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Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD
[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: 2021.08.30 at 11:05:22 AM BST 
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  *                   </sequence>
169  *                   <attGroup ref="{www.jalview.org}swingwindow"/>
170  *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
171  *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
172  *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
173  *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
174  *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
175  *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
176  *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
177  *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
178  *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
179  *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
180  *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
181  *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
182  *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
183  *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
184  *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185  *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186  *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
187  *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
188  *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
189  *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
190  *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
191  *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
192  *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
193  *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
194  *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
195  *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
196  *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
197  *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
198  *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
199  *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
200  *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
201  *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
202  *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
203  *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
204  *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
205  *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
206  *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
207  *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
208  *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
209  *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
210  *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
211  *                   <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
212  *                   <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
213  *                 </restriction>
214  *               </complexContent>
215  *             </complexType>
216  *           </element>
217  *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
218  *             <complexType>
219  *               <complexContent>
220  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
221  *                   <sequence>
222  *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
223  *                   </sequence>
224  *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
225  *                 </restriction>
226  *               </complexContent>
227  *             </complexType>
228  *           </element>
229  *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
230  *             <complexType>
231  *               <complexContent>
232  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
233  *                   <sequence minOccurs="0">
234  *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
235  *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
236  *                   </sequence>
237  *                   <attGroup ref="{www.jalview.org}swingwindow"/>
238  *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
239  *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
240  *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
241  *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
242  *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
243  *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
244  *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
245  *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
246  *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
247  *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
248  *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
249  *                 </restriction>
250  *               </complexContent>
251  *             </complexType>
252  *           </element>
253  *           <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
254  *             <complexType>
255  *               <complexContent>
256  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
257  *                   <sequence>
258  *                     <element name="sequencePoint" maxOccurs="unbounded">
259  *                       <complexType>
260  *                         <complexContent>
261  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
262  *                             <attGroup ref="{www.jalview.org}position"/>
263  *                             <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
264  *                           </restriction>
265  *                         </complexContent>
266  *                       </complexType>
267  *                     </element>
268  *                     <element name="axis" maxOccurs="3" minOccurs="3">
269  *                       <complexType>
270  *                         <complexContent>
271  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
272  *                             <attGroup ref="{www.jalview.org}position"/>
273  *                           </restriction>
274  *                         </complexContent>
275  *                       </complexType>
276  *                     </element>
277  *                     <element name="seqPointMin">
278  *                       <complexType>
279  *                         <complexContent>
280  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
281  *                             <attGroup ref="{www.jalview.org}position"/>
282  *                           </restriction>
283  *                         </complexContent>
284  *                       </complexType>
285  *                     </element>
286  *                     <element name="seqPointMax">
287  *                       <complexType>
288  *                         <complexContent>
289  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
290  *                             <attGroup ref="{www.jalview.org}position"/>
291  *                           </restriction>
292  *                         </complexContent>
293  *                       </complexType>
294  *                     </element>
295  *                     <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
296  *                   </sequence>
297  *                   <attGroup ref="{www.jalview.org}swingwindow"/>
298  *                   <attGroup ref="{www.jalview.org}SimilarityParams"/>
299  *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
300  *                   <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
301  *                   <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
302  *                   <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
303  *                   <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
304  *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
305  *                   <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
306  *                   <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
307  *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
308  *                 </restriction>
309  *               </complexContent>
310  *             </complexType>
311  *           </element>
312  *           <element name="FeatureSettings" minOccurs="0">
313  *             <complexType>
314  *               <complexContent>
315  *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
316  *                   <sequence>
317  *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
318  *                       <complexType>
319  *                         <complexContent>
320  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
321  *                             <sequence>
322  *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
323  *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
324  *                             </sequence>
325  *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
326  *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
327  *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
328  *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
329  *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
330  *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
331  *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
332  *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
333  *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
334  *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
335  *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
336  *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
337  *                           </restriction>
338  *                         </complexContent>
339  *                       </complexType>
340  *                     </element>
341  *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
342  *                       <complexType>
343  *                         <complexContent>
344  *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
345  *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
346  *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
347  *                           </restriction>
348  *                         </complexContent>
349  *                       </complexType>
350  *                     </element>
351  *                   </sequence>
352  *                 </restriction>
353  *               </complexContent>
354  *             </complexType>
355  *           </element>
356  *         </sequence>
357  *       </sequence>
358  *     </restriction>
359  *   </complexContent>
360  * </complexType>
361  * </pre>
362  * 
363  * 
364  */
365 @XmlAccessorType(XmlAccessType.FIELD)
366 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
367     "creationDate",
368     "version",
369     "vamsasModel",
370     "jSeq",
371     "jGroup",
372     "viewport",
373     "userColours",
374     "tree",
375     "pcaViewer",
376     "featureSettings"
377 })
378 public class JalviewModel {
379
380     @XmlElement(required = true)
381     @XmlSchemaType(name = "dateTime")
382     protected XMLGregorianCalendar creationDate;
383     @XmlElement(required = true)
384     protected String version;
385     @XmlElement(required = true)
386     protected VAMSAS vamsasModel;
387     @XmlElement(name = "JSeq")
388     protected List<JalviewModel.JSeq> jSeq;
389     @XmlElement(name = "JGroup")
390     protected List<JalviewModel.JGroup> jGroup;
391     @XmlElement(name = "Viewport")
392     protected List<JalviewModel.Viewport> viewport;
393     @XmlElement(name = "UserColours")
394     protected List<JalviewModel.UserColours> userColours;
395     protected List<JalviewModel.Tree> tree;
396     @XmlElement(name = "PcaViewer")
397     protected List<JalviewModel.PcaViewer> pcaViewer;
398     @XmlElement(name = "FeatureSettings")
399     protected JalviewModel.FeatureSettings featureSettings;
400
401     /**
402      * Gets the value of the creationDate property.
403      * 
404      * @return
405      *     possible object is
406      *     {@link XMLGregorianCalendar }
407      *     
408      */
409     public XMLGregorianCalendar getCreationDate() {
410         return creationDate;
411     }
412
413     /**
414      * Sets the value of the creationDate property.
415      * 
416      * @param value
417      *     allowed object is
418      *     {@link XMLGregorianCalendar }
419      *     
420      */
421     public void setCreationDate(XMLGregorianCalendar value) {
422         this.creationDate = value;
423     }
424
425     /**
426      * Gets the value of the version property.
427      * 
428      * @return
429      *     possible object is
430      *     {@link String }
431      *     
432      */
433     public String getVersion() {
434         return version;
435     }
436
437     /**
438      * Sets the value of the version property.
439      * 
440      * @param value
441      *     allowed object is
442      *     {@link String }
443      *     
444      */
445     public void setVersion(String value) {
446         this.version = value;
447     }
448
449     /**
450      * Gets the value of the vamsasModel property.
451      * 
452      * @return
453      *     possible object is
454      *     {@link VAMSAS }
455      *     
456      */
457     public VAMSAS getVamsasModel() {
458         return vamsasModel;
459     }
460
461     /**
462      * Sets the value of the vamsasModel property.
463      * 
464      * @param value
465      *     allowed object is
466      *     {@link VAMSAS }
467      *     
468      */
469     public void setVamsasModel(VAMSAS value) {
470         this.vamsasModel = value;
471     }
472
473     /**
474      * Gets the value of the jSeq property.
475      * 
476      * &lt;p&gt;
477      * This accessor method returns a reference to the live list,
478      * not a snapshot. Therefore any modification you make to the
479      * returned list will be present inside the JAXB object.
