915              *     
2916              */
2917             public void setXpos(Integer value) {
2918                 this.xpos = value;
2919             }
2920
2921             /**
2922              * Gets the value of the ypos property.
2923              * 
2924              * @return
2925              *     possible object is
2926              *     {@link Integer }
2927              *     
2928              */
2929             public Integer getYpos() {
2930                 return ypos;
2931             }
2932
2933             /**
2934              * Sets the value of the ypos property.
2935              * 
2936              * @param value
2937              *     allowed object is
2938              *     {@link Integer }
2939              *     
2940              */
2941             public void setYpos(Integer value) {
2942                 this.ypos = value;
2943             }
2944
2945
2946             /**
2947              * &lt;p&gt;Java class for anonymous complex type.
2948              * 
2949              * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2950              * 
2951              * &lt;pre&gt;
2952              * &amp;lt;complexType&amp;gt;
2953              *   &amp;lt;complexContent&amp;gt;
2954              *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2955              *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2956              *       &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2957              *       &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2958              *       &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2959              *     &amp;lt;/restriction&amp;gt;
2960              *   &amp;lt;/complexContent&amp;gt;
2961              * &amp;lt;/complexType&amp;gt;
2962              * &lt;/pre&gt;
2963              * 
2964              * 
2965              */
2966             @XmlAccessorType(XmlAccessType.FIELD)
2967             @XmlType(name = "")
2968             public static class SecondaryStructure {
2969
2970                 @XmlAttribute(name = "title")
2971                 protected String title;
2972                 @XmlAttribute(name = "annotationId", required = true)
2973                 protected String annotationId;
2974                 @XmlAttribute(name = "gapped")
2975                 protected Boolean gapped;
2976                 @XmlAttribute(name = "viewerState")
2977                 protected String viewerState;
2978
2979                 /**
2980                  * Gets the value of the title property.
2981                  * 
2982                  * @return
2983                  *     possible object is
2984                  *     {@link String }
2985                  *     
2986                  */
2987                 public String getTitle() {
2988                     return title;
2989                 }
2990
2991                 /**
2992                  * Sets the value of the title property.
2993                  * 
2994                  * @param value
2995                  *     allowed object is
2996                  *     {@link String }
2997                  *     
2998                  */
2999                 public void setTitle(String value) {
3000                     this.title = value;
3001                 }
3002
3003                 /**
3004                  * Gets the value of the annotationId property.
3005                  * 
3006                  * @return
3007                  *     possible object is
3008                  *     {@link String }
3009                  *     
3010                  */
3011                 public String getAnnotationId() {
3012                     return annotationId;
3013                 }
3014
3015                 /**
3016                  * Sets the value of the annotationId property.
3017                  * 
3018                  * @param value
3019                  *     allowed object is
3020                  *     {@link String }
3021                  *     
3022                  */
3023                 public void setAnnotationId(String value) {
3024                     this.annotationId = value;
3025                 }
3026
3027                 /**
3028                  * Gets the value of the gapped property.
3029                  * 
3030                  * @return
3031                  *     possible object is
3032                  *     {@link Boolean }
3033                  *     
3034                  */
3035                 public Boolean isGapped() {
3036                     return gapped;
3037                 }
3038
3039                 /**
3040                  * Sets the value of the gapped property.
3041                  * 
3042                  * @param value
3043                  *     allowed object is
3044                  *     {@link Boolean }
3045                  *     
3046                  */
3047                 public void setGapped(Boolean value) {
3048                     this.gapped = value;
3049                 }
3050
3051                 /**
3052                  * Gets the value of the viewerState property.
3053                  * 
3054                  * @return
3055                  *     possible object is
3056                  *     {@link String }
3057                  *     
3058                  */
3059                 public String getViewerState() {
3060                     return viewerState;
3061                 }
3062
3063                 /**
3064                  * Sets the value of the viewerState property.
3065                  * 
3066                  * @param value
3067                  *     allowed object is
3068                  *     {@link String }
3069                  *     
3070                  */
3071                 public void setViewerState(String value) {
3072                     this.viewerState = value;
3073                 }
3074
3075             }
3076
3077         }
3078
3079     }
3080
3081
3082     /**
3083      * &lt;p&gt;Java class for anonymous complex type.
3084      * 
3085      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3086      * 
3087      * &lt;pre&gt;
3088      * &amp;lt;complexType&amp;gt;
3089      *   &amp;lt;complexContent&amp;gt;
3090      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3091      *       &amp;lt;sequence&amp;gt;
3092      *         &amp;lt;element name="sequencePoint" maxOccurs="unbounded"&amp;gt;
3093      *           &amp;lt;complexType&amp;gt;
3094      *             &amp;lt;complexContent&amp;gt;
3095      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3096      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3097      *                 &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3098      *               &amp;lt;/restriction&amp;gt;
3099      *             &amp;lt;/complexContent&amp;gt;
3100      *           &amp;lt;/complexType&amp;gt;
3101      *         &amp;lt;/element&amp;gt;
3102      *         &amp;lt;element name="axis" maxOccurs="3" minOccurs="3"&amp;gt;
3103      *           &amp;lt;complexType&amp;gt;
3104      *             &amp;lt;complexContent&amp;gt;
3105      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3106      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3107      *               &amp;lt;/restriction&amp;gt;
3108      *             &amp;lt;/complexContent&amp;gt;
3109      *           &amp;lt;/complexType&amp;gt;
3110      *         &amp;lt;/element&amp;gt;
3111      *         &amp;lt;element name="seqPointMin"&amp;gt;
3112      *           &amp;lt;complexType&amp;gt;
3113      *             &amp;lt;complexContent&amp;gt;
3114      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3115      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3116      *               &amp;lt;/restriction&amp;gt;
3117      *             &amp;lt;/complexContent&amp;gt;
3118      *           &amp;lt;/complexType&amp;gt;
3119      *         &amp;lt;/element&amp;gt;
3120      *         &amp;lt;element name="seqPointMax"&amp;gt;
3121      *           &amp;lt;complexType&amp;gt;
3122      *             &amp;lt;complexContent&amp;gt;
3123      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3124      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3125      *               &amp;lt;/restriction&amp;gt;
3126      *             &amp;lt;/complexContent&amp;gt;
3127      *           &amp;lt;/complexType&amp;gt;
3128      *         &amp;lt;/element&amp;gt;
3129      *         &amp;lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&amp;gt;
3130      *       &amp;lt;/sequence&amp;gt;
3131      *       &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
3132      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
3133      *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3134      *       &amp;lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3135      *       &amp;lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3136      *       &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3137      *       &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3138      *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3139      *       &amp;lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
3140      *       &amp;lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3141      *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3142      *     &amp;lt;/restriction&amp;gt;
3143      *   &amp;lt;/complexContent&amp;gt;
3144      * &amp;lt;/complexType&amp;gt;
3145      * &lt;/pre&gt;
3146      * 
3147      * 
3148      */
3149     @XmlAccessorType(XmlAccessType.FIELD)
3150     @XmlType(name = "", propOrder = {
3151         "sequencePoint",
3152         "axis",
3153         "seqPointMin",
3154         "seqPointMax",
3155         "pcaData"
3156     })
3157     public static class PcaViewer {
3158
3159         @XmlElement(namespace = "www.jalview.org", required = true)
3160         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3161         @XmlElement(namespace = "www.jalview.org", required = true)
3162         protected List<JalviewModel.PcaViewer.Axis> axis;
3163         @XmlElement(namespace = "www.jalview.org", required = true)
3164         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3165         @XmlElement(namespace = "www.jalview.org", required = true)
3166         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3167         @XmlElement(namespace = "www.jalview.org", required = true)
3168         protected PcaDataType pcaData;
3169         @XmlAttribute(name = "title")
3170         protected String title;
3171         @XmlAttribute(name = "scoreModelName")
3172         protected String scoreModelName;
3173         @XmlAttribute(name = "xDim")
3174         protected Integer xDim;
3175         @XmlAttribute(name = "yDim")
3176         protected Integer yDim;
3177         @XmlAttribute(name = "zDim")
3178         protected Integer zDim;
3179         @XmlAttribute(name = "bgColour")
3180         protected Integer bgColour;
3181         @XmlAttribute(name = "scaleFactor")
3182         protected Float scaleFactor;
3183         @XmlAttribute(name = "showLabels")
3184         protected Boolean showLabels;
3185         @XmlAttribute(name = "linkToAllViews")
3186         protected Boolean linkToAllViews;
3187         @XmlAttribute(name = "includeGaps")
3188         protected Boolean includeGaps;
3189         @XmlAttribute(name = "matchGaps")
3190         protected Boolean matchGaps;
3191         @XmlAttribute(name = "includeGappedColumns")
3192         protected Boolean includeGappedColumns;
3193         @XmlAttribute(name = "denominateByShortestLength")
3194         protected Boolean denominateByShortestLength;
3195         @XmlAttribute(name = "width")
3196         protected Integer width;
3197         @XmlAttribute(name = "height")
3198         protected Integer height;
3199         @XmlAttribute(name = "xpos")
3200         protected Integer xpos;
3201         @XmlAttribute(name = "ypos")
3202         protected Integer ypos;
3203
3204         /**
3205          * Gets the value of the sequencePoint property.
3206          * 
3207          * &lt;p&gt;
3208          * This accessor method returns a reference to the live list,
3209          * not a snapshot. Therefore any modification you make to the
3210          * returned list will be present inside the JAXB object.
3211          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
3212          * 
3213          * &lt;p&gt;
3214          * For example, to add a new item, do as follows:
3215          * &lt;pre&gt;
3216          *    getSequencePoint().add(newItem);
3217          * &lt;/pre&gt;
3218          * 
3219          * 
3220          * &lt;p&gt;
3221          * Objects of the following type(s) are allowed in the list
3222          * {@link JalviewModel.PcaViewer.SequencePoint }
3223          * 
3224          * 
3225          */
3226         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3227             if (sequencePoint == null) {
3228                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3229             }
3230             return this.sequencePoint;
3231         }
3232
3233         /**
3234          * Gets the value of the axis property.
3235          * 
3236          * &lt;p&gt;
3237          * This accessor method returns a reference to the live list,
3238          * not a snapshot. Therefore any modification you make to the
3239          * returned list will be present inside the JAXB object.
3240          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
3241          * 
3242          * &lt;p&gt;
3243          * For example, to add a new item, do as follows:
3244          * &lt;pre&gt;
3245          *    getAxis().add(newItem);
3246          * &lt;/pre&gt;
3247          * 
3248          * 
3249          * &lt;p&gt;
3250          * Objects of the following type(s) are allowed in the list
3251          * {@link JalviewModel.PcaViewer.Axis }
3252          * 
3253          * 
3254          */
3255         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3256             if (axis == null) {
3257                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3258             }
3259             return this.axis;
3260         }
3261
3262         /**
3263          * Gets the value of the seqPointMin property.
3264          * 
3265          * @return
3266          *     possible object is
3267          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3268          *     
3269          */
3270         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3271             return seqPointMin;
3272         }
3273
3274         /**
3275          * Sets the value of the seqPointMin property.
3276          * 
3277          * @param value
3278          *     allowed object is
3279          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3280          *     
3281          */
3282         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3283             this.seqPointMin = value;
3284         }
3285
3286         /**
3287          * Gets the value of the seqPointMax property.
3288          * 
3289          * @return
3290          *     possible object is
3291          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3292          *     
3293          */
3294         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3295             return seqPointMax;
3296         }
3297
3298         /**
3299          * Sets the value of the seqPointMax property.
3300          * 
3301          * @param value
3302          *     allowed object is
3303          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3304          *     
3305          */
3306         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3307             this.seqPointMax = value;
3308         }
3309
3310         /**
3311          * Gets the value of the pcaData property.
3312          * 
3313          * @return
3314          *     possible object is
3315          *     {@link PcaDataType }
3316          *     
3317          */
3318         public PcaDataType getPcaData() {
3319             return pcaData;
3320         }
3321
3322         /**
3323          * Sets the value of the pcaData property.
3324          * 
3325          * @param value
3326          *     allowed object is
3327          *     {@link PcaDataType }
3328          *     
3329          */
3330         public void setPcaData(PcaDataType value) {
3331             this.pcaData = value;
3332         }
3333
3334         /**
3335          * Gets the value of the title property.
3336          * 
3337          * @return
3338          *     possible object is
3339          *     {@link String }
3340          *     
3341          */
3342         public String getTitle() {
3343             return title;
3344         }
3345
3346         /**
3347          * Sets the value of the title property.