480      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
481      * 
482      * &lt;p&gt;
483      * For example, to add a new item, do as follows:
484      * &lt;pre&gt;
485      *    getJSeq().add(newItem);
486      * &lt;/pre&gt;
487      * 
488      * 
489      * &lt;p&gt;
490      * Objects of the following type(s) are allowed in the list
491      * {@link JalviewModel.JSeq }
492      * 
493      * 
494      */
495     public List<JalviewModel.JSeq> getJSeq() {
496         if (jSeq == null) {
497             jSeq = new ArrayList<JalviewModel.JSeq>();
498         }
499         return this.jSeq;
500     }
501
502     /**
503      * Gets the value of the jGroup property.
504      * 
505      * &lt;p&gt;
506      * This accessor method returns a reference to the live list,
507      * not a snapshot. Therefore any modification you make to the
508      * returned list will be present inside the JAXB object.
509      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
510      * 
511      * &lt;p&gt;
512      * For example, to add a new item, do as follows:
513      * &lt;pre&gt;
514      *    getJGroup().add(newItem);
515      * &lt;/pre&gt;
516      * 
517      * 
518      * &lt;p&gt;
519      * Objects of the following type(s) are allowed in the list
520      * {@link JalviewModel.JGroup }
521      * 
522      * 
523      */
524     public List<JalviewModel.JGroup> getJGroup() {
525         if (jGroup == null) {
526             jGroup = new ArrayList<JalviewModel.JGroup>();
527         }
528         return this.jGroup;
529     }
530
531     /**
532      * Gets the value of the viewport property.
533      * 
534      * &lt;p&gt;
535      * This accessor method returns a reference to the live list,
536      * not a snapshot. Therefore any modification you make to the
537      * returned list will be present inside the JAXB object.
538      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
539      * 
540      * &lt;p&gt;
541      * For example, to add a new item, do as follows:
542      * &lt;pre&gt;
543      *    getViewport().add(newItem);
544      * &lt;/pre&gt;
545      * 
546      * 
547      * &lt;p&gt;
548      * Objects of the following type(s) are allowed in the list
549      * {@link JalviewModel.Viewport }
550      * 
551      * 
552      */
553     public List<JalviewModel.Viewport> getViewport() {
554         if (viewport == null) {
555             viewport = new ArrayList<JalviewModel.Viewport>();
556         }
557         return this.viewport;
558     }
559
560     /**
561      * Gets the value of the userColours property.
562      * 
563      * &lt;p&gt;
564      * This accessor method returns a reference to the live list,
565      * not a snapshot. Therefore any modification you make to the
566      * returned list will be present inside the JAXB object.
567      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
568      * 
569      * &lt;p&gt;
570      * For example, to add a new item, do as follows:
571      * &lt;pre&gt;
572      *    getUserColours().add(newItem);
573      * &lt;/pre&gt;
574      * 
575      * 
576      * &lt;p&gt;
577      * Objects of the following type(s) are allowed in the list
578      * {@link JalviewModel.UserColours }
579      * 
580      * 
581      */
582     public List<JalviewModel.UserColours> getUserColours() {
583         if (userColours == null) {
584             userColours = new ArrayList<JalviewModel.UserColours>();
585         }
586         return this.userColours;
587     }
588
589     /**
590      * Gets the value of the tree property.
591      * 
592      * &lt;p&gt;
593      * This accessor method returns a reference to the live list,
594      * not a snapshot. Therefore any modification you make to the
595      * returned list will be present inside the JAXB object.
596      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
597      * 
598      * &lt;p&gt;
599      * For example, to add a new item, do as follows:
600      * &lt;pre&gt;
601      *    getTree().add(newItem);
602      * &lt;/pre&gt;
603      * 
604      * 
605      * &lt;p&gt;
606      * Objects of the following type(s) are allowed in the list
607      * {@link JalviewModel.Tree }
608      * 
609      * 
610      */
611     public List<JalviewModel.Tree> getTree() {
612         if (tree == null) {
613             tree = new ArrayList<JalviewModel.Tree>();
614         }
615         return this.tree;
616     }
617
618     /**
619      * Gets the value of the pcaViewer property.
620      * 
621      * &lt;p&gt;
622      * This accessor method returns a reference to the live list,
623      * not a snapshot. Therefore any modification you make to the
624      * returned list will be present inside the JAXB object.
625      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
626      * 
627      * &lt;p&gt;
628      * For example, to add a new item, do as follows:
629      * &lt;pre&gt;
630      *    getPcaViewer().add(newItem);
631      * &lt;/pre&gt;
632      * 
633      * 
634      * &lt;p&gt;
635      * Objects of the following type(s) are allowed in the list
636      * {@link JalviewModel.PcaViewer }
637      * 
638      * 
639      */
640     public List<JalviewModel.PcaViewer> getPcaViewer() {
641         if (pcaViewer == null) {
642             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
643         }
644         return this.pcaViewer;
645     }
646
647     /**
648      * Gets the value of the featureSettings property.
649      * 
650      * @return
651      *     possible object is
652      *     {@link JalviewModel.FeatureSettings }
653      *     
654      */
655     public JalviewModel.FeatureSettings getFeatureSettings() {
656         return featureSettings;
657     }
658
659     /**
660      * Sets the value of the featureSettings property.
661      * 
662      * @param value
663      *     allowed object is
664      *     {@link JalviewModel.FeatureSettings }
665      *     
666      */
667     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
668         this.featureSettings = value;
669     }
670
671
672     /**
673      * &lt;p&gt;Java class for anonymous complex type.
674      * 
675      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
676      * 
677      * &lt;pre&gt;
678      * &amp;lt;complexType&amp;gt;
679      *   &amp;lt;complexContent&amp;gt;
680      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
681      *       &amp;lt;sequence&amp;gt;
682      *         &amp;lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&amp;gt;
683      *           &amp;lt;complexType&amp;gt;
684      *             &amp;lt;complexContent&amp;gt;
685      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
686      *                 &amp;lt;sequence&amp;gt;
687      *                   &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
688      *                   &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
689      *                 &amp;lt;/sequence&amp;gt;
690      *                 &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
691      *                 &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
692      *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
693      *                 &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
694      *                 &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
695      *                 &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
696      *                 &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
697      *                 &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
698      *                 &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
699      *                 &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
700      *                 &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
701      *                 &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
702      *               &amp;lt;/restriction&amp;gt;
703      *             &amp;lt;/complexContent&amp;gt;
704      *           &amp;lt;/complexType&amp;gt;
705      *         &amp;lt;/element&amp;gt;
706      *         &amp;lt;element name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
707      *           &amp;lt;complexType&amp;gt;
708      *             &amp;lt;complexContent&amp;gt;
709      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
710      *                 &amp;lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
711      *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
712      *               &amp;lt;/restriction&amp;gt;
713      *             &amp;lt;/complexContent&amp;gt;
714      *           &amp;lt;/complexType&amp;gt;
715      *         &amp;lt;/element&amp;gt;
716      *       &amp;lt;/sequence&amp;gt;
717      *     &amp;lt;/restriction&amp;gt;
718      *   &amp;lt;/complexContent&amp;gt;
719      * &amp;lt;/complexType&amp;gt;
720      * &lt;/pre&gt;
721      * 
722      * 
723      */
724     @XmlAccessorType(XmlAccessType.FIELD)
725     @XmlType(name = "", propOrder = {
726         "setting",
727         "group"
728     })
729     public static class FeatureSettings {
730
731         @XmlElement(namespace = "www.jalview.org")
732         protected List<JalviewModel.FeatureSettings.Setting> setting;
733         @XmlElement(namespace = "www.jalview.org")
734         protected List<JalviewModel.FeatureSettings.Group> group;
735
736         /**
737          * Gets the value of the setting property.
738          * 
739          * &lt;p&gt;
740          * This accessor method returns a reference to the live list,
741          * not a snapshot. Therefore any modification you make to the
742          * returned list will be present inside the JAXB object.
743          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
744          * 
745          * &lt;p&gt;
746          * For example, to add a new item, do as follows:
747          * &lt;pre&gt;
748          *    getSetting().add(newItem);
749          * &lt;/pre&gt;
750          * 
751          * 
752          * &lt;p&gt;
753          * Objects of the following type(s) are allowed in the list
754          * {@link JalviewModel.FeatureSettings.Setting }
755          * 
756          * 
757          */
758         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
759             if (setting == null) {
760                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
761             }
762             return this.setting;
763         }
764
765         /**
766          * Gets the value of the group property.
767          * 
768          * &lt;p&gt;
769          * This accessor method returns a reference to the live list,
770          * not a snapshot. Therefore any modification you make to the
771          * returned list will be present inside the JAXB object.
772          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
773          * 
774          * &lt;p&gt;
775          * For example, to add a new item, do as follows:
776          * &lt;pre&gt;
777          *    getGroup().add(newItem);
778          * &lt;/pre&gt;
779          * 
780          * 
781          * &lt;p&gt;
782          * Objects of the following type(s) are allowed in the list
783          * {@link JalviewModel.FeatureSettings.Group }
784          * 
785          * 
786          */
787         public List<JalviewModel.FeatureSettings.Group> getGroup() {
788             if (group == null) {
789                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
790             }
791             return this.group;
792         }
793
794
795         /**
796          * &lt;p&gt;Java class for anonymous complex type.
797          * 
798          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
799          * 
800          * &lt;pre&gt;
801          * &amp;lt;complexType&amp;gt;
802          *   &amp;lt;complexContent&amp;gt;
803          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
804          *       &amp;lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
805          *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
806          *     &amp;lt;/restriction&amp;gt;
807          *   &amp;lt;/complexContent&amp;gt;
808          * &amp;lt;/complexType&amp;gt;
809          * &lt;/pre&gt;
810          * 
811          * 
812          */
813         @XmlAccessorType(XmlAccessType.FIELD)
814         @XmlType(name = "")
815         public static class Group {
816
817             @XmlAttribute(name = "name", required = true)
818             protected String name;
819             @XmlAttribute(name = "display", required = true)
820             protected boolean display;
821
822             /**
823              * Gets the value of the name property.
824              * 
825              * @return
826              *     possible object is
827              *     {@link String }
828              *     
829              */
830             public String getName() {
831                 return name;
832             }
833
834             /**
835              * Sets the value of the name property.
836              * 
837              * @param value
838              *     allowed object is
839              *     {@link String }
840              *     
841              */
842             public void setName(String value) {
843                 this.name = value;
844             }
845
846             /**
847              * Gets the value of the display property.
848              * 
849              */
850             public boolean isDisplay() {
851                 return display;
852             }
853
854             /**
855              * Sets the value of the display property.
856              * 
857              */
858             public void setDisplay(boolean value) {
859                 this.display = value;
860             }
861
862         }
863
864
865         /**
866          * &lt;p&gt;Java class for anonymous complex type.
867          * 
868          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
869          * 
870          * &lt;pre&gt;
871          * &amp;lt;complexType&amp;gt;
872          *   &amp;lt;complexContent&amp;gt;
873          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
874          *       &amp;lt;sequence&amp;gt;
875          *         &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
876          *         &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
877          *       &amp;lt;/sequence&amp;gt;
878          *       &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
879          *       &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
880          *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
881          *       &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
882          *       &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
883          *       &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
884          *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
885          *       &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
886          *       &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
887          *       &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
888          *       &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
889          *       &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
890          *     &amp;lt;/restriction&amp;gt;
891          *   &amp;lt;/complexContent&amp;gt;
892          * &amp;lt;/complexType&amp;gt;
893          * &lt;/pre&gt;
894          * 
895          * 
896          */
897         @XmlAccessorType(XmlAccessType.FIELD)
898         @XmlType(name = "", propOrder = {
899             "attributeName",
900             "matcherSet"
901         })
902         public static class Setting {
903
904             @XmlElement(namespace = "www.jalview.org")
905             protected List<String> attributeName;
906             @XmlElement(namespace = "www.jalview.org")
907             protected FeatureMatcherSet matcherSet;
908             @XmlAttribute(name = "type", required = true)
909             protected String type;
910             @XmlAttribute(name = "colour", required = true)
911             protected int colour;
912             @XmlAttribute(name = "display", required = true)
913             protected boolean display;
914             @XmlAttribute(name = "order")
915             protected Float order;
916             @XmlAttribute(name = "mincolour")
917             protected Integer mincolour;
918             @XmlAttribute(name = "noValueColour")
919             protected NoValueColour noValueColour;
920             @XmlAttribute(name = "threshold")
921             protected Float threshold;
922             @XmlAttribute(name = "threshstate")
923             protected Integer threshstate;
924             @XmlAttribute(name = "max")
925             protected Float max;
926             @XmlAttribute(name = "min")
927             protected Float min;
928             @XmlAttribute(name = "colourByLabel")
929             protected Boolean colourByLabel;
930             @XmlAttribute(name = "autoScale")
931             protected Boolean autoScale;
932
933             /**
934              * Gets the value of the attributeName property.
935              * 
936              * &lt;p&gt;
937              * This accessor method returns a reference to the live list,
938              * not a snapshot. Therefore any modification you make to the
939              * returned list will be present inside the JAXB object.
940              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
941              * 
942              * &lt;p&gt;
943              * For example, to add a new item, do as follows:
944              * &lt;pre&gt;
945              *    getAttributeName().add(newItem);
946              * &lt;/pre&gt;
947              * 
948              * 
949              * &lt;p&gt;
950              * Objects of the following type(s) are allowed in the list
951              * {@link String }
952              * 
953              * 
954              */
955             public List<String> getAttributeName() {
956                 if (attributeName == null) {
957                     attributeName = new ArrayList<String>();
958                 }
959                 return this.attributeName;
960             }
961
962             /**
963              * Gets the value of the matcherSet property.
964              * 
965              * @return
966              *     possible object is
967              *     {@link FeatureMatcherSet }
968              *     
969              */
970             public FeatureMatcherSet getMatcherSet() {
971                 return matcherSet;
972             }
973
974             /**
975              * Sets the value of the matcherSet property.
976              * 
977              * @param value
978              *     allowed object is
979              *     {@link FeatureMatcherSet }
980              *     
981              */
982             public void setMatcherSet(FeatureMatcherSet value) {
983                 this.matcherSet = value;
984             }
985
986             /**
987              * Gets the value of the type property.
988              * 
989              * @return
990              *     possible object is
991              *     {@link String }
992              *     
993              */
994             public String getType() {
995                 return type;
996             }
997
998             /**
999              * Sets the value of the type property.
1000              * 
1001              * @param value
1002              *     allowed object is
1003              *     {@link String }
1004              *     
1005              */
1006             public void setType(String value) {
1007                 this.type = value;
1008             }
1009
1010             /**
1011              * Gets the value of the colour property.
1012              * 
1013              */
1014             public int getColour() {
1015                 return colour;
1016             }
1017
1018             /**
1019              * Sets the value of the colour property.
1020              * 
1021              */
1022             public void setColour(int value) {
1023                 this.colour = value;
1024             }
1025
1026             /**
1027              * Gets the value of the display property.
1028              * 
1029              */
1030             public boolean isDisplay() {
1031                 return display;
1032             }
1033
1034             /**
1035              * Sets the value of the display property.
1036              * 
1037              */
1038             public void setDisplay(boolean value) {
1039                 this.display = value;
1040             }
1041
1042             /**
1043              * Gets the value of the order property.
1044              * 
1045              * @return
1046              *     possible object is
1047              *     {@link Float }
1048              *     
1049              */
1050             public Float getOrder() {
1051                 return order;
1052             }
1053
1054             /**
1055              * Sets the value of the order property.