3348          * 
3349          * @param value
3350          *     allowed object is
3351          *     {@link String }
3352          *     
3353          */
3354         public void setTitle(String value) {
3355             this.title = value;
3356         }
3357
3358         /**
3359          * Gets the value of the scoreModelName property.
3360          * 
3361          * @return
3362          *     possible object is
3363          *     {@link String }
3364          *     
3365          */
3366         public String getScoreModelName() {
3367             return scoreModelName;
3368         }
3369
3370         /**
3371          * Sets the value of the scoreModelName property.
3372          * 
3373          * @param value
3374          *     allowed object is
3375          *     {@link String }
3376          *     
3377          */
3378         public void setScoreModelName(String value) {
3379             this.scoreModelName = value;
3380         }
3381
3382         /**
3383          * Gets the value of the xDim property.
3384          * 
3385          * @return
3386          *     possible object is
3387          *     {@link Integer }
3388          *     
3389          */
3390         public Integer getXDim() {
3391             return xDim;
3392         }
3393
3394         /**
3395          * Sets the value of the xDim property.
3396          * 
3397          * @param value
3398          *     allowed object is
3399          *     {@link Integer }
3400          *     
3401          */
3402         public void setXDim(Integer value) {
3403             this.xDim = value;
3404         }
3405
3406         /**
3407          * Gets the value of the yDim property.
3408          * 
3409          * @return
3410          *     possible object is
3411          *     {@link Integer }
3412          *     
3413          */
3414         public Integer getYDim() {
3415             return yDim;
3416         }
3417
3418         /**
3419          * Sets the value of the yDim property.
3420          * 
3421          * @param value
3422          *     allowed object is
3423          *     {@link Integer }
3424          *     
3425          */
3426         public void setYDim(Integer value) {
3427             this.yDim = value;
3428         }
3429
3430         /**
3431          * Gets the value of the zDim property.
3432          * 
3433          * @return
3434          *     possible object is
3435          *     {@link Integer }
3436          *     
3437          */
3438         public Integer getZDim() {
3439             return zDim;
3440         }
3441
3442         /**
3443          * Sets the value of the zDim property.
3444          * 
3445          * @param value
3446          *     allowed object is
3447          *     {@link Integer }
3448          *     
3449          */
3450         public void setZDim(Integer value) {
3451             this.zDim = value;
3452         }
3453
3454         /**
3455          * Gets the value of the bgColour property.
3456          * 
3457          * @return
3458          *     possible object is
3459          *     {@link Integer }
3460          *     
3461          */
3462         public Integer getBgColour() {
3463             return bgColour;
3464         }
3465
3466         /**
3467          * Sets the value of the bgColour property.
3468          * 
3469          * @param value
3470          *     allowed object is
3471          *     {@link Integer }
3472          *     
3473          */
3474         public void setBgColour(Integer value) {
3475             this.bgColour = value;
3476         }
3477
3478         /**
3479          * Gets the value of the scaleFactor property.
3480          * 
3481          * @return
3482          *     possible object is
3483          *     {@link Float }
3484          *     
3485          */
3486         public Float getScaleFactor() {
3487             return scaleFactor;
3488         }
3489
3490         /**
3491          * Sets the value of the scaleFactor property.
3492          * 
3493          * @param value
3494          *     allowed object is
3495          *     {@link Float }
3496          *     
3497          */
3498         public void setScaleFactor(Float value) {
3499             this.scaleFactor = value;
3500         }
3501
3502         /**
3503          * Gets the value of the showLabels property.
3504          * 
3505          * @return
3506          *     possible object is
3507          *     {@link Boolean }
3508          *     
3509          */
3510         public Boolean isShowLabels() {
3511             return showLabels;
3512         }
3513
3514         /**
3515          * Sets the value of the showLabels property.
3516          * 
3517          * @param value
3518          *     allowed object is
3519          *     {@link Boolean }
3520          *     
3521          */
3522         public void setShowLabels(Boolean value) {
3523             this.showLabels = value;
3524         }
3525
3526         /**
3527          * Gets the value of the linkToAllViews property.
3528          * 
3529          * @return
3530          *     possible object is
3531          *     {@link Boolean }
3532          *     
3533          */
3534         public Boolean isLinkToAllViews() {
3535             return linkToAllViews;
3536         }
3537
3538         /**
3539          * Sets the value of the linkToAllViews property.
3540          * 
3541          * @param value
3542          *     allowed object is
3543          *     {@link Boolean }
3544          *     
3545          */
3546         public void setLinkToAllViews(Boolean value) {
3547             this.linkToAllViews = value;
3548         }
3549
3550         /**
3551          * Gets the value of the includeGaps property.
3552          * 
3553          * @return
3554          *     possible object is
3555          *     {@link Boolean }
3556          *     
3557          */
3558         public Boolean isIncludeGaps() {
3559             return includeGaps;
3560         }
3561
3562         /**
3563          * Sets the value of the includeGaps property.
3564          * 
3565          * @param value
3566          *     allowed object is
3567          *     {@link Boolean }
3568          *     
3569          */
3570         public void setIncludeGaps(Boolean value) {
3571             this.includeGaps = value;
3572         }
3573
3574         /**
3575          * Gets the value of the matchGaps property.
3576          * 
3577          * @return
3578          *     possible object is
3579          *     {@link Boolean }
3580          *     
3581          */
3582         public Boolean isMatchGaps() {
3583             return matchGaps;
3584         }
3585
3586         /**
3587          * Sets the value of the matchGaps property.
3588          * 
3589          * @param value
3590          *     allowed object is
3591          *     {@link Boolean }
3592          *     
3593          */
3594         public void setMatchGaps(Boolean value) {
3595             this.matchGaps = value;
3596         }
3597
3598         /**
3599          * Gets the value of the includeGappedColumns property.
3600          * 
3601          * @return
3602          *     possible object is
3603          *     {@link Boolean }
3604          *     
3605          */
3606         public Boolean isIncludeGappedColumns() {
3607             return includeGappedColumns;
3608         }
3609
3610         /**
3611          * Sets the value of the includeGappedColumns property.
3612          * 
3613          * @param value
3614          *     allowed object is
3615          *     {@link Boolean }
3616          *     
3617          */
3618         public void setIncludeGappedColumns(Boolean value) {
3619             this.includeGappedColumns = value;
3620         }
3621
3622         /**
3623          * Gets the value of the denominateByShortestLength property.
3624          * 
3625          * @return
3626          *     possible object is
3627          *     {@link Boolean }
3628          *     
3629          */
3630         public Boolean isDenominateByShortestLength() {
3631             return denominateByShortestLength;
3632         }
3633
3634         /**
3635          * Sets the value of the denominateByShortestLength property.
3636          * 
3637          * @param value
3638          *     allowed object is
3639          *     {@link Boolean }
3640          *     
3641          */
3642         public void setDenominateByShortestLength(Boolean value) {
3643             this.denominateByShortestLength = value;
3644         }
3645
3646         /**
3647          * Gets the value of the width property.
3648          * 
3649          * @return
3650          *     possible object is
3651          *     {@link Integer }
3652          *     
3653          */
3654         public Integer getWidth() {
3655             return width;
3656         }
3657
3658         /**
3659          * Sets the value of the width property.
3660          * 
3661          * @param value
3662          *     allowed object is
3663          *     {@link Integer }
3664          *     
3665          */
3666         public void setWidth(Integer value) {
3667             this.width = value;
3668         }
3669
3670         /**
3671          * Gets the value of the height property.
3672          * 
3673          * @return
3674          *     possible object is
3675          *     {@link Integer }
3676          *     
3677          */
3678         public Integer getHeight() {
3679             return height;
3680         }
3681
3682         /**
3683          * Sets the value of the height property.
3684          * 
3685          * @param value
3686          *     allowed object is
3687          *     {@link Integer }
3688          *     
3689          */
3690         public void setHeight(Integer value) {
3691             this.height = value;
3692         }
3693
3694         /**
3695          * Gets the value of the xpos property.
3696          * 
3697          * @return
3698          *     possible object is
3699          *     {@link Integer }
3700          *     
3701          */
3702         public Integer getXpos() {
3703             return xpos;
3704         }
3705
3706         /**
3707          * Sets the value of the xpos property.
3708          * 
3709          * @param value
3710          *     allowed object is
3711          *     {@link Integer }
3712          *     
3713          */
3714         public void setXpos(Integer value) {
3715             this.xpos = value;
3716         }
3717
3718         /**
3719          * Gets the value of the ypos property.
3720          * 
3721          * @return
3722          *     possible object is
3723          *     {@link Integer }
3724          *     
3725          */
3726         public Integer getYpos() {
3727             return ypos;
3728         }
3729
3730         /**
3731          * Sets the value of the ypos property.
3732          * 
3733          * @param value
3734          *     allowed object is
3735          *     {@link Integer }
3736          *     
3737          */
3738         public void setYpos(Integer value) {
3739             this.ypos = value;
3740         }
3741
3742
3743         /**
3744          * &lt;p&gt;Java class for anonymous complex type.
3745          * 
3746          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3747          * 
3748          * &lt;pre&gt;
3749          * &amp;lt;complexType&amp;gt;
3750          *   &amp;lt;complexContent&amp;gt;
3751          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3752          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3753          *     &amp;lt;/restriction&amp;gt;
3754          *   &amp;lt;/complexContent&amp;gt;
3755          * &amp;lt;/complexType&amp;gt;
3756          * &lt;/pre&gt;
3757          * 
3758          * 
3759          */
3760         @XmlAccessorType(XmlAccessType.FIELD)
3761         @XmlType(name = "")
3762         public static class Axis {
3763
3764             @XmlAttribute(name = "xPos")
3765             protected Float xPos;
3766             @XmlAttribute(name = "yPos")
3767             protected Float yPos;
3768             @XmlAttribute(name = "zPos")
3769             protected Float zPos;
3770
3771             /**
3772              * Gets the value of the xPos property.
3773              * 
3774              * @return
3775              *     possible object is
3776              *     {@link Float }
3777              *     
3778              */
3779             public Float getXPos() {
3780                 return xPos;
3781             }
3782
3783             /**
3784              * Sets the value of the xPos property.
3785              * 
3786              * @param value
3787              *     allowed object is
3788              *     {@link Float }
3789              *     
3790              */
3791             public void setXPos(Float value) {
3792                 this.xPos = value;
3793             }
3794
3795             /**
3796              * Gets the value of the yPos property.
3797              * 
3798              * @return
3799              *     possible object is
3800              *     {@link Float }
3801              *     
3802              */
3803             public Float getYPos() {
3804                 return yPos;
3805             }
3806
3807             /**
3808              * Sets the value of the yPos property.
3809              * 
3810              * @param value
3811              *     allowed object is
3812              *     {@link Float }
3813              *     
3814              */
3815             public void setYPos(Float value) {
3816                 this.yPos = value;
3817             }
3818
3819             /**
3820              * Gets the value of the zPos property.
3821              * 
3822              * @return
3823              *     possible object is
3824              *     {@link Float }
3825              *     
3826              */
3827             public Float getZPos() {
3828                 return zPos;
3829             }
3830
3831             /**
3832              * Sets the value of the zPos property.
3833              * 
3834              * @param value
3835              *     allowed object is
3836              *     {@link Float }
3837              *     
3838              */
3839             public void setZPos(Float value) {
3840                 this.zPos = value;
3841             }
3842
3843         }
3844
3845
3846         /**
3847          * &lt;p&gt;Java class for anonymous complex type.
3848          * 
3849          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3850          * 
3851          * &lt;pre&gt;
3852          * &amp;lt;complexType&amp;gt;
3853          *   &amp;lt;complexContent&amp;gt;
3854          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3855          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3856          *     &amp;lt;/restriction&amp;gt;
3857          *   &amp;lt;/complexContent&amp;gt;
3858          * &amp;lt;/complexType&amp;gt;
3859          * &lt;/pre&gt;
3860          * 
3861          * 
3862          */
3863         @XmlAccessorType(XmlAccessType.FIELD)
3864         @XmlType(name = "")
3865         public static class SeqPointMax {
3866
3867             @XmlAttribute(name = "xPos")
3868             protected Float xPos;
3869             @XmlAttribute(name = "yPos")
3870             protected Float yPos;
3871             @XmlAttribute(name = "zPos")
3872             protected Float zPos;
3873
3874             /**
3875              * Gets the value of the xPos property.