1056              * 
1057              * @param value
1058              *     allowed object is
1059              *     {@link Float }
1060              *     
1061              */
1062             public void setOrder(Float value) {
1063                 this.order = value;
1064             }
1065
1066             /**
1067              * Gets the value of the mincolour property.
1068              * 
1069              * @return
1070              *     possible object is
1071              *     {@link Integer }
1072              *     
1073              */
1074             public Integer getMincolour() {
1075                 return mincolour;
1076             }
1077
1078             /**
1079              * Sets the value of the mincolour property.
1080              * 
1081              * @param value
1082              *     allowed object is
1083              *     {@link Integer }
1084              *     
1085              */
1086             public void setMincolour(Integer value) {
1087                 this.mincolour = value;
1088             }
1089
1090             /**
1091              * Gets the value of the noValueColour property.
1092              * 
1093              * @return
1094              *     possible object is
1095              *     {@link NoValueColour }
1096              *     
1097              */
1098             public NoValueColour getNoValueColour() {
1099                 if (noValueColour == null) {
1100                     return NoValueColour.MIN;
1101                 } else {
1102                     return noValueColour;
1103                 }
1104             }
1105
1106             /**
1107              * Sets the value of the noValueColour property.
1108              * 
1109              * @param value
1110              *     allowed object is
1111              *     {@link NoValueColour }
1112              *     
1113              */
1114             public void setNoValueColour(NoValueColour value) {
1115                 this.noValueColour = value;
1116             }
1117
1118             /**
1119              * Gets the value of the threshold property.
1120              * 
1121              * @return
1122              *     possible object is
1123              *     {@link Float }
1124              *     
1125              */
1126             public Float getThreshold() {
1127                 return threshold;
1128             }
1129
1130             /**
1131              * Sets the value of the threshold property.
1132              * 
1133              * @param value
1134              *     allowed object is
1135              *     {@link Float }
1136              *     
1137              */
1138             public void setThreshold(Float value) {
1139                 this.threshold = value;
1140             }
1141
1142             /**
1143              * Gets the value of the threshstate property.
1144              * 
1145              * @return
1146              *     possible object is
1147              *     {@link Integer }
1148              *     
1149              */
1150             public Integer getThreshstate() {
1151                 return threshstate;
1152             }
1153
1154             /**
1155              * Sets the value of the threshstate property.
1156              * 
1157              * @param value
1158              *     allowed object is
1159              *     {@link Integer }
1160              *     
1161              */
1162             public void setThreshstate(Integer value) {
1163                 this.threshstate = value;
1164             }
1165
1166             /**
1167              * Gets the value of the max property.
1168              * 
1169              * @return
1170              *     possible object is
1171              *     {@link Float }
1172              *     
1173              */
1174             public Float getMax() {
1175                 return max;
1176             }
1177
1178             /**
1179              * Sets the value of the max property.
1180              * 
1181              * @param value
1182              *     allowed object is
1183              *     {@link Float }
1184              *     
1185              */
1186             public void setMax(Float value) {
1187                 this.max = value;
1188             }
1189
1190             /**
1191              * Gets the value of the min property.
1192              * 
1193              * @return
1194              *     possible object is
1195              *     {@link Float }
1196              *     
1197              */
1198             public Float getMin() {
1199                 return min;
1200             }
1201
1202             /**
1203              * Sets the value of the min property.
1204              * 
1205              * @param value
1206              *     allowed object is
1207              *     {@link Float }
1208              *     
1209              */
1210             public void setMin(Float value) {
1211                 this.min = value;
1212             }
1213
1214             /**
1215              * Gets the value of the colourByLabel property.
1216              * 
1217              * @return
1218              *     possible object is
1219              *     {@link Boolean }
1220              *     
1221              */
1222             public Boolean isColourByLabel() {
1223                 return colourByLabel;
1224             }
1225
1226             /**
1227              * Sets the value of the colourByLabel property.
1228              * 
1229              * @param value
1230              *     allowed object is
1231              *     {@link Boolean }
1232              *     
1233              */
1234             public void setColourByLabel(Boolean value) {
1235                 this.colourByLabel = value;
1236             }
1237
1238             /**
1239              * Gets the value of the autoScale property.
1240              * 
1241              * @return
1242              *     possible object is
1243              *     {@link Boolean }
1244              *     
1245              */
1246             public Boolean isAutoScale() {
1247                 return autoScale;
1248             }
1249
1250             /**
1251              * Sets the value of the autoScale property.
1252              * 
1253              * @param value
1254              *     allowed object is
1255              *     {@link Boolean }
1256              *     
1257              */
1258             public void setAutoScale(Boolean value) {
1259                 this.autoScale = value;
1260             }
1261
1262         }
1263
1264     }
1265
1266
1267     /**
1268      * &lt;p&gt;Java class for anonymous complex type.
1269      * 
1270      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
1271      * 
1272      * &lt;pre&gt;
1273      * &amp;lt;complexType&amp;gt;
1274      *   &amp;lt;complexContent&amp;gt;
1275      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1276      *       &amp;lt;sequence&amp;gt;
1277      *         &amp;lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&amp;gt;
1278      *         &amp;lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
1279      *       &amp;lt;/sequence&amp;gt;
1280      *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1281      *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1282      *       &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1283      *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1284      *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1285      *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1286      *       &amp;lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1287      *       &amp;lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1288      *       &amp;lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1289      *       &amp;lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1290      *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1291      *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1292      *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1293      *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1294      *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1295      *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1296      *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1297      *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1298      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1299      *     &amp;lt;/restriction&amp;gt;
1300      *   &amp;lt;/complexContent&amp;gt;
1301      * &amp;lt;/complexType&amp;gt;
1302      * &lt;/pre&gt;
1303      * 
1304      * 
1305      */
1306     @XmlAccessorType(XmlAccessType.FIELD)
1307     @XmlType(name = "", propOrder = {
1308         "seq",
1309         "annotationColours"
1310     })
1311     public static class JGroup {
1312
1313         @XmlElement(namespace = "www.jalview.org", required = true)
1314         protected List<String> seq;
1315         @XmlElement(namespace = "www.jalview.org")
1316         protected AnnotationColourScheme annotationColours;
1317         @XmlAttribute(name = "start")
1318         protected Integer start;
1319         @XmlAttribute(name = "end")
1320         protected Integer end;
1321         @XmlAttribute(name = "name")
1322         protected String name;
1323         @XmlAttribute(name = "colour")
1324         protected String colour;
1325         @XmlAttribute(name = "consThreshold")
1326         protected Integer consThreshold;
1327         @XmlAttribute(name = "pidThreshold")
1328         protected Integer pidThreshold;
1329         @XmlAttribute(name = "outlineColour")
1330         protected Integer outlineColour;
1331         @XmlAttribute(name = "displayBoxes")
1332         protected Boolean displayBoxes;
1333         @XmlAttribute(name = "displayText")
1334         protected Boolean displayText;
1335         @XmlAttribute(name = "colourText")
1336         protected Boolean colourText;
1337         @XmlAttribute(name = "textCol1")
1338         protected Integer textCol1;
1339         @XmlAttribute(name = "textCol2")
1340         protected Integer textCol2;
1341         @XmlAttribute(name = "textColThreshold")
1342         protected Integer textColThreshold;
1343         @XmlAttribute(name = "showUnconserved")
1344         protected Boolean showUnconserved;
1345         @XmlAttribute(name = "ignoreGapsinConsensus")
1346         protected Boolean ignoreGapsinConsensus;
1347         @XmlAttribute(name = "showConsensusHistogram")
1348         protected Boolean showConsensusHistogram;
1349         @XmlAttribute(name = "showSequenceLogo")
1350         protected Boolean showSequenceLogo;
1351         @XmlAttribute(name = "normaliseSequenceLogo")
1352         protected Boolean normaliseSequenceLogo;
1353         @XmlAttribute(name = "id")
1354         protected String id;
1355
1356         /**
1357          * Gets the value of the seq property.
1358          * 
1359          * &lt;p&gt;
1360          * This accessor method returns a reference to the live list,
1361          * not a snapshot. Therefore any modification you make to the
1362          * returned list will be present inside the JAXB object.
1363          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
1364          * 
1365          * &lt;p&gt;
1366          * For example, to add a new item, do as follows:
1367          * &lt;pre&gt;
1368          *    getSeq().add(newItem);
1369          * &lt;/pre&gt;
1370          * 
1371          * 
1372          * &lt;p&gt;
1373          * Objects of the following type(s) are allowed in the list
1374          * {@link String }
1375          * 
1376          * 
1377          */
1378         public List<String> getSeq() {
1379             if (seq == null) {
1380                 seq = new ArrayList<String>();
1381             }
1382             return this.seq;
1383         }
1384
1385         /**
1386          * Gets the value of the annotationColours property.
1387          * 
1388          * @return
1389          *     possible object is
1390          *     {@link AnnotationColourScheme }
1391          *     
1392          */
1393         public AnnotationColourScheme getAnnotationColours() {
1394             return annotationColours;
1395         }
1396
1397         /**
1398          * Sets the value of the annotationColours property.
1399          * 
1400          * @param value
1401          *     allowed object is
1402          *     {@link AnnotationColourScheme }
1403          *     
1404          */
1405         public void setAnnotationColours(AnnotationColourScheme value) {
1406             this.annotationColours = value;
1407         }
1408
1409         /**
1410          * Gets the value of the start property.
1411          * 
1412          * @return
1413          *     possible object is
1414          *     {@link Integer }
1415          *     
1416          */
1417         public Integer getStart() {
1418             return start;
1419         }
1420
1421         /**
1422          * Sets the value of the start property.
1423          * 
1424          * @param value
1425          *     allowed object is
1426          *     {@link Integer }
1427          *     
1428          */
1429         public void setStart(Integer value) {
1430             this.start = value;
1431         }
1432
1433         /**
1434          * Gets the value of the end property.
1435          * 
1436          * @return
1437          *     possible object is
1438          *     {@link Integer }
1439          *     
1440          */
1441         public Integer getEnd() {
1442             return end;
1443         }
1444
1445         /**
1446          * Sets the value of the end property.
1447          * 
1448          * @param value
1449          *     allowed object is
1450          *     {@link Integer }
1451          *     
1452          */
1453         public void setEnd(Integer value) {
1454             this.end = value;
1455         }
1456
1457         /**
1458          * Gets the value of the name property.
1459          * 
1460          * @return
1461          *     possible object is
1462          *     {@link String }
1463          *     
1464          */
1465         public String getName() {
1466             return name;
1467         }
1468
1469         /**
1470          * Sets the value of the name property.
1471          * 
1472          * @param value
1473          *     allowed object is
1474          *     {@link String }
1475          *     
1476          */
1477         public void setName(String value) {
1478             this.name = value;
1479         }
1480
1481         /**
1482          * Gets the value of the colour property.
1483          * 
1484          * @return
1485          *     possible object is
1486          *     {@link String }
1487          *     
1488          */
1489         public String getColour() {
1490             return colour;
1491         }
1492
1493         /**
1494          * Sets the value of the colour property.
1495          * 
1496          * @param value
1497          *     allowed object is
1498          *     {@link String }
1499          *     
1500          */
1501         public void setColour(String value) {
1502             this.colour = value;
1503         }
1504
1505         /**
1506          * Gets the value of the consThreshold property.
1507          * 
1508          * @return
1509          *     possible object is
1510          *     {@link Integer }
1511          *     
1512          */
1513         public Integer getConsThreshold() {
1514             return consThreshold;
1515         }
1516
1517         /**
1518          * Sets the value of the consThreshold property.
1519          * 
1520          * @param value
1521          *     allowed object is
1522          *     {@link Integer }
1523          *     
1524          */
1525         public void setConsThreshold(Integer value) {
1526             this.consThreshold = value;
1527         }
1528
1529         /**
1530          * Gets the value of the pidThreshold property.
1531          * 
1532          * @return
1533          *     possible object is
1534          *     {@link Integer }
1535          *     
1536          */
1537         public Integer getPidThreshold() {
1538             return pidThreshold;
1539         }
1540
1541         /**
1542          * Sets the value of the pidThreshold property.
1543          * 
1544          * @param value
1545          *     allowed object is
1546          *     {@link Integer }
1547          *     
1548          */
1549         public void setPidThreshold(Integer value) {
1550             this.pidThreshold = value;
1551         }
1552
1553         /**
1554          * Gets the value of the outlineColour property.
1555          * 
1556          * @return
1557          *     possible object is
1558          *     {@link Integer }
1559          *     
1560          */
1561         public Integer getOutlineColour() {
1562             return outlineColour;
1563         }
1564
1565         /**
1566          * Sets the value of the outlineColour property.
1567          * 
1568          * @param value
1569          *     allowed object is
1570          *     {@link Integer }
1571          *     
1572          */
1573         public void setOutlineColour(Integer value) {
1574             this.outlineColour = value;
1575         }
1576
1577         /**
1578          * Gets the value of the displayBoxes property.
1579          * 
1580          * @return
1581          *     possible object is
1582          *     {@link Boolean }
1583          *     
1584          */
1585         public Boolean isDisplayBoxes() {
1586             return displayBoxes;
1587         }
1588
1589         /**
1590          * Sets the value of the displayBoxes property.
1591          * 
1592          * @param value
1593          *     allowed object is
1594          *     {@link Boolean }
1595          *     
1596          */
1597         public void setDisplayBoxes(Boolean value) {
1598             this.displayBoxes = value;
1599         }
1600
1601         /**
1602          * Gets the value of the displayText property.
1603          * 
1604          * @return
1605          *     possible object is
1606          *     {@link Boolean }
1607          *     
1608          */
1609         public Boolean isDisplayText() {
1610             return displayText;
1611         }
1612
1613         /**
1614          * Sets the value of the displayText property.
1615          * 
1616          * @param value
1617          *     allowed object is
1618          *     {@link Boolean }
1619          *     
1620          */
1621         public void setDisplayText(Boolean value) {
1622             this.displayText = value;
1623         }
1624
1625         /**
1626          * Gets the value of the colourText property.
1627          * 
1628          * @return
1629          *     possible object is
1630          *     {@link Boolean }
1631          *     
1632          */
1633         public Boolean isColourText() {
1634             return colourText;
1635         }
1636
1637         /**
1638          * Sets the value of the colourText property.
1639          * 
1640          * @param value
1641          *     allowed object is
1642          *     {@link Boolean }
1643          *     
1644          */
1645         public void setColourText(Boolean value) {
1646             this.colourText = value;
1647         }
1648
1649         /**
1650          * Gets the value of the textCol1 property.
1651          * 
1652          * @return
1653          *     possible object is
1654          *     {@link Integer }
1655          *     
1656          */
1657         public Integer getTextCol1() {
1658             return textCol1;
1659         }
1660
1661         /**
1662          * Sets the value of the textCol1 property.
1663          * 
1664          * @param value
1665          *     allowed object is
1666          *     {@link Integer }
1667          *     
1668          */
1669         public void setTextCol1(Integer value) {
1670             this.textCol1 = value;
1671         }
1672
1673         /**
1674          * Gets the value of the textCol2 property.