3876              * 
3877              * @return
3878              *     possible object is
3879              *     {@link Float }
3880              *     
3881              */
3882             public Float getXPos() {
3883                 return xPos;
3884             }
3885
3886             /**
3887              * Sets the value of the xPos property.
3888              * 
3889              * @param value
3890              *     allowed object is
3891              *     {@link Float }
3892              *     
3893              */
3894             public void setXPos(Float value) {
3895                 this.xPos = value;
3896             }
3897
3898             /**
3899              * Gets the value of the yPos property.
3900              * 
3901              * @return
3902              *     possible object is
3903              *     {@link Float }
3904              *     
3905              */
3906             public Float getYPos() {
3907                 return yPos;
3908             }
3909
3910             /**
3911              * Sets the value of the yPos property.
3912              * 
3913              * @param value
3914              *     allowed object is
3915              *     {@link Float }
3916              *     
3917              */
3918             public void setYPos(Float value) {
3919                 this.yPos = value;
3920             }
3921
3922             /**
3923              * Gets the value of the zPos property.
3924              * 
3925              * @return
3926              *     possible object is
3927              *     {@link Float }
3928              *     
3929              */
3930             public Float getZPos() {
3931                 return zPos;
3932             }
3933
3934             /**
3935              * Sets the value of the zPos property.
3936              * 
3937              * @param value
3938              *     allowed object is
3939              *     {@link Float }
3940              *     
3941              */
3942             public void setZPos(Float value) {
3943                 this.zPos = value;
3944             }
3945
3946         }
3947
3948
3949         /**
3950          * &lt;p&gt;Java class for anonymous complex type.
3951          * 
3952          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3953          * 
3954          * &lt;pre&gt;
3955          * &amp;lt;complexType&amp;gt;
3956          *   &amp;lt;complexContent&amp;gt;
3957          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3958          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3959          *     &amp;lt;/restriction&amp;gt;
3960          *   &amp;lt;/complexContent&amp;gt;
3961          * &amp;lt;/complexType&amp;gt;
3962          * &lt;/pre&gt;
3963          * 
3964          * 
3965          */
3966         @XmlAccessorType(XmlAccessType.FIELD)
3967         @XmlType(name = "")
3968         public static class SeqPointMin {
3969
3970             @XmlAttribute(name = "xPos")
3971             protected Float xPos;
3972             @XmlAttribute(name = "yPos")
3973             protected Float yPos;
3974             @XmlAttribute(name = "zPos")
3975             protected Float zPos;
3976
3977             /**
3978              * Gets the value of the xPos property.
3979              * 
3980              * @return
3981              *     possible object is
3982              *     {@link Float }
3983              *     
3984              */
3985             public Float getXPos() {
3986                 return xPos;
3987             }
3988
3989             /**
3990              * Sets the value of the xPos property.
3991              * 
3992              * @param value
3993              *     allowed object is
3994              *     {@link Float }
3995              *     
3996              */
3997             public void setXPos(Float value) {
3998                 this.xPos = value;
3999             }
4000
4001             /**
4002              * Gets the value of the yPos property.
4003              * 
4004              * @return
4005              *     possible object is
4006              *     {@link Float }
4007              *     
4008              */
4009             public Float getYPos() {
4010                 return yPos;
4011             }
4012
4013             /**
4014              * Sets the value of the yPos property.
4015              * 
4016              * @param value
4017              *     allowed object is
4018              *     {@link Float }
4019              *     
4020              */
4021             public void setYPos(Float value) {
4022                 this.yPos = value;
4023             }
4024
4025             /**
4026              * Gets the value of the zPos property.
4027              * 
4028              * @return
4029              *     possible object is
4030              *     {@link Float }
4031              *     
4032              */
4033             public Float getZPos() {
4034                 return zPos;
4035             }
4036
4037             /**
4038              * Sets the value of the zPos property.
4039              * 
4040              * @param value
4041              *     allowed object is
4042              *     {@link Float }
4043              *     
4044              */
4045             public void setZPos(Float value) {
4046                 this.zPos = value;
4047             }
4048
4049         }
4050
4051
4052         /**
4053          * &lt;p&gt;Java class for anonymous complex type.
4054          * 
4055          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4056          * 
4057          * &lt;pre&gt;
4058          * &amp;lt;complexType&amp;gt;
4059          *   &amp;lt;complexContent&amp;gt;
4060          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4061          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
4062          *       &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4063          *     &amp;lt;/restriction&amp;gt;
4064          *   &amp;lt;/complexContent&amp;gt;
4065          * &amp;lt;/complexType&amp;gt;
4066          * &lt;/pre&gt;
4067          * 
4068          * 
4069          */
4070         @XmlAccessorType(XmlAccessType.FIELD)
4071         @XmlType(name = "")
4072         public static class SequencePoint {
4073
4074             @XmlAttribute(name = "sequenceRef")
4075             protected String sequenceRef;
4076             @XmlAttribute(name = "xPos")
4077             protected Float xPos;
4078             @XmlAttribute(name = "yPos")
4079             protected Float yPos;
4080             @XmlAttribute(name = "zPos")
4081             protected Float zPos;
4082
4083             /**
4084              * Gets the value of the sequenceRef property.
4085              * 
4086              * @return
4087              *     possible object is
4088              *     {@link String }
4089              *     
4090              */
4091             public String getSequenceRef() {
4092                 return sequenceRef;
4093             }
4094
4095             /**
4096              * Sets the value of the sequenceRef property.
4097              * 
4098              * @param value
4099              *     allowed object is
4100              *     {@link String }
4101              *     
4102              */
4103             public void setSequenceRef(String value) {
4104                 this.sequenceRef = value;
4105             }
4106
4107             /**
4108              * Gets the value of the xPos property.
4109              * 
4110              * @return
4111              *     possible object is
4112              *     {@link Float }
4113              *     
4114              */
4115             public Float getXPos() {
4116                 return xPos;
4117             }
4118
4119             /**
4120              * Sets the value of the xPos property.
4121              * 
4122              * @param value
4123              *     allowed object is
4124              *     {@link Float }
4125              *     
4126              */
4127             public void setXPos(Float value) {
4128                 this.xPos = value;
4129             }
4130
4131             /**
4132              * Gets the value of the yPos property.
4133              * 
4134              * @return
4135              *     possible object is
4136              *     {@link Float }
4137              *     
4138              */
4139             public Float getYPos() {
4140                 return yPos;
4141             }
4142
4143             /**
4144              * Sets the value of the yPos property.
4145              * 
4146              * @param value
4147              *     allowed object is
4148              *     {@link Float }
4149              *     
4150              */
4151             public void setYPos(Float value) {
4152                 this.yPos = value;
4153             }
4154
4155             /**
4156              * Gets the value of the zPos property.
4157              * 
4158              * @return
4159              *     possible object is
4160              *     {@link Float }
4161              *     
4162              */
4163             public Float getZPos() {
4164                 return zPos;
4165             }
4166
4167             /**
4168              * Sets the value of the zPos property.
4169              * 
4170              * @param value
4171              *     allowed object is
4172              *     {@link Float }
4173              *     
4174              */
4175             public void setZPos(Float value) {
4176                 this.zPos = value;
4177             }
4178
4179         }
4180
4181     }
4182
4183
4184     /**
4185      * &lt;p&gt;Java class for anonymous complex type.
4186      * 
4187      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4188      * 
4189      * &lt;pre&gt;
4190      * &amp;lt;complexType&amp;gt;
4191      *   &amp;lt;complexContent&amp;gt;
4192      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4193      *       &amp;lt;sequence minOccurs="0"&amp;gt;
4194      *         &amp;lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4195      *         &amp;lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4196      *       &amp;lt;/sequence&amp;gt;
4197      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
4198      *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4199      *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4200      *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4201      *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
4202      *       &amp;lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4203      *       &amp;lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4204      *       &amp;lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4205      *       &amp;lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4206      *       &amp;lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4207      *       &amp;lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4208      *       &amp;lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4209      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4210      *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4211      *     &amp;lt;/restriction&amp;gt;
4212      *   &amp;lt;/complexContent&amp;gt;
4213      * &amp;lt;/complexType&amp;gt;
4214      * &lt;/pre&gt;
4215      * 
4216      * 
4217      */
4218     @XmlAccessorType(XmlAccessType.FIELD)
4219     @XmlType(name = "", propOrder = {
4220         "title",
4221         "newick"
4222     })
4223     public static class Tree {
4224
4225         @XmlElement(namespace = "www.jalview.org")
4226         protected String title;
4227         @XmlElement(namespace = "www.jalview.org")
4228         protected String newick;
4229         @XmlAttribute(name = "fontName")
4230         protected String fontName;
4231         @XmlAttribute(name = "fontSize")
4232         protected Integer fontSize;
4233         @XmlAttribute(name = "fontStyle")
4234         protected Integer fontStyle;
4235         @XmlAttribute(name = "threshold")
4236         protected Float threshold;
4237         @XmlAttribute(name = "showBootstrap")
4238         protected Boolean showBootstrap;
4239         @XmlAttribute(name = "showDistances")
4240         protected Boolean showDistances;
4241         @XmlAttribute(name = "markUnlinked")
4242         protected Boolean markUnlinked;
4243         @XmlAttribute(name = "fitToWindow")
4244         protected Boolean fitToWindow;
4245         @XmlAttribute(name = "currentTree")
4246         protected Boolean currentTree;
4247         @XmlAttribute(name = "columnWise")
4248         protected Boolean columnWise;
4249         @XmlAttribute(name = "columnReference")
4250         protected String columnReference;
4251         @XmlAttribute(name = "id")
4252         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4253         @XmlID
4254         @XmlSchemaType(name = "ID")
4255         protected String id;
4256         @XmlAttribute(name = "linkToAllViews")
4257         protected Boolean linkToAllViews;
4258         @XmlAttribute(name = "width")
4259         protected Integer width;
4260         @XmlAttribute(name = "height")
4261         protected Integer height;
4262         @XmlAttribute(name = "xpos")
4263         protected Integer xpos;
4264         @XmlAttribute(name = "ypos")
4265         protected Integer ypos;
4266
4267         /**
4268          * Gets the value of the title property.
4269          * 
4270          * @return
4271          *     possible object is
4272          *     {@link String }
4273          *     
4274          */
4275         public String getTitle() {
4276             return title;
4277         }
4278
4279         /**
4280          * Sets the value of the title property.
4281          * 
4282          * @param value
4283          *     allowed object is
4284          *     {@link String }
4285          *     
4286          */
4287         public void setTitle(String value) {
4288             this.title = value;
4289         }
4290
4291         /**
4292          * Gets the value of the newick property.
4293          * 
4294          * @return
4295          *     possible object is
4296          *     {@link String }
4297          *     
4298          */
4299         public String getNewick() {
4300             return newick;
4301         }
4302
4303         /**
4304          * Sets the value of the newick property.
4305          * 
4306          * @param value
4307          *     allowed object is
4308          *     {@link String }
4309          *     
4310          */
4311         public void setNewick(String value) {
4312             this.newick = value;
4313         }
4314
4315         /**
4316          * Gets the value of the fontName property.
4317          * 
4318          * @return
4319          *     possible object is
4320          *     {@link String }
4321          *     
4322          */
4323         public String getFontName() {
4324             return fontName;
4325         }
4326
4327         /**
4328          * Sets the value of the fontName property.
4329          * 
4330          * @param value
4331          *     allowed object is
4332          *     {@link String }
4333          *     
4334          */
4335         public void setFontName(String value) {
4336             this.fontName = value;
4337         }
4338
4339         /**
4340          * Gets the value of the fontSize property.
4341          * 
4342          * @return
4343          *     possible object is
4344          *     {@link Integer }
4345          *     
4346          */
4347         public Integer getFontSize() {
4348             return fontSize;
4349         }
4350
4351         /**
4352          * Sets the value of the fontSize property.
4353          * 
4354          * @param value
4355          *     allowed object is
4356          *     {@link Integer }
4357          *     
4358          */
4359         public void setFontSize(Integer value) {
4360             this.fontSize = value;
4361         }
4362
4363         /**
4364          * Gets the value of the fontStyle property.
4365          * 
4366          * @return
4367          *     possible object is
4368          *     {@link Integer }
4369          *     
4370          */
4371         public Integer getFontStyle() {
4372             return fontStyle;
4373         }
4374
4375         /**
4376          * Sets the value of the fontStyle property.
4377          * 
4378          * @param value
4379          *     allowed object is
4380          *     {@link Integer }
4381          *     
4382          */
4383         public void setFontStyle(Integer value) {
4384             this.fontStyle = value;
4385         }
4386
4387         /**
4388          * Gets the value of the threshold property.
4389          * 
4390          * @return
4391          *     possible object is
4392          *     {@link Float }
4393          *     
4394          */
4395         public Float getThreshold() {
4396             return threshold;
4397         }
4398
4399         /**
4400          * Sets the value of the threshold property.
4401          * 
4402          * @param value
4403          *     allowed object is
4404          *     {@link Float }
4405          *     
4406          */
4407         public void setThreshold(Float value) {
4408             this.threshold = value;
4409         }
4410
4411         /**
4412          * Gets the value of the showBootstrap property.
4413          * 
4414          * @return
4415          *     possible object is
4416          *     {@link Boolean }
4417          *     
4418          */
4419         public Boolean isShowBootstrap() {
4420             return showBootstrap;
4421         }
4422
4423         /**
4424          * Sets the value of the showBootstrap property.
4425          * 
4426          * @param value
4427          *     allowed object is
4428          *     {@link Boolean }
4429          *     
4430          */
4431         public void setShowBootstrap(Boolean value) {
4432             this.showBootstrap = value;
4433         }
4434
4435         /**
4436          * Gets the value of the showDistances property.
4437          * 
4438          * @return
4439          *     possible object is
4440          *     {@link Boolean }
4441          *     
4442          */
4443         public Boolean isShowDistances() {
4444             return showDistances;
4445         }
4446
4447         /**
4448          * Sets the value of the showDistances property.
4449          * 
4450          * @param value
4451          *     allowed object is
4452          *     {@link Boolean }
4453          *     
4454          */
4455         public void setShowDistances(Boolean value) {
4456             this.showDistances = value;
4457         }
4458
4459         /**
4460          * Gets the value of the markUnlinked property.
4461          * 
4462          * @return
4463          *     possible object is
4464          *     {@link Boolean }
4465          *     
4466          */
4467         public Boolean isMarkUnlinked() {
4468             return markUnlinked;
4469         }
4470
4471         /**
4472          * Sets the value of the markUnlinked property.
4473          * 
4474          * @param value
4475          *     allowed object is
4476          *     {@link Boolean }
4477          *     
4478          */
4479         public void setMarkUnlinked(Boolean value) {
4480             this.markUnlinked = value;
4481         }
4482
4483         /**
4484          * Gets the value of the fitToWindow property.
4485          * 
4486          * @return
4487          *     possible object is
4488          *     {@link Boolean }
4489          *     
4490          */
4491         public Boolean isFitToWindow() {
4492             return fitToWindow;
4493         }
4494
4495         /**
4496          * Sets the value of the fitToWindow property.
4497          * 
4498          * @param value
4499          *     allowed object is
4500          *     {@link Boolean }
4501          *     
4502          */
4503         public void setFitToWindow(Boolean value) {
4504             this.fitToWindow = value;
4505         }
4506
4507         /**
4508          * Gets the value of the currentTree property.
4509          * 
4510          * @return
4511          *     possible object is
4512          *     {@link Boolean }
4513          *     
4514          */
4515         public Boolean isCurrentTree() {
4516             return currentTree;
4517         }
4518
4519         /**
4520          * Sets the value of the currentTree property.
4521          * 
4522          * @param value
4523          *     allowed object is
4524          *     {@link Boolean }
4525          *     
4526          */
4527         public void setCurrentTree(Boolean value) {
4528             this.currentTree = value;
4529         }
4530
4531         /**
4532          * Gets the value of the columnWise property.
4533          * 
4534          * @return
4535          *     possible object is
4536          *     {@link Boolean }
4537          *     
4538          */
4539         public boolean isColumnWise() {
4540             if (columnWise == null) {
4541                 return false;
4542             } else {
4543                 return columnWise;
4544             }
4545         }
4546
4547         /**
4548          * Sets the value of the columnWise property.
4549          * 
4550          * @param value
4551          *     allowed object is
4552          *     {@link Boolean }
4553          *     
4554          */
4555         public void setColumnWise(Boolean value) {
4556             this.columnWise = value;
4557         }
4558
4559         /**
4560          * Gets the value of the columnReference property.
4561          * 
4562          * @return
4563          *     possible object is
4564          *     {@link String }
4565          *     
4566          */
4567         public String getColumnReference() {
4568             return columnReference;
4569         }
4570
4571         /**
4572          * Sets the value of the columnReference property.
4573          * 
4574          * @param value
4575          *     allowed object is
4576          *     {@link String }
4577          *     
4578          */
4579         public void setColumnReference(String value) {
4580             this.columnReference = value;
4581         }
4582
4583         /**
4584          * Gets the value of the id property.
4585          * 
4586          * @return
4587          *     possible object is
4588          *     {@link String }
4589          *     
4590          */
4591         public String getId() {
4592             return id;
4593         }
4594
4595         /**
4596          * Sets the value of the id property.
4597          * 
4598          * @param value
4599          *     allowed object is
4600          *     {@link String }
4601          *     
4602          */
4603         public void setId(String value) {
4604             this.id = value;
4605         }
4606
4607         /**
4608          * Gets the value of the linkToAllViews property.
4609          * 
4610          * @return
4611          *     possible object is
4612          *     {@link Boolean }
4613          *     
4614          */
4615         public boolean isLinkToAllViews() {
4616             if (linkToAllViews == null) {
4617                 return false;
4618             } else {
4619                 return linkToAllViews;
4620             }
4621         }
4622
4623         /**
4624          * Sets the value of the linkToAllViews property.
4625          * 
4626          * @param value
4627          *     allowed object is
4628          *     {@link Boolean }
4629          *     
4630          */
4631         public void setLinkToAllViews(Boolean value) {
4632             this.linkToAllViews = value;
4633         }
4634
4635         /**
4636          * Gets the value of the width property.
4637          * 
4638          * @return
4639          *     possible object is
4640          *     {@link Integer }
4641          *     
4642          */
4643         public Integer getWidth() {
4644             return width;
4645         }
4646
4647         /**
4648          * Sets the value of the width property.
4649          * 
4650          * @param value
4651          *     allowed object is
4652          *     {@link Integer }
4653          *     
4654          */
4655         public void setWidth(Integer value) {
4656             this.width = value;
4657         }
4658
4659         /**
4660          * Gets the value of the height property.
4661          * 
4662          * @return
4663          *     possible object is
4664          *     {@link Integer }
4665          *     
4666          */
4667         public Integer getHeight() {
4668             return height;
4669         }
4670
4671         /**
4672          * Sets the value of the height property.
4673          * 
4674          * @param value
4675          *     allowed object is
4676          *     {@link Integer }
4677          *     
4678          */
4679         public void setHeight(Integer value) {
4680             this.height = value;
4681         }
4682
4683         /**
4684          * Gets the value of the xpos property.
4685          * 
4686          * @return
4687          *     possible object is
4688          *     {@link Integer }
4689          *     
4690          */
4691         public Integer getXpos() {
4692             return xpos;
4693         }
4694
4695         /**
4696          * Sets the value of the xpos property.
4697          * 
4698          * @param value
4699          *     allowed object is
4700          *     {@link Integer }
4701          *     
4702          */
4703         public void setXpos(Integer value) {
4704             this.xpos = value;
4705         }
4706
4707         /**
4708          * Gets the value of the ypos property.
4709          * 
4710          * @return
4711          *     possible object is
4712          *     {@link Integer }
4713          *     
4714          */
4715         public Integer getYpos() {
4716             return ypos;
4717         }
4718
4719         /**
4720          * Sets the value of the ypos property.
4721          * 
4722          * @param value
4723          *     allowed object is
4724          *     {@link Integer }
4725          *     
4726          */
4727         public void setYpos(Integer value) {
4728             this.ypos = value;
4729         }
4730
4731     }
4732
4733
4734     /**
4735      * &lt;p&gt;Java class for anonymous complex type.
4736      * 
4737      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4738      * 
4739      * &lt;pre&gt;
4740      * &amp;lt;complexType&amp;gt;
4741      *   &amp;lt;complexContent&amp;gt;
4742      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4743      *       &amp;lt;sequence&amp;gt;
4744      *         &amp;lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
4745      *       &amp;lt;/sequence&amp;gt;
4746      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4747      *     &amp;lt;/restriction&amp;gt;
4748      *   &amp;lt;/complexContent&amp;gt;
4749      * &amp;lt;/complexType&amp;gt;
4750      * &lt;/pre&gt;
4751      * 
4752      * 
4753      */
4754     @XmlAccessorType(XmlAccessType.FIELD)
4755     @XmlType(name = "", propOrder = {
4756         "userColourScheme"
4757     })
4758     public static class UserColours {
4759
4760         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4761         protected JalviewUserColours userColourScheme;
4762         @XmlAttribute(name = "id")
4763         protected String id;
4764
4765         /**
4766          * Gets the value of the userColourScheme property.
4767          * 
4768          * @return
4769          *     possible object is
4770          *     {@link JalviewUserColours }
4771          *     
4772          */
4773         public JalviewUserColours getUserColourScheme() {
4774             return userColourScheme;
4775         }
4776
4777         /**
4778          * Sets the value of the userColourScheme property.
4779          * 
4780          * @param value
4781          *     allowed object is
4782          *     {@link JalviewUserColours }
4783          *     
4784          */
4785         public void setUserColourScheme(JalviewUserColours value) {
4786             this.userColourScheme = value;
4787         }
4788
4789         /**
4790          * Gets the value of the id property.
4791          * 
4792          * @return
4793          *     possible object is
4794          *     {@link String }
4795          *     
4796          */
4797         public String getId() {
4798             return id;
4799         }
4800
4801         /**
4802          * Sets the value of the id property.
4803          * 
4804          * @param value
4805          *     allowed object is
4806          *     {@link String }
4807          *     
4808          */
4809         public void setId(String value) {
4810             this.id = value;
4811         }
4812
4813     }
4814
4815
4816     /**
4817      * &lt;p&gt;Java class for anonymous complex type.