1675          * 
1676          * @return
1677          *     possible object is
1678          *     {@link Integer }
1679          *     
1680          */
1681         public Integer getTextCol2() {
1682             return textCol2;
1683         }
1684
1685         /**
1686          * Sets the value of the textCol2 property.
1687          * 
1688          * @param value
1689          *     allowed object is
1690          *     {@link Integer }
1691          *     
1692          */
1693         public void setTextCol2(Integer value) {
1694             this.textCol2 = value;
1695         }
1696
1697         /**
1698          * Gets the value of the textColThreshold property.
1699          * 
1700          * @return
1701          *     possible object is
1702          *     {@link Integer }
1703          *     
1704          */
1705         public Integer getTextColThreshold() {
1706             return textColThreshold;
1707         }
1708
1709         /**
1710          * Sets the value of the textColThreshold property.
1711          * 
1712          * @param value
1713          *     allowed object is
1714          *     {@link Integer }
1715          *     
1716          */
1717         public void setTextColThreshold(Integer value) {
1718             this.textColThreshold = value;
1719         }
1720
1721         /**
1722          * Gets the value of the showUnconserved property.
1723          * 
1724          * @return
1725          *     possible object is
1726          *     {@link Boolean }
1727          *     
1728          */
1729         public Boolean isShowUnconserved() {
1730             return showUnconserved;
1731         }
1732
1733         /**
1734          * Sets the value of the showUnconserved property.
1735          * 
1736          * @param value
1737          *     allowed object is
1738          *     {@link Boolean }
1739          *     
1740          */
1741         public void setShowUnconserved(Boolean value) {
1742             this.showUnconserved = value;
1743         }
1744
1745         /**
1746          * Gets the value of the ignoreGapsinConsensus property.
1747          * 
1748          * @return
1749          *     possible object is
1750          *     {@link Boolean }
1751          *     
1752          */
1753         public boolean isIgnoreGapsinConsensus() {
1754             if (ignoreGapsinConsensus == null) {
1755                 return true;
1756             } else {
1757                 return ignoreGapsinConsensus;
1758             }
1759         }
1760
1761         /**
1762          * Sets the value of the ignoreGapsinConsensus property.
1763          * 
1764          * @param value
1765          *     allowed object is
1766          *     {@link Boolean }
1767          *     
1768          */
1769         public void setIgnoreGapsinConsensus(Boolean value) {
1770             this.ignoreGapsinConsensus = value;
1771         }
1772
1773         /**
1774          * Gets the value of the showConsensusHistogram property.
1775          * 
1776          * @return
1777          *     possible object is
1778          *     {@link Boolean }
1779          *     
1780          */
1781         public boolean isShowConsensusHistogram() {
1782             if (showConsensusHistogram == null) {
1783                 return true;
1784             } else {
1785                 return showConsensusHistogram;
1786             }
1787         }
1788
1789         /**
1790          * Sets the value of the showConsensusHistogram property.
1791          * 
1792          * @param value
1793          *     allowed object is
1794          *     {@link Boolean }
1795          *     
1796          */
1797         public void setShowConsensusHistogram(Boolean value) {
1798             this.showConsensusHistogram = value;
1799         }
1800
1801         /**
1802          * Gets the value of the showSequenceLogo property.
1803          * 
1804          * @return
1805          *     possible object is
1806          *     {@link Boolean }
1807          *     
1808          */
1809         public boolean isShowSequenceLogo() {
1810             if (showSequenceLogo == null) {
1811                 return false;
1812             } else {
1813                 return showSequenceLogo;
1814             }
1815         }
1816
1817         /**
1818          * Sets the value of the showSequenceLogo property.
1819          * 
1820          * @param value
1821          *     allowed object is
1822          *     {@link Boolean }
1823          *     
1824          */
1825         public void setShowSequenceLogo(Boolean value) {
1826             this.showSequenceLogo = value;
1827         }
1828
1829         /**
1830          * Gets the value of the normaliseSequenceLogo property.
1831          * 
1832          * @return
1833          *     possible object is
1834          *     {@link Boolean }
1835          *     
1836          */
1837         public boolean isNormaliseSequenceLogo() {
1838             if (normaliseSequenceLogo == null) {
1839                 return false;
1840             } else {
1841                 return normaliseSequenceLogo;
1842             }
1843         }
1844
1845         /**
1846          * Sets the value of the normaliseSequenceLogo property.
1847          * 
1848          * @param value
1849          *     allowed object is
1850          *     {@link Boolean }
1851          *     
1852          */
1853         public void setNormaliseSequenceLogo(Boolean value) {
1854             this.normaliseSequenceLogo = value;
1855         }
1856
1857         /**
1858          * Gets the value of the id property.
1859          * 
1860          * @return
1861          *     possible object is
1862          *     {@link String }
1863          *     
1864          */
1865         public String getId() {
1866             return id;
1867         }
1868
1869         /**
1870          * Sets the value of the id property.
1871          * 
1872          * @param value
1873          *     allowed object is
1874          *     {@link String }
1875          *     
1876          */
1877         public void setId(String value) {
1878             this.id = value;
1879         }
1880
1881     }
1882
1883
1884     /**
1885      * &lt;p&gt;Java class for anonymous complex type.
1886      * 
1887      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
1888      * 
1889      * &lt;pre&gt;
1890      * &amp;lt;complexType&amp;gt;
1891      *   &amp;lt;complexContent&amp;gt;
1892      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1893      *       &amp;lt;sequence&amp;gt;
1894      *         &amp;lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
1895      *         &amp;lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&amp;gt;
1896      *           &amp;lt;complexType&amp;gt;
1897      *             &amp;lt;complexContent&amp;gt;
1898      *               &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
1899      *                 &amp;lt;sequence&amp;gt;
1900      *                   &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
1901      *                     &amp;lt;complexType&amp;gt;
1902      *                       &amp;lt;simpleContent&amp;gt;
1903      *                         &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
1904      *                           &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
1905      *                           &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1906      *                           &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1907      *                           &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1908      *                           &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1909      *                           &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1910      *                           &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1911      *                         &amp;lt;/extension&amp;gt;
1912      *                       &amp;lt;/simpleContent&amp;gt;
1913      *                     &amp;lt;/complexType&amp;gt;
1914      *                   &amp;lt;/element&amp;gt;
1915      *                 &amp;lt;/sequence&amp;gt;
1916      *               &amp;lt;/extension&amp;gt;
1917      *             &amp;lt;/complexContent&amp;gt;
1918      *           &amp;lt;/complexType&amp;gt;
1919      *         &amp;lt;/element&amp;gt;
1920      *         &amp;lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
1921      *         &amp;lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&amp;gt;
1922      *           &amp;lt;complexType&amp;gt;
1923      *             &amp;lt;complexContent&amp;gt;
1924      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1925      *                 &amp;lt;sequence&amp;gt;
1926      *                   &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
1927      *                     &amp;lt;complexType&amp;gt;
1928      *                       &amp;lt;complexContent&amp;gt;
1929      *                         &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1930      *                           &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1931      *                           &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1932      *                           &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1933      *                           &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1934      *                         &amp;lt;/restriction&amp;gt;
1935      *                       &amp;lt;/complexContent&amp;gt;
1936      *                     &amp;lt;/complexType&amp;gt;
1937      *                   &amp;lt;/element&amp;gt;
1938      *                 &amp;lt;/sequence&amp;gt;
1939      *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
1940      *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1941      *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1942      *                 &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1943      *                 &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1944      *               &amp;lt;/restriction&amp;gt;
1945      *             &amp;lt;/complexContent&amp;gt;
1946      *           &amp;lt;/complexType&amp;gt;
1947      *         &amp;lt;/element&amp;gt;
1948      *       &amp;lt;/sequence&amp;gt;
1949      *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1950      *       &amp;lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1951      *       &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1952      *       &amp;lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1953      *       &amp;lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1954      *       &amp;lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1955      *     &amp;lt;/restriction&amp;gt;
1956      *   &amp;lt;/complexContent&amp;gt;
1957      * &amp;lt;/complexType&amp;gt;
1958      * &lt;/pre&gt;
1959      * 
1960      * 
1961      */
1962     @XmlAccessorType(XmlAccessType.FIELD)
1963     @XmlType(name = "", propOrder = {
1964         "features",
1965         "pdbids",
1966         "hiddenSequences",
1967         "rnaViewer",
1968         "hmmerProfile"
1969     })
1970     public static class JSeq {
1971
1972         @XmlElement(namespace = "www.jalview.org")
1973         protected List<Feature> features;
1974         @XmlElement(namespace = "www.jalview.org")
1975         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1976         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1977         protected List<Integer> hiddenSequences;
1978         @XmlElement(namespace = "www.jalview.org")
1979         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1980         @XmlElement(namespace = "www.jalview.org")
1981         protected String hmmerProfile;
1982         @XmlAttribute(name = "colour")
1983         protected Integer colour;
1984         @XmlAttribute(name = "start", required = true)
1985         protected int start;
1986         @XmlAttribute(name = "end", required = true)
1987         protected int end;
1988         @XmlAttribute(name = "id", required = true)
1989         protected String id;
1990         @XmlAttribute(name = "hidden")
1991         protected Boolean hidden;
1992         @XmlAttribute(name = "viewreference")
1993         protected Boolean viewreference;
1994
1995         /**
1996          * Gets the value of the features property.
1997          * 
1998          * &lt;p&gt;
1999          * This accessor method returns a reference to the live list,
2000          * not a snapshot. Therefore any modification you make to the
2001          * returned list will be present inside the JAXB object.
2002          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
2003          * 
2004          * &lt;p&gt;
2005          * For example, to add a new item, do as follows:
2006          * &lt;pre&gt;
2007          *    getFeatures().add(newItem);
2008          * &lt;/pre&gt;
2009          * 
2010          * 
2011          * &lt;p&gt;
2012          * Objects of the following type(s) are allowed in the list
2013          * {@link Feature }
2014          * 
2015          * 
2016          */
2017         public List<Feature> getFeatures() {
2018             if (features == null) {
2019                 features = new ArrayList<Feature>();
2020             }
2021             return this.features;
2022         }
2023
2024         /**
2025          * Gets the value of the pdbids property.
2026          * 
2027          * &lt;p&gt;
2028          * This accessor method returns a reference to the live list,
2029          * not a snapshot. Therefore any modification you make to the
2030          * returned list will be present inside the JAXB object.
2031          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
2032          * 
2033          * &lt;p&gt;
2034          * For example, to add a new item, do as follows:
2035          * &lt;pre&gt;
2036          *    getPdbids().add(newItem);
2037          * &lt;/pre&gt;
2038          * 
2039          * 
2040          * &lt;p&gt;
2041          * Objects of the following type(s) are allowed in the list
2042          * {@link JalviewModel.JSeq.Pdbids }
2043          * 
2044          * 
2045          */
2046         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2047             if (pdbids == null) {
2048                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2049             }
2050             return this.pdbids;
2051         }
2052
2053         /**
2054          * Gets the value of the hiddenSequences property.
2055          * 
2056          * &lt;p&gt;
2057          * This accessor method returns a reference to the live list,
2058          * not a snapshot. Therefore any modification you make to the
2059          * returned list will be present inside the JAXB object.
2060          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
2061          * 
2062          * &lt;p&gt;
2063          * For example, to add a new item, do as follows:
2064          * &lt;pre&gt;
2065          *    getHiddenSequences().add(newItem);
2066          * &lt;/pre&gt;
2067          * 
2068          * 
2069          * &lt;p&gt;
2070          * Objects of the following type(s) are allowed in the list
2071          * {@link Integer }
2072          * 
2073          * 
2074          */
2075         public List<Integer> getHiddenSequences() {
2076             if (hiddenSequences == null) {
2077                 hiddenSequences = new ArrayList<Integer>();
2078             }
2079             return this.hiddenSequences;
2080         }
2081
2082         /**
2083          * Gets the value of the rnaViewer property.
2084          * 
2085          * &lt;p&gt;
2086          * This accessor method returns a reference to the live list,
2087          * not a snapshot. Therefore any modification you make to the
2088          * returned list will be present inside the JAXB object.
2089          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
2090          * 
2091          * &lt;p&gt;
2092          * For example, to add a new item, do as follows:
2093          * &lt;pre&gt;
2094          *    getRnaViewer().add(newItem);
2095          * &lt;/pre&gt;
2096          * 
2097          * 
2098          * &lt;p&gt;
2099          * Objects of the following type(s) are allowed in the list
2100          * {@link JalviewModel.JSeq.RnaViewer }
2101          * 
2102          * 
2103          */
2104         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2105             if (rnaViewer == null) {
2106                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2107             }
2108             return this.rnaViewer;
2109         }
2110
2111         /**
2112          * Gets the value of the hmmerProfile property.
2113          * 
2114          * @return
2115          *     possible object is
2116          *     {@link String }
2117          *     
2118          */
2119         public String getHmmerProfile() {
2120             return hmmerProfile;
2121         }
2122
2123         /**
2124          * Sets the value of the hmmerProfile property.
2125          * 
2126          * @param value
2127          *     allowed object is
2128          *     {@link String }
2129          *     
2130          */
2131         public void setHmmerProfile(String value) {
2132             this.hmmerProfile = value;
2133         }
2134
2135         /**
2136          * Gets the value of the colour property.
2137          * 
2138          * @return
2139          *     possible object is
2140          *     {@link Integer }
2141          *     
2142          */
2143         public Integer getColour() {
2144             return colour;
2145         }
2146
2147         /**
2148          * Sets the value of the colour property.
2149          * 
2150          * @param value
2151          *     allowed object is
2152          *     {@link Integer }
2153          *     
2154          */
2155         public void setColour(Integer value) {
2156             this.colour = value;
2157         }
2158
2159         /**
2160          * Gets the value of the start property.
2161          * 
2162          */
2163         public int getStart() {
2164             return start;
2165         }
2166
2167         /**
2168          * Sets the value of the start property.
2169          * 
2170          */
2171         public void setStart(int value) {
2172             this.start = value;
2173         }
2174
2175         /**
2176          * Gets the value of the end property.
2177          * 
2178          */
2179         public int getEnd() {
2180             return end;
2181         }
2182
2183         /**
2184          * Sets the value of the end property.
2185          * 
2186          */
2187         public void setEnd(int value) {
2188             this.end = value;
2189         }
2190
2191         /**
2192          * Gets the value of the id property.
2193          * 
2194          * @return
2195          *     possible object is
2196          *     {@link String }
2197          *     
2198          */
2199         public String getId() {
2200             return id;
2201         }
2202
2203         /**
2204          * Sets the value of the id property.
2205          * 
2206          * @param value
2207          *     allowed object is
2208          *     {@link String }
2209          *     
2210          */
2211         public void setId(String value) {
2212             this.id = value;
2213         }
2214
2215         /**
2216          * Gets the value of the hidden property.
2217          * 
2218          * @return
2219          *     possible object is
2220          *     {@link Boolean }
2221          *     
2222          */
2223         public Boolean isHidden() {
2224             return hidden;
2225         }
2226
2227         /**
2228          * Sets the value of the hidden property.
2229          * 
2230          * @param value
2231          *     allowed object is
2232          *     {@link Boolean }
2233          *     
2234          */
2235         public void setHidden(Boolean value) {
2236             this.hidden = value;
2237         }
2238
2239         /**
2240          * Gets the value of the viewreference property.