4818      * 
4819      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4820      * 
4821      * &lt;pre&gt;
4822      * &amp;lt;complexType&amp;gt;
4823      *   &amp;lt;complexContent&amp;gt;
4824      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4825      *       &amp;lt;sequence&amp;gt;
4826      *         &amp;lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
4827      *         &amp;lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4828      *           &amp;lt;complexType&amp;gt;
4829      *             &amp;lt;complexContent&amp;gt;
4830      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4831      *                 &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4832      *                 &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4833      *               &amp;lt;/restriction&amp;gt;
4834      *             &amp;lt;/complexContent&amp;gt;
4835      *           &amp;lt;/complexType&amp;gt;
4836      *         &amp;lt;/element&amp;gt;
4837      *         &amp;lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4838      *           &amp;lt;complexType&amp;gt;
4839      *             &amp;lt;complexContent&amp;gt;
4840      *               &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
4841      *                 &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4842      *                 &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4843      *                 &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4844      *               &amp;lt;/extension&amp;gt;
4845      *             &amp;lt;/complexContent&amp;gt;
4846      *           &amp;lt;/complexType&amp;gt;
4847      *         &amp;lt;/element&amp;gt;
4848      *         &amp;lt;element name="overview" minOccurs="0"&amp;gt;
4849      *           &amp;lt;complexType&amp;gt;
4850      *             &amp;lt;complexContent&amp;gt;
4851      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4852      *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
4853      *                 &amp;lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4854      *                 &amp;lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4855      *                 &amp;lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4856      *                 &amp;lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4857      *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4858      *               &amp;lt;/restriction&amp;gt;
4859      *             &amp;lt;/complexContent&amp;gt;
4860      *           &amp;lt;/complexType&amp;gt;
4861      *         &amp;lt;/element&amp;gt;
4862      *       &amp;lt;/sequence&amp;gt;
4863      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
4864      *       &amp;lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4865      *       &amp;lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4866      *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4867      *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4868      *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4869      *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4870      *       &amp;lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4871      *       &amp;lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4872      *       &amp;lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4873      *       &amp;lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4874      *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4875      *       &amp;lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4876      *       &amp;lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4877      *       &amp;lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4878      *       &amp;lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4879      *       &amp;lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4880      *       &amp;lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4881      *       &amp;lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4882      *       &amp;lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4883      *       &amp;lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4884      *       &amp;lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4885      *       &amp;lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4886      *       &amp;lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4887      *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4888      *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4889      *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4890      *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4891      *       &amp;lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4892      *       &amp;lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4893      *       &amp;lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4894      *       &amp;lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4895      *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4896      *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4897      *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4898      *       &amp;lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4899      *       &amp;lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4900      *       &amp;lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4901      *       &amp;lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4902      *       &amp;lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4903      *       &amp;lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4904      *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4905      *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4906      *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4907      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4908      *       &amp;lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4909      *       &amp;lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4910      *       &amp;lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4911      *     &amp;lt;/restriction&amp;gt;
4912      *   &amp;lt;/complexContent&amp;gt;
4913      * &amp;lt;/complexType&amp;gt;
4914      * &lt;/pre&gt;
4915      * 
4916      * 
4917      */
4918     @XmlAccessorType(XmlAccessType.FIELD)
4919     @XmlType(name = "", propOrder = {
4920         "annotationColours",
4921         "hiddenColumns",
4922         "calcIdParam",
4923         "overview"
4924     })
4925     public static class Viewport {
4926
4927         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4928         protected AnnotationColourScheme annotationColours;
4929         @XmlElement(namespace = "www.jalview.org")
4930         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4931         @XmlElement(namespace = "www.jalview.org")
4932         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4933         @XmlElement(namespace = "www.jalview.org")
4934         protected JalviewModel.Viewport.Overview overview;
4935         @XmlAttribute(name = "conservationSelected")
4936         protected Boolean conservationSelected;
4937         @XmlAttribute(name = "pidSelected")
4938         protected Boolean pidSelected;
4939         @XmlAttribute(name = "bgColour")
4940         protected String bgColour;
4941         @XmlAttribute(name = "consThreshold")
4942         protected Integer consThreshold;
4943         @XmlAttribute(name = "pidThreshold")
4944         protected Integer pidThreshold;
4945         @XmlAttribute(name = "title")
4946         protected String title;
4947         @XmlAttribute(name = "showFullId")
4948         protected Boolean showFullId;
4949         @XmlAttribute(name = "rightAlignIds")
4950         protected Boolean rightAlignIds;
4951         @XmlAttribute(name = "showText")
4952         protected Boolean showText;
4953         @XmlAttribute(name = "showColourText")
4954         protected Boolean showColourText;
4955         @XmlAttribute(name = "showUnconserved")
4956         protected Boolean showUnconserved;
4957         @XmlAttribute(name = "showBoxes")
4958         protected Boolean showBoxes;
4959         @XmlAttribute(name = "wrapAlignment")
4960         protected Boolean wrapAlignment;
4961         @XmlAttribute(name = "renderGaps")
4962         protected Boolean renderGaps;
4963         @XmlAttribute(name = "showSequenceFeatures")
4964         protected Boolean showSequenceFeatures;
4965         @XmlAttribute(name = "showNPfeatureTooltip")
4966         protected Boolean showNPfeatureTooltip;
4967         @XmlAttribute(name = "showDbRefTooltip")
4968         protected Boolean showDbRefTooltip;
4969         @XmlAttribute(name = "followHighlight")
4970         protected Boolean followHighlight;
4971         @XmlAttribute(name = "followSelection")
4972         protected Boolean followSelection;
4973         @XmlAttribute(name = "showAnnotation")
4974         protected Boolean showAnnotation;
4975         @XmlAttribute(name = "centreColumnLabels")
4976         protected Boolean centreColumnLabels;
4977         @XmlAttribute(name = "showGroupConservation")
4978         protected Boolean showGroupConservation;
4979         @XmlAttribute(name = "showGroupConsensus")
4980         protected Boolean showGroupConsensus;
4981         @XmlAttribute(name = "showConsensusHistogram")
4982         protected Boolean showConsensusHistogram;
4983         @XmlAttribute(name = "showSequenceLogo")
4984         protected Boolean showSequenceLogo;
4985         @XmlAttribute(name = "normaliseSequenceLogo")
4986         protected Boolean normaliseSequenceLogo;
4987         @XmlAttribute(name = "ignoreGapsinConsensus")
4988         protected Boolean ignoreGapsinConsensus;
4989         @XmlAttribute(name = "startRes")
4990         protected Integer startRes;
4991         @XmlAttribute(name = "startSeq")
4992         protected Integer startSeq;
4993         @XmlAttribute(name = "charWidth")
4994         protected Integer charWidth;
4995         @XmlAttribute(name = "charHeight")
4996         protected Integer charHeight;
4997         @XmlAttribute(name = "fontName")
4998         protected String fontName;
4999         @XmlAttribute(name = "fontSize")
5000         protected Integer fontSize;
5001         @XmlAttribute(name = "fontStyle")
5002         protected Integer fontStyle;
5003         @XmlAttribute(name = "idWidth")
5004         protected Integer idWidth;
5005         @XmlAttribute(name = "idWidthManuallyAdjusted")
5006         protected Boolean idWidthManuallyAdjusted;
5007         @XmlAttribute(name = "scaleProteinAsCdna")
5008         protected Boolean scaleProteinAsCdna;
5009         @XmlAttribute(name = "viewName")
5010         protected String viewName;
5011         @XmlAttribute(name = "sequenceSetId")
5012         protected String sequenceSetId;
5013         @XmlAttribute(name = "gatheredViews")
5014         protected Boolean gatheredViews;
5015         @XmlAttribute(name = "textCol1")
5016         protected Integer textCol1;
5017         @XmlAttribute(name = "textCol2")
5018         protected Integer textCol2;
5019         @XmlAttribute(name = "textColThreshold")
5020         protected Integer textColThreshold;
5021         @XmlAttribute(name = "id")
5022         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5023         @XmlID
5024         @XmlSchemaType(name = "ID")
5025         protected String id;
5026         @XmlAttribute(name = "complementId")
5027         protected String complementId;
5028         @XmlAttribute(name = "showComplementFeatures")
5029         protected Boolean showComplementFeatures;
5030         @XmlAttribute(name = "showComplementFeaturesOnTop")
5031         protected Boolean showComplementFeaturesOnTop;
5032         @XmlAttribute(name = "width")
5033         protected Integer width;
5034         @XmlAttribute(name = "height")
5035         protected Integer height;
5036         @XmlAttribute(name = "xpos")
5037         protected Integer xpos;
5038         @XmlAttribute(name = "ypos")
5039         protected Integer ypos;
5040
5041         /**
5042          * Gets the value of the annotationColours property.
5043          * 
5044          * @return
5045          *     possible object is
5046          *     {@link AnnotationColourScheme }
5047          *     
5048          */
5049         public AnnotationColourScheme getAnnotationColours() {
5050             return annotationColours;
5051         }
5052
5053         /**
5054          * Sets the value of the annotationColours property.
5055          * 
5056          * @param value
5057          *     allowed object is
5058          *     {@link AnnotationColourScheme }
5059          *     
5060          */
5061         public void setAnnotationColours(AnnotationColourScheme value) {
5062             this.annotationColours = value;
5063         }
5064
5065         /**
5066          * Gets the value of the hiddenColumns property.
5067          * 
5068          * &lt;p&gt;
5069          * This accessor method returns a reference to the live list,
5070          * not a snapshot. Therefore any modification you make to the
5071          * returned list will be present inside the JAXB object.
5072          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
5073          * 
5074          * &lt;p&gt;
5075          * For example, to add a new item, do as follows:
5076          * &lt;pre&gt;
5077          *    getHiddenColumns().add(newItem);
5078          * &lt;/pre&gt;
5079          * 
5080          * 
5081          * &lt;p&gt;
5082          * Objects of the following type(s) are allowed in the list
5083          * {@link JalviewModel.Viewport.HiddenColumns }
5084          * 
5085          * 
5086          */
5087         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5088             if (hiddenColumns == null) {
5089                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5090             }
5091             return this.hiddenColumns;
5092         }
5093
5094         /**
5095          * Gets the value of the calcIdParam property.
5096          * 
5097          * &lt;p&gt;
5098          * This accessor method returns a reference to the live list,
5099          * not a snapshot. Therefore any modification you make to the
5100          * returned list will be present inside the JAXB object.
5101          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
5102          * 
5103          * &lt;p&gt;
5104          * For example, to add a new item, do as follows:
5105          * &lt;pre&gt;
5106          *    getCalcIdParam().add(newItem);
5107          * &lt;/pre&gt;
5108          * 
5109          * 
5110          * &lt;p&gt;
5111          * Objects of the following type(s) are allowed in the list
5112          * {@link JalviewModel.Viewport.CalcIdParam }
5113          * 
5114          * 
5115          */
5116         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5117             if (calcIdParam == null) {
5118                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5119             }
5120             return this.calcIdParam;
5121         }
5122
5123         /**
5124          * Gets the value of the overview property.
5125          * 
5126          * @return
5127          *     possible object is
5128          *     {@link JalviewModel.Viewport.Overview }
5129          *     
5130          */
5131         public JalviewModel.Viewport.Overview getOverview() {
5132             return overview;
5133         }
5134
5135         /**
5136          * Sets the value of the overview property.
5137          * 
5138          * @param value
5139          *     allowed object is
5140          *     {@link JalviewModel.Viewport.Overview }
5141          *     
5142          */
5143         public void setOverview(JalviewModel.Viewport.Overview value) {
5144             this.overview = value;
5145         }
5146
5147         /**
5148          * Gets the value of the conservationSelected property.
5149          * 
5150          * @return
5151          *     possible object is
5152          *     {@link Boolean }
5153          *     
5154          */
5155         public Boolean isConservationSelected() {
5156             return conservationSelected;
5157         }
5158
5159         /**
5160          * Sets the value of the conservationSelected property.
5161          * 
5162          * @param value
5163          *     allowed object is
5164          *     {@link Boolean }
5165          *     
5166          */
5167         public void setConservationSelected(Boolean value) {
5168             this.conservationSelected = value;
5169         }
5170
5171         /**
5172          * Gets the value of the pidSelected property.
5173          * 
5174          * @return
5175          *     possible object is
5176          *     {@link Boolean }
5177          *     
5178          */
5179         public Boolean isPidSelected() {
5180             return pidSelected;
5181         }
5182
5183         /**
5184          * Sets the value of the pidSelected property.
5185          * 
5186          * @param value
5187          *     allowed object is
5188          *     {@link Boolean }
5189          *     
5190          */
5191         public void setPidSelected(Boolean value) {
5192             this.pidSelected = value;
5193         }
5194
5195         /**
5196          * Gets the value of the bgColour property.
5197          * 
5198          * @return
5199          *     possible object is
5200          *     {@link String }
5201          *     
5202          */
5203         public String getBgColour() {
5204             return bgColour;
5205         }
5206
5207         /**
5208          * Sets the value of the bgColour property.
5209          * 
5210          * @param value
5211          *     allowed object is
5212          *     {@link String }
5213          *     
5214          */
5215         public void setBgColour(String value) {
5216             this.bgColour = value;
5217         }
5218
5219         /**
5220          * Gets the value of the consThreshold property.
5221          * 
5222          * @return
5223          *     possible object is
5224          *     {@link Integer }
5225          *     
5226          */
5227         public Integer getConsThreshold() {
5228             return consThreshold;
5229         }
5230
5231         /**
5232          * Sets the value of the consThreshold property.
5233          * 
5234          * @param value
5235          *     allowed object is
5236          *     {@link Integer }
5237          *     
5238          */
5239         public void setConsThreshold(Integer value) {
5240             this.consThreshold = value;
5241         }
5242
5243         /**
5244          * Gets the value of the pidThreshold property.
5245          * 
5246          * @return
5247          *     possible object is
5248          *     {@link Integer }
5249          *     
5250          */
5251         public Integer getPidThreshold() {
5252             return pidThreshold;
5253         }
5254
5255         /**
5256          * Sets the value of the pidThreshold property.
5257          * 
5258          * @param value
5259          *     allowed object is
5260          *     {@link Integer }
5261          *     
5262          */
5263         public void setPidThreshold(Integer value) {
5264             this.pidThreshold = value;
5265         }
5266
5267         /**
5268          * Gets the value of the title property.
5269          * 
5270          * @return
5271          *     possible object is
5272          *     {@link String }
5273          *     
5274          */
5275         public String getTitle() {
5276             return title;
5277         }
5278
5279         /**
5280          * Sets the value of the title property.
5281          * 
5282          * @param value
5283          *     allowed object is
5284          *     {@link String }
5285          *     
5286          */
5287         public void setTitle(String value) {
5288             this.title = value;
5289         }
5290
5291         /**
5292          * Gets the value of the showFullId property.
5293          * 
5294          * @return
5295          *     possible object is
5296          *     {@link Boolean }
5297          *     
5298          */
5299         public Boolean isShowFullId() {
5300             return showFullId;
5301         }
5302
5303         /**
5304          * Sets the value of the showFullId property.
5305          * 
5306          * @param value
5307          *     allowed object is
5308          *     {@link Boolean }
5309          *     
5310          */
5311         public void setShowFullId(Boolean value) {
5312             this.showFullId = value;
5313         }
5314
5315         /**
5316          * Gets the value of the rightAlignIds property.
5317          * 
5318          * @return
5319          *     possible object is
5320          *     {@link Boolean }
5321          *     
5322          */
5323         public Boolean isRightAlignIds() {
5324             return rightAlignIds;
5325         }
5326
5327         /**
5328          * Sets the value of the rightAlignIds property.
5329          * 
5330          * @param value
5331          *     allowed object is
5332          *     {@link Boolean }
5333          *     
5334          */
5335         public void setRightAlignIds(Boolean value) {
5336             this.rightAlignIds = value;
5337         }
5338
5339         /**
5340          * Gets the value of the showText property.
5341          * 
5342          * @return
5343          *     possible object is
5344          *     {@link Boolean }
5345          *     
5346          */
5347         public Boolean isShowText() {
5348             return showText;
5349         }
5350
5351         /**
5352          * Sets the value of the showText property.
5353          * 
5354          * @param value
5355          *     allowed object is
5356          *     {@link Boolean }
5357          *     
5358          */
5359         public void setShowText(Boolean value) {
5360             this.showText = value;
5361         }
5362
5363         /**
5364          * Gets the value of the showColourText property.
5365          * 
5366          * @return
5367          *     possible object is
5368          *     {@link Boolean }
5369          *     
5370          */
5371         public Boolean isShowColourText() {
5372             return showColourText;
5373         }
5374
5375         /**
5376          * Sets the value of the showColourText property.
5377          * 
5378          * @param value
5379          *     allowed object is
5380          *     {@link Boolean }
5381          *     
5382          */
5383         public void setShowColourText(Boolean value) {
5384             this.showColourText = value;
5385         }
5386
5387         /**
5388          * Gets the value of the showUnconserved property.
5389          * 
5390          * @return
5391          *     possible object is
5392          *     {@link Boolean }
5393          *     
5394          */
5395         public boolean isShowUnconserved() {
5396             if (showUnconserved == null) {
5397                 return false;
5398             } else {
5399                 return showUnconserved;
5400             }
5401         }
5402
5403         /**
5404          * Sets the value of the showUnconserved property.
5405          * 
5406          * @param value
5407          *     allowed object is
5408          *     {@link Boolean }
5409          *     
5410          */
5411         public void setShowUnconserved(Boolean value) {
5412             this.showUnconserved = value;
5413         }
5414
5415         /**
5416          * Gets the value of the showBoxes property.
5417          * 
5418          * @return
5419          *     possible object is
5420          *     {@link Boolean }
5421          *     
5422          */
5423         public Boolean isShowBoxes() {
5424             return showBoxes;
5425         }
5426
5427         /**
5428          * Sets the value of the showBoxes property.
5429          * 
5430          * @param value
5431          *     allowed object is
5432          *     {@link Boolean }
5433          *     
5434          */
5435         public void setShowBoxes(Boolean value) {
5436             this.showBoxes = value;
5437         }
5438
5439         /**
5440          * Gets the value of the wrapAlignment property.
5441          * 
5442          * @return
5443          *     possible object is
5444          *     {@link Boolean }
5445          *     
5446          */
5447         public Boolean isWrapAlignment() {
5448             return wrapAlignment;
5449         }
5450
5451         /**
5452          * Sets the value of the wrapAlignment property.
5453          * 
5454          * @param value
5455          *     allowed object is
5456          *     {@link Boolean }
5457          *     
5458          */
5459         public void setWrapAlignment(Boolean value) {
5460             this.wrapAlignment = value;
5461         }
5462
5463         /**
5464          * Gets the value of the renderGaps property.
5465          * 
5466          * @return
5467          *     possible object is
5468          *     {@link Boolean }
5469          *     
5470          */
5471         public Boolean isRenderGaps() {
5472             return renderGaps;
5473         }
5474
5475         /**
5476          * Sets the value of the renderGaps property.
5477          * 
5478          * @param value
5479          *     allowed object is
5480          *     {@link Boolean }
5481          *     
5482          */
5483         public void setRenderGaps(Boolean value) {
5484             this.renderGaps = value;
5485         }
5486
5487         /**
5488          * Gets the value of the showSequenceFeatures property.
5489          * 
5490          * @return
5491          *     possible object is
5492          *     {@link Boolean }
5493          *     
5494          */
5495         public Boolean isShowSequenceFeatures() {
5496             return showSequenceFeatures;
5497         }
5498
5499         /**
5500          * Sets the value of the showSequenceFeatures property.
5501          * 
5502          * @param value
5503          *     allowed object is
5504          *     {@link Boolean }
5505          *     
5506          */
5507         public void setShowSequenceFeatures(Boolean value) {
5508             this.showSequenceFeatures = value;
5509         }
5510
5511         /**
5512          * Gets the value of the showNPfeatureTooltip property.
5513          * 
5514          * @return
5515          *     possible object is
5516          *     {@link Boolean }
5517          *     
5518          */
5519         public Boolean isShowNPfeatureTooltip() {
5520             return showNPfeatureTooltip;
5521         }
5522
5523         /**
5524          * Sets the value of the showNPfeatureTooltip property.
5525          * 
5526          * @param value
5527          *     allowed object is
5528          *     {@link Boolean }
5529          *     
5530          */
5531         public void setShowNPfeatureTooltip(Boolean value) {
5532             this.showNPfeatureTooltip = value;
5533         }
5534
5535         /**
5536          * Gets the value of the showDbRefTooltip property.
5537          * 
5538          * @return
5539          *     possible object is
5540          *     {@link Boolean }
5541          *     
5542          */
5543         public Boolean isShowDbRefTooltip() {
5544             return showDbRefTooltip;
5545         }
5546
5547         /**
5548          * Sets the value of the showDbRefTooltip property.
5549          * 
5550          * @param value
5551          *     allowed object is
5552          *     {@link Boolean }
5553          *     
5554          */
5555         public void setShowDbRefTooltip(Boolean value) {
5556             this.showDbRefTooltip = value;
5557         }
5558
5559         /**
5560          * Gets the value of the followHighlight property.
5561          * 
5562          * @return
5563          *     possible object is
5564          *     {@link Boolean }
5565          *     
5566          */
5567         public boolean isFollowHighlight() {
5568             if (followHighlight == null) {
5569                 return true;
5570             } else {
5571                 return followHighlight;
5572             }
5573         }
5574
5575         /**
5576          * Sets the value of the followHighlight property.
5577          * 
5578          * @param value
5579          *     allowed object is
5580          *     {@link Boolean }
5581          *     
5582          */
5583         public void setFollowHighlight(Boolean value) {
5584             this.followHighlight = value;
5585         }
5586
5587         /**
5588          * Gets the value of the followSelection property.
5589          * 
5590          * @return
5591          *     possible object is
5592          *     {@link Boolean }
5593          *     
5594          */
5595         public boolean isFollowSelection() {
5596             if (followSelection == null) {
5597                 return true;
5598             } else {
5599                 return followSelection;
5600             }
5601         }
5602
5603         /**
5604          * Sets the value of the followSelection property.
5605          * 
5606          * @param value
5607          *     allowed object is
5608          *     {@link Boolean }
5609          *     
5610          */
5611         public void setFollowSelection(Boolean value) {
5612             this.followSelection = value;
5613         }
5614
5615         /**
5616          * Gets the value of the showAnnotation property.
5617          * 
5618          * @return
5619          *     possible object is
5620          *     {@link Boolean }
5621          *     
5622          */
5623         public Boolean isShowAnnotation() {
5624             return showAnnotation;
5625         }
5626
5627         /**
5628          * Sets the value of the showAnnotation property.
5629          * 
5630          * @param value
5631          *     allowed object is
5632          *     {@link Boolean }
5633          *     
5634          */
5635         public void setShowAnnotation(Boolean value) {
5636             this.showAnnotation = value;
5637         }
5638
5639         /**
5640          * Gets the value of the centreColumnLabels property.
5641          * 
5642          * @return
5643          *     possible object is
5644          *     {@link Boolean }
5645          *     
5646          */
5647         public boolean isCentreColumnLabels() {
5648             if (centreColumnLabels == null) {
5649                 return false;
5650             } else {
5651                 return centreColumnLabels;
5652             }
5653         }
5654
5655         /**
5656          * Sets the value of the centreColumnLabels property.
5657          * 
5658          * @param value
5659          *     allowed object is
5660          *     {@link Boolean }
5661          *     
5662          */
5663         public void setCentreColumnLabels(Boolean value) {
5664             this.centreColumnLabels = value;
5665         }
5666
5667         /**
5668          * Gets the value of the showGroupConservation property.
5669          * 
5670          * @return
5671          *     possible object is
5672          *     {@link Boolean }
5673          *     
5674          */
5675         public boolean isShowGroupConservation() {
5676             if (showGroupConservation == null) {
5677                 return false;
5678             } else {
5679                 return showGroupConservation;
5680             }
5681         }
5682
5683         /**
5684          * Sets the value of the showGroupConservation property.
5685          * 
5686          * @param value
5687          *     allowed object is
5688          *     {@link Boolean }
5689          *     
5690          */
5691         public void setShowGroupConservation(Boolean value) {
5692             this.showGroupConservation = value;
5693         }
5694
5695         /**
5696          * Gets the value of the showGroupConsensus property.
5697          * 
5698          * @return
5699          *     possible object is
5700          *     {@link Boolean }
5701          *     
5702          */
5703         public boolean isShowGroupConsensus() {
5704             if (showGroupConsensus == null) {
5705                 return false;
5706             } else {
5707                 return showGroupConsensus;
5708             }
5709         }
5710
5711         /**
5712          * Sets the value of the showGroupConsensus property.
5713          * 
5714          * @param value
5715          *     allowed object is
5716          *     {@link Boolean }
5717          *     
5718          */
5719         public void setShowGroupConsensus(Boolean value) {
5720             this.showGroupConsensus = value;
5721         }
5722
5723         /**
5724          * Gets the value of the showConsensusHistogram property.
5725          * 
5726          * @return
5727          *     possible object is
5728          *     {@link Boolean }
5729          *     
5730          */
5731         public boolean isShowConsensusHistogram() {
5732             if (showConsensusHistogram == null) {
5733                 return true;
5734             } else {
5735                 return showConsensusHistogram;
5736             }
5737         }
5738
5739         /**
5740          * Sets the value of the showConsensusHistogram property.
5741          * 
5742          * @param value
5743          *     allowed object is
5744          *     {@link Boolean }
5745          *     
5746          */
5747         public void setShowConsensusHistogram(Boolean value) {
5748             this.showConsensusHistogram = value;
5749         }
5750
5751         /**
5752          * Gets the value of the showSequenceLogo property.
5753          * 
5754          * @return
5755          *     possible object is
5756          *     {@link Boolean }
5757          *     
5758          */
5759         public boolean isShowSequenceLogo() {
5760             if (showSequenceLogo == null) {
5761                 return false;
5762             } else {
5763                 return showSequenceLogo;
5764             }
5765         }
5766
5767         /**
5768          * Sets the value of the showSequenceLogo property.
5769          * 
5770          * @param value
5771          *     allowed object is
5772          *     {@link Boolean }
5773          *     
5774          */
5775         public void setShowSequenceLogo(Boolean value) {
5776             this.showSequenceLogo = value;
5777         }
5778
5779         /**
5780          * Gets the value of the normaliseSequenceLogo property.
5781          * 
5782          * @return
5783          *     possible object is
5784          *     {@link Boolean }
5785          *     
5786          */
5787         public boolean isNormaliseSequenceLogo() {
5788             if (normaliseSequenceLogo == null) {
5789                 return false;
5790             } else {
5791                 return normaliseSequenceLogo;
5792             }
5793         }
5794
5795         /**
5796          * Sets the value of the normaliseSequenceLogo property.
5797          * 
5798          * @param value
5799          *     allowed object is
5800          *     {@link Boolean }
5801          *     
5802          */
5803         public void setNormaliseSequenceLogo(Boolean value) {
5804             this.normaliseSequenceLogo = value;
5805         }
5806
5807         /**
5808          * Gets the value of the ignoreGapsinConsensus property.
5809          * 
5810          * @return
5811          *     possible object is
5812          *     {@link Boolean }
5813          *     
5814          */
5815         public boolean isIgnoreGapsinConsensus() {
5816             if (ignoreGapsinConsensus == null) {
5817                 return true;
5818             } else {
5819                 return ignoreGapsinConsensus;
5820             }
5821         }
5822
5823         /**
5824          * Sets the value of the ignoreGapsinConsensus property.
5825          * 
5826          * @param value
5827          *     allowed object is
5828          *     {@link Boolean }
5829          *     
5830          */
5831         public void setIgnoreGapsinConsensus(Boolean value) {
5832             this.ignoreGapsinConsensus = value;
5833         }
5834
5835         /**
5836          * Gets the value of the startRes property.
5837          * 
5838          * @return
5839          *     possible object is
5840          *     {@link Integer }
5841          *     
5842          */
5843         public Integer getStartRes() {
5844             return startRes;
5845         }
5846
5847         /**
5848          * Sets the value of the startRes property.
5849          * 
5850          * @param value
5851          *     allowed object is
5852          *     {@link Integer }
5853          *     
5854          */
5855         public void setStartRes(Integer value) {
5856             this.startRes = value;
5857         }
5858
5859         /**
5860          * Gets the value of the startSeq property.
5861          * 
5862          * @return
5863          *     possible object is
5864          *     {@link Integer }
5865          *     
5866          */
5867         public Integer getStartSeq() {
5868             return startSeq;
5869         }
5870
5871         /**
5872          * Sets the value of the startSeq property.
5873          * 
5874          * @param value
5875          *     allowed object is
5876          *     {@link Integer }
5877          *     
5878          */
5879         public void setStartSeq(Integer value) {
5880             this.startSeq = value;
5881         }
5882
5883         /**
5884          * Gets the value of the charWidth property.
5885          * 
5886          * @return
5887          *     possible object is
5888          *     {@link Integer }
5889          *     
5890          */
5891         public Integer getCharWidth() {
5892             return charWidth;
5893         }
5894
5895         /**
5896          * Sets the value of the charWidth property.
5897          * 
5898          * @param value
5899          *     allowed object is
5900          *     {@link Integer }
5901          *     
5902          */
5903         public void setCharWidth(Integer value) {
5904             this.charWidth = value;
5905         }
5906
5907         /**
5908          * Gets the value of the charHeight property.
5909          * 
5910          * @return
5911          *     possible object is
5912          *     {@link Integer }
5913          *     
5914          */
5915         public Integer getCharHeight() {
5916             return charHeight;
5917         }
5918
5919         /**
5920          * Sets the value of the charHeight property.
5921          * 
5922          * @param value
5923          *     allowed object is
5924          *     {@link Integer }
5925          *     
5926          */
5927         public void setCharHeight(Integer value) {
5928             this.charHeight = value;
5929         }
5930
5931         /**
5932          * Gets the value of the fontName property.
5933          * 
5934          * @return
5935          *     possible object is
5936          *     {@link String }
5937          *     
5938          */
5939         public String getFontName() {
5940             return fontName;
5941         }
5942
5943         /**
5944          * Sets the value of the fontName property.
5945          * 
5946          * @param value
5947          *     allowed object is
5948          *     {@link String }
5949          *     
5950          */
5951         public void setFontName(String value) {
5952             this.fontName = value;
5953         }
5954
5955         /**
5956          * Gets the value of the fontSize property.
5957          * 
5958          * @return
5959          *     possible object is
5960          *     {@link Integer }
5961          *     
5962          */
5963         public Integer getFontSize() {
5964             return fontSize;
5965         }
5966
5967         /**
5968          * Sets the value of the fontSize property.
5969          * 
5970          * @param value
5971          *     allowed object is
5972          *     {@link Integer }
5973          *     
5974          */
5975         public void setFontSize(Integer value) {
5976             this.fontSize = value;
5977         }
5978
5979         /**
5980          * Gets the value of the fontStyle property.
5981          * 
5982          * @return
5983          *     possible object is
5984          *     {@link Integer }
5985          *     
5986          */
5987         public Integer getFontStyle() {
5988             return fontStyle;
5989         }
5990
5991         /**
5992          * Sets the value of the fontStyle property.
5993          * 
5994          * @param value
5995          *     allowed object is
5996          *     {@link Integer }
5997          *     
5998          */
5999         public void setFontStyle(Integer value) {
6000             this.fontStyle = value;
6001         }
6002
6003         /**
6004          * Gets the value of the idWidth property.
6005          * 
6006          * @return
6007          *     possible object is
6008          *     {@link Integer }
6009          *     
6010          */
6011         public Integer getIdWidth() {
6012             return idWidth;
6013         }
6014
6015         /**
6016          * Sets the value of the idWidth property.
6017          * 
6018          * @param value
6019          *     allowed object is
6020          *     {@link Integer }
6021          *     
6022          */
6023         public void setIdWidth(Integer value) {
6024             this.idWidth = value;
6025         }
6026
6027         /**
6028          * Gets the value of the idWidthManuallyAdjusted property.
6029          * 
6030          * @return
6031          *     possible object is
6032          *     {@link Boolean }
6033          *     
6034          */
6035         public Boolean isIdWidthManuallyAdjusted() {
6036             return idWidthManuallyAdjusted;
6037         }
6038
6039         /**
6040          * Sets the value of the idWidthManuallyAdjusted property.
6041          * 
6042          * @param value
6043          *     allowed object is
6044          *     {@link Boolean }
6045          *     
6046          */
6047         public void setIdWidthManuallyAdjusted(Boolean value) {
6048             this.idWidthManuallyAdjusted = value;
6049         }
6050
6051         /**
6052          * Gets the value of the scaleProteinAsCdna property.
6053          * 
6054          * @return
6055          *     possible object is
6056          *     {@link Boolean }
6057          *     
6058          */
6059         public boolean isScaleProteinAsCdna() {
6060             if (scaleProteinAsCdna == null) {
6061                 return true;
6062             } else {
6063                 return scaleProteinAsCdna;
6064             }
6065         }
6066
6067         /**
6068          * Sets the value of the scaleProteinAsCdna property.
6069          * 
6070          * @param value
6071          *     allowed object is
6072          *     {@link Boolean }
6073          *     
6074          */
6075         public void setScaleProteinAsCdna(Boolean value) {
6076             this.scaleProteinAsCdna = value;
6077         }
6078
6079         /**
6080          * Gets the value of the viewName property.
6081          * 
6082          * @return
6083          *     possible object is
6084          *     {@link String }
6085          *     
6086          */
6087         public String getViewName() {
6088             return viewName;
6089         }
6090
6091         /**
6092          * Sets the value of the viewName property.
6093          * 
6094          * @param value
6095          *     allowed object is
6096          *     {@link String }
6097          *     
6098          */
6099         public void setViewName(String value) {
6100             this.viewName = value;
6101         }
6102
6103         /**
6104          * Gets the value of the sequenceSetId property.
6105          * 
6106          * @return
6107          *     possible object is
6108          *     {@link String }
6109          *     
6110          */
6111         public String getSequenceSetId() {
6112             return sequenceSetId;
6113         }
6114
6115         /**
6116          * Sets the value of the sequenceSetId property.
6117          * 
6118          * @param value
6119          *     allowed object is
6120          *     {@link String }
6121          *     
6122          */
6123         public void setSequenceSetId(String value) {
6124             this.sequenceSetId = value;
6125         }
6126
6127         /**
6128          * Gets the value of the gatheredViews property.
6129          * 
6130          * @return
6131          *     possible object is
6132          *     {@link Boolean }
6133          *     
6134          */
6135         public Boolean isGatheredViews() {
6136             return gatheredViews;
6137         }
6138
6139         /**
6140          * Sets the value of the gatheredViews property.
6141          * 
6142          * @param value
6143          *     allowed object is
6144          *     {@link Boolean }
6145          *     
6146          */
6147         public void setGatheredViews(Boolean value) {
6148             this.gatheredViews = value;
6149         }
6150
6151         /**
6152          * Gets the value of the textCol1 property.
6153          * 
6154          * @return
6155          *     possible object is
6156          *     {@link Integer }
6157          *     
6158          */
6159         public Integer getTextCol1() {
6160             return textCol1;
6161         }
6162
6163         /**
6164          * Sets the value of the textCol1 property.
6165          * 
6166          * @param value
6167          *     allowed object is
6168          *     {@link Integer }
6169          *     
6170          */
6171         public void setTextCol1(Integer value) {
6172             this.textCol1 = value;
6173         }
6174
6175         /**
6176          * Gets the value of the textCol2 property.
6177          * 
6178          * @return
6179          *     possible object is
6180          *     {@link Integer }
6181          *     
6182          */
6183         public Integer getTextCol2() {
6184             return textCol2;
6185         }
6186
6187         /**
6188          * Sets the value of the textCol2 property.
6189          * 
6190          * @param value
6191          *     allowed object is
6192          *     {@link Integer }
6193          *     
6194          */
6195         public void setTextCol2(Integer value) {
6196             this.textCol2 = value;
6197         }
6198
6199         /**
6200          * Gets the value of the textColThreshold property.
6201          * 
6202          * @return
6203          *     possible object is
6204          *     {@link Integer }
6205          *     
6206          */
6207         public Integer getTextColThreshold() {
6208             return textColThreshold;
6209         }
6210
6211         /**
6212          * Sets the value of the textColThreshold property.
6213          * 
6214          * @param value
6215          *     allowed object is
6216          *     {@link Integer }
6217          *     
6218          */
6219         public void setTextColThreshold(Integer value) {
6220             this.textColThreshold = value;
6221         }
6222
6223         /**
6224          * Gets the value of the id property.
6225          * 
6226          * @return
6227          *     possible object is
6228          *     {@link String }
6229          *     
6230          */
6231         public String getId() {
6232             return id;
6233         }
6234
6235         /**
6236          * Sets the value of the id property.
6237          * 
6238          * @param value
6239          *     allowed object is
6240          *     {@link String }
6241          *     
6242          */
6243         public void setId(String value) {
6244             this.id = value;
6245         }
6246
6247         /**
6248          * Gets the value of the complementId property.
6249          * 
6250          * @return
6251          *     possible object is
6252          *     {@link String }
6253          *     
6254          */
6255         public String getComplementId() {
6256             return complementId;
6257         }
6258
6259         /**
6260          * Sets the value of the complementId property.
6261          * 
6262          * @param value
6263          *     allowed object is
6264          *     {@link String }
6265          *     
6266          */
6267         public void setComplementId(String value) {
6268             this.complementId = value;
6269         }
6270
6271         /**
6272          * Gets the value of the showComplementFeatures property.
6273          * 
6274          * @return
6275          *     possible object is
6276          *     {@link Boolean }
6277          *     
6278          */
6279         public boolean isShowComplementFeatures() {
6280             if (showComplementFeatures == null) {
6281                 return false;
6282             } else {
6283                 return showComplementFeatures;
6284             }
6285         }
6286
6287         /**
6288          * Sets the value of the showComplementFeatures property.
6289          * 
6290          * @param value
6291          *     allowed object is
6292          *     {@link Boolean }
6293          *     
6294          */
6295         public void setShowComplementFeatures(Boolean value) {
6296             this.showComplementFeatures = value;
6297         }
6298
6299         /**
6300          * Gets the value of the showComplementFeaturesOnTop property.
6301          * 
6302          * @return
6303          *     possible object is
6304          *     {@link Boolean }
6305          *     
6306          */
6307         public boolean isShowComplementFeaturesOnTop() {
6308             if (showComplementFeaturesOnTop == null) {
6309                 return false;
6310             } else {
6311                 return showComplementFeaturesOnTop;
6312             }
6313         }
6314
6315         /**
6316          * Sets the value of the showComplementFeaturesOnTop property.
6317          * 
6318          * @param value
6319          *     allowed object is
6320          *     {@link Boolean }
6321          *     
6322          */
6323         public void setShowComplementFeaturesOnTop(Boolean value) {
6324             this.showComplementFeaturesOnTop = value;
6325         }
6326
6327         /**
6328          * Gets the value of the width property.
6329          * 
6330          * @return
6331          *     possible object is
6332          *     {@link Integer }
6333          *     
6334          */
6335         public Integer getWidth() {
6336             return width;
6337         }
6338
6339         /**
6340          * Sets the value of the width property.
6341          * 
6342          * @param value
6343          *     allowed object is
6344          *     {@link Integer }
6345          *     
6346          */
6347         public void setWidth(Integer value) {
6348             this.width = value;
6349         }
6350
6351         /**
6352          * Gets the value of the height property.
6353          * 
6354          * @return
6355          *     possible object is
6356          *     {@link Integer }
6357          *     
6358          */
6359         public Integer getHeight() {
6360             return height;
6361         }
6362
6363         /**
6364          * Sets the value of the height property.
6365          * 
6366          * @param value
6367          *     allowed object is
6368          *     {@link Integer }
6369          *     
6370          */
6371         public void setHeight(Integer value) {
6372             this.height = value;
6373         }
6374
6375         /**
6376          * Gets the value of the xpos property.
6377          * 
6378          * @return
6379          *     possible object is
6380          *     {@link Integer }
6381          *     
6382          */
6383         public Integer getXpos() {
6384             return xpos;
6385         }
6386
6387         /**
6388          * Sets the value of the xpos property.
6389          * 
6390          * @param value
6391          *     allowed object is
6392          *     {@link Integer }
6393          *     
6394          */
6395         public void setXpos(Integer value) {
6396             this.xpos = value;
6397         }
6398
6399         /**
6400          * Gets the value of the ypos property.
6401          * 
6402          * @return
6403          *     possible object is
6404          *     {@link Integer }
6405          *     
6406          */
6407         public Integer getYpos() {
6408             return ypos;
6409         }
6410
6411         /**
6412          * Sets the value of the ypos property.
6413          * 
6414          * @param value
6415          *     allowed object is
6416          *     {@link Integer }
6417          *     
6418          */
6419         public void setYpos(Integer value) {
6420             this.ypos = value;
6421         }
6422
6423
6424         /**
6425          * &lt;p&gt;Java class for anonymous complex type.
6426          * 
6427          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
6428          * 
6429          * &lt;pre&gt;
6430          * &amp;lt;complexType&amp;gt;
6431          *   &amp;lt;complexContent&amp;gt;
6432          *     &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
6433          *       &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6434          *       &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
6435          *       &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
6436          *     &amp;lt;/extension&amp;gt;
6437          *   &amp;lt;/complexContent&amp;gt;
6438          * &amp;lt;/complexType&amp;gt;
6439          * &lt;/pre&gt;
6440          * 
6441          * 
6442          */
6443         @XmlAccessorType(XmlAccessType.FIELD)
6444         @XmlType(name = "")
6445         public static class CalcIdParam
6446             extends WebServiceParameterSet
6447         {
6448
6449             @XmlAttribute(name = "calcId", required = true)
6450             protected String calcId;
6451             @XmlAttribute(name = "needsUpdate")
6452             protected Boolean needsUpdate;
6453             @XmlAttribute(name = "autoUpdate", required = true)
6454             protected boolean autoUpdate;
6455
6456             /**
6457              * Gets the value of the calcId property.
6458              * 
6459              * @return
6460              *     possible object is
6461              *     {@link String }
6462              *     
6463              */
6464             public String getCalcId() {
6465                 return calcId;
6466             }
6467
6468             /**
6469              * Sets the value of the calcId property.
6470              * 
6471              * @param value
6472              *     allowed object is
6473              *     {@link String }
6474              *     
6475              */
6476             public void setCalcId(String value) {
6477                 this.calcId = value;
6478             }
6479
6480             /**
6481              * Gets the value of the needsUpdate property.
6482              * 
6483              * @return
6484              *     possible object is
6485              *     {@link Boolean }
6486              *     
6487              */
6488             public boolean isNeedsUpdate() {
6489                 if (needsUpdate == null) {
6490                     return false;
6491                 } else {
6492                     return needsUpdate;
6493                 }
6494             }
6495
6496             /**
6497              * Sets the value of the needsUpdate property.
6498              * 
6499              * @param value
6500              *     allowed object is
6501              *     {@link Boolean }
6502              *     
6503              */
6504             public void setNeedsUpdate(Boolean value) {
6505                 this.needsUpdate = value;
6506             }
6507
6508             /**
6509              * Gets the value of the autoUpdate property.
6510              * 
6511              */
6512             public boolean isAutoUpdate() {
6513                 return autoUpdate;
6514             }
6515
6516             /**
6517              * Sets the value of the autoUpdate property.
6518              * 
6519              */
6520             public void setAutoUpdate(boolean value) {
6521                 this.autoUpdate = value;
6522             }
6523
6524         }
6525
6526
6527         /**
6528          * &lt;p&gt;Java class for anonymous complex type.
6529          * 
6530          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
6531          * 
6532          * &lt;pre&gt;
6533          * &amp;lt;complexType&amp;gt;
6534          *   &amp;lt;complexContent&amp;gt;
6535          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
6536          *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6537          *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6538          *     &amp;lt;/restriction&amp;gt;
6539          *   &amp;lt;/complexContent&amp;gt;
6540          * &amp;lt;/complexType&amp;gt;
6541          * &lt;/pre&gt;
6542          * 
6543          * 
6544          */
6545         @XmlAccessorType(XmlAccessType.FIELD)
6546         @XmlType(name = "")
6547         public static class HiddenColumns {
6548
6549             @XmlAttribute(name = "start")
6550             protected Integer start;
6551             @XmlAttribute(name = "end")
6552             protected Integer end;
6553
6554             /**
6555              * Gets the value of the start property.
6556              * 
6557              * @return
6558              *     possible object is
6559              *     {@link Integer }
6560              *     
6561              */
6562             public Integer getStart() {
6563                 return start;
6564             }
6565
6566             /**
6567              * Sets the value of the start property.
6568              * 
6569              * @param value
6570              *     allowed object is
6571              *     {@link Integer }
6572              *     
6573              */
6574             public void setStart(Integer value) {
6575                 this.start = value;
6576             }
6577
6578             /**
6579              * Gets the value of the end property.
6580              * 
6581              * @return
6582              *     possible object is
6583              *     {@link Integer }
6584              *     
6585              */
6586             public Integer getEnd() {
6587                 return end;
6588             }
6589
6590             /**
6591              * Sets the value of the end property.
6592              * 
6593              * @param value
6594              *     allowed object is
6595              *     {@link Integer }
6596              *     
6597              */
6598             public void setEnd(Integer value) {
6599                 this.end = value;
6600             }
6601
6602         }
6603
6604
6605         /**
6606          * &lt;p&gt;Java class for anonymous complex type.
6607          * 
6608          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
6609          * 
6610          * &lt;pre&gt;
6611          * &amp;lt;complexType&amp;gt;
6612          *   &amp;lt;complexContent&amp;gt;
6613          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
6614          *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
6615          *       &amp;lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
6616          *       &amp;lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6617          *       &amp;lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6618          *       &amp;lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6619          *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6620          *     &amp;lt;/restriction&amp;gt;
6621          *   &amp;lt;/complexContent&amp;gt;
6622          * &amp;lt;/complexType&amp;gt;
6623          * &lt;/pre&gt;
6624          * 
6625          * 
6626          */
6627         @XmlAccessorType(XmlAccessType.FIELD)
6628         @XmlType(name = "")
6629         public static class Overview {
6630
6631             @XmlAttribute(name = "showHidden")
6632             protected Boolean showHidden;
6633             @XmlAttribute(name = "residueColour")
6634             protected Integer residueColour;
6635             @XmlAttribute(name = "gapColour")
6636             protected Integer gapColour;
6637             @XmlAttribute(name = "hiddenColour")
6638             protected Integer hiddenColour;
6639             @XmlAttribute(name = "title")
6640             protected String title;
6641             @XmlAttribute(name = "width")
6642             protected Integer width;
6643             @XmlAttribute(name = "height")
6644             protected Integer height;
6645             @XmlAttribute(name = "xpos")
6646             protected Integer xpos;
6647             @XmlAttribute(name = "ypos")
6648             protected Integer ypos;
6649
6650             /**
6651              * Gets the value of the showHidden property.
6652              * 
6653              * @return
6654              *     possible object is
6655              *     {@link Boolean }
6656              *     
6657              */
6658             public Boolean isShowHidden() {
6659                 return showHidden;
6660             }
6661
6662             /**
6663              * Sets the value of the showHidden property.
6664              * 
6665              * @param value
6666              *     allowed object is
6667              *     {@link Boolean }
6668              *     
6669              */
6670             public void setShowHidden(Boolean value) {
6671                 this.showHidden = value;
6672             }
6673
6674             /**
6675              * Gets the value of the residueColour property.
6676              * 
6677              * @return
6678              *     possible object is
6679              *     {@link Integer }
6680              *     
6681              */
6682             public Integer getResidueColour() {
6683                 return residueColour;
6684             }
6685
6686             /**
6687              * Sets the value of the residueColour property.
6688              * 
6689              * @param value
6690              *     allowed object is
6691              *     {@link Integer }
6692              *     
6693              */
6694             public void setResidueColour(Integer value) {
6695                 this.residueColour = value;
6696             }
6697
6698             /**
6699              * Gets the value of the gapColour property.
6700              * 
6701              * @return
6702              *     possible object is
6703              *     {@link Integer }
6704              *     
6705              */
6706             public Integer getGapColour() {
6707                 return gapColour;
6708             }
6709
6710             /**
6711              * Sets the value of the gapColour property.
6712              * 
6713              * @param value
6714              *     allowed object is
6715              *     {@link Integer }
6716              *     
6717              */
6718             public void setGapColour(Integer value) {
6719                 this.gapColour = value;
6720             }
6721
6722             /**
6723              * Gets the value of the hiddenColour property.
6724              * 
6725              * @return
6726              *     possible object is
6727              *     {@link Integer }
6728              *     
6729              */
6730             public Integer getHiddenColour() {
6731                 return hiddenColour;
6732             }
6733
6734             /**
6735              * Sets the value of the hiddenColour property.
6736              * 
6737              * @param value
6738              *     allowed object is
6739              *     {@link Integer }
6740              *     
6741              */
6742             public void setHiddenColour(Integer value) {
6743                 this.hiddenColour = value;
6744             }
6745
6746             /**
6747              * Gets the value of the title property.
6748              * 
6749              * @return
6750              *     possible object is
6751              *     {@link String }
6752              *     
6753              */
6754             public String getTitle() {
6755                 return title;
6756             }
6757
6758             /**
6759              * Sets the value of the title property.
6760              * 
6761              * @param value
6762              *     allowed object is
6763              *     {@link String }
6764              *     
6765              */
6766             public void setTitle(String value) {
6767                 this.title = value;
6768             }
6769
6770             /**
6771              * Gets the value of the width property.
6772              * 
6773              * @return
6774              *     possible object is
6775              *     {@link Integer }
6776              *     
6777              */
6778             public Integer getWidth() {
6779                 return width;
6780             }
6781
6782             /**
6783              * Sets the value of the width property.
6784              * 
6785              * @param value
6786              *     allowed object is
6787              *     {@link Integer }
6788              *     
6789              */
6790             public void setWidth(Integer value) {
6791                 this.width = value;
6792             }
6793
6794             /**
6795              * Gets the value of the height property.
6796              * 
6797              * @return
6798              *     possible object is
6799              *     {@link Integer }
6800              *     
6801              */
6802             public Integer getHeight() {
6803                 return height;
6804             }
6805
6806             /**
6807              * Sets the value of the height property.
6808              * 
6809              * @param value
6810              *     allowed object is
6811              *     {@link Integer }
6812              *     
6813              */
6814             public void setHeight(Integer value) {
6815                 this.height = value;
6816             }
6817
6818             /**
6819              * Gets the value of the xpos property.
6820              * 
6821              * @return
6822              *     possible object is
6823              *     {@link Integer }
6824              *     
6825              */
6826             public Integer getXpos() {
6827                 return xpos;
6828             }
6829
6830             /**
6831              * Sets the value of the xpos property.
6832              * 
6833              * @param value
6834              *     allowed object is
6835              *     {@link Integer }
6836              *     
6837              */
6838             public void setXpos(Integer value) {
6839                 this.xpos = value;
6840             }
6841
6842             /**
6843              * Gets the value of the ypos property.
6844              * 
6845              * @return
6846              *     possible object is
6847              *     {@link Integer }
6848              *     
6849              */
6850             public Integer getYpos() {
6851                 return ypos;
6852             }
6853
6854             /**
6855              * Sets the value of the ypos property.
6856              * 
6857              * @param value
6858              *     allowed object is
6859              *     {@link Integer }
6860              *     
6861              */
6862             public void setYpos(Integer value) {
6863                 this.ypos = value;
6864             }
6865
6866         }
6867
6868     }
6869
6870 }