2241          * 
2242          * @return
2243          *     possible object is
2244          *     {@link Boolean }
2245          *     
2246          */
2247         public Boolean isViewreference() {
2248             return viewreference;
2249         }
2250
2251         /**
2252          * Sets the value of the viewreference property.
2253          * 
2254          * @param value
2255          *     allowed object is
2256          *     {@link Boolean }
2257          *     
2258          */
2259         public void setViewreference(Boolean value) {
2260             this.viewreference = value;
2261         }
2262
2263
2264         /**
2265          * &lt;p&gt;Java class for anonymous complex type.
2266          * 
2267          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2268          * 
2269          * &lt;pre&gt;
2270          * &amp;lt;complexType&amp;gt;
2271          *   &amp;lt;complexContent&amp;gt;
2272          *     &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
2273          *       &amp;lt;sequence&amp;gt;
2274          *         &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
2275          *           &amp;lt;complexType&amp;gt;
2276          *             &amp;lt;simpleContent&amp;gt;
2277          *               &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2278          *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2279          *                 &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2280          *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2281          *                 &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2282          *                 &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
2283          *                 &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2284          *                 &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2285          *               &amp;lt;/extension&amp;gt;
2286          *             &amp;lt;/simpleContent&amp;gt;
2287          *           &amp;lt;/complexType&amp;gt;
2288          *         &amp;lt;/element&amp;gt;
2289          *       &amp;lt;/sequence&amp;gt;
2290          *     &amp;lt;/extension&amp;gt;
2291          *   &amp;lt;/complexContent&amp;gt;
2292          * &amp;lt;/complexType&amp;gt;
2293          * &lt;/pre&gt;
2294          * 
2295          * 
2296          */
2297         @XmlAccessorType(XmlAccessType.FIELD)
2298         @XmlType(name = "", propOrder = {
2299             "structureState"
2300         })
2301         public static class Pdbids
2302             extends Pdbentry
2303         {
2304
2305             @XmlElement(namespace = "www.jalview.org")
2306             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2307
2308             /**
2309              * Gets the value of the structureState property.
2310              * 
2311              * &lt;p&gt;
2312              * This accessor method returns a reference to the live list,
2313              * not a snapshot. Therefore any modification you make to the
2314              * returned list will be present inside the JAXB object.
2315              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
2316              * 
2317              * &lt;p&gt;
2318              * For example, to add a new item, do as follows:
2319              * &lt;pre&gt;
2320              *    getStructureState().add(newItem);
2321              * &lt;/pre&gt;
2322              * 
2323              * 
2324              * &lt;p&gt;
2325              * Objects of the following type(s) are allowed in the list
2326              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2327              * 
2328              * 
2329              */
2330             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2331                 if (structureState == null) {
2332                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2333                 }
2334                 return this.structureState;
2335             }
2336
2337
2338             /**
2339              * &lt;p&gt;Java class for anonymous complex type.
2340              * 
2341              * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2342              * 
2343              * &lt;pre&gt;
2344              * &amp;lt;complexType&amp;gt;
2345              *   &amp;lt;simpleContent&amp;gt;
2346              *     &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2347              *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2348              *       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2349              *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2350              *       &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2351              *       &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
2352              *       &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2353              *       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2354              *     &amp;lt;/extension&amp;gt;
2355              *   &amp;lt;/simpleContent&amp;gt;
2356              * &amp;lt;/complexType&amp;gt;
2357              * &lt;/pre&gt;
2358              * 
2359              * 
2360              */
2361             @XmlAccessorType(XmlAccessType.FIELD)
2362             @XmlType(name = "", propOrder = {
2363                 "value"
2364             })
2365             public static class StructureState {
2366
2367                 @XmlValue
2368                 protected String value;
2369                 @XmlAttribute(name = "visible")
2370                 protected Boolean visible;
2371                 @XmlAttribute(name = "viewId")
2372                 protected String viewId;
2373                 @XmlAttribute(name = "alignwithAlignPanel")
2374                 protected Boolean alignwithAlignPanel;
2375                 @XmlAttribute(name = "colourwithAlignPanel")
2376                 protected Boolean colourwithAlignPanel;
2377                 @XmlAttribute(name = "colourByJmol")
2378                 protected Boolean colourByJmol;
2379                 @XmlAttribute(name = "type")
2380                 protected String type;
2381                 @XmlAttribute(name = "width")
2382                 protected Integer width;
2383                 @XmlAttribute(name = "height")
2384                 protected Integer height;
2385                 @XmlAttribute(name = "xpos")
2386                 protected Integer xpos;
2387                 @XmlAttribute(name = "ypos")
2388                 protected Integer ypos;
2389
2390                 /**
2391                  * Gets the value of the value property.
2392                  * 
2393                  * @return
2394                  *     possible object is
2395                  *     {@link String }
2396                  *     
2397                  */
2398                 public String getValue() {
2399                     return value;
2400                 }
2401
2402                 /**
2403                  * Sets the value of the value property.
2404                  * 
2405                  * @param value
2406                  *     allowed object is
2407                  *     {@link String }
2408                  *     
2409                  */
2410                 public void setValue(String value) {
2411                     this.value = value;
2412                 }
2413
2414                 /**
2415                  * Gets the value of the visible property.
2416                  * 
2417                  * @return
2418                  *     possible object is
2419                  *     {@link Boolean }
2420                  *     
2421                  */
2422                 public Boolean isVisible() {
2423                     return visible;
2424                 }
2425
2426                 /**
2427                  * Sets the value of the visible property.
2428                  * 
2429                  * @param value
2430                  *     allowed object is
2431                  *     {@link Boolean }
2432                  *     
2433                  */
2434                 public void setVisible(Boolean value) {
2435                     this.visible = value;
2436                 }
2437
2438                 /**
2439                  * Gets the value of the viewId property.
2440                  * 
2441                  * @return
2442                  *     possible object is
2443                  *     {@link String }
2444                  *     
2445                  */
2446                 public String getViewId() {
2447                     return viewId;
2448                 }
2449
2450                 /**
2451                  * Sets the value of the viewId property.
2452                  * 
2453                  * @param value
2454                  *     allowed object is
2455                  *     {@link String }
2456                  *     
2457                  */
2458                 public void setViewId(String value) {
2459                     this.viewId = value;
2460                 }
2461
2462                 /**
2463                  * Gets the value of the alignwithAlignPanel property.
2464                  * 
2465                  * @return
2466                  *     possible object is
2467                  *     {@link Boolean }
2468                  *     
2469                  */
2470                 public boolean isAlignwithAlignPanel() {
2471                     if (alignwithAlignPanel == null) {
2472                         return true;
2473                     } else {
2474                         return alignwithAlignPanel;
2475                     }
2476                 }
2477
2478                 /**
2479                  * Sets the value of the alignwithAlignPanel property.
2480                  * 
2481                  * @param value
2482                  *     allowed object is
2483                  *     {@link Boolean }
2484                  *     
2485                  */
2486                 public void setAlignwithAlignPanel(Boolean value) {
2487                     this.alignwithAlignPanel = value;
2488                 }
2489
2490                 /**
2491                  * Gets the value of the colourwithAlignPanel property.
2492                  * 
2493                  * @return
2494                  *     possible object is
2495                  *     {@link Boolean }
2496                  *     
2497                  */
2498                 public boolean isColourwithAlignPanel() {
2499                     if (colourwithAlignPanel == null) {
2500                         return false;
2501                     } else {
2502                         return colourwithAlignPanel;
2503                     }
2504                 }
2505
2506                 /**
2507                  * Sets the value of the colourwithAlignPanel property.
2508                  * 
2509                  * @param value
2510                  *     allowed object is
2511                  *     {@link Boolean }
2512                  *     
2513                  */
2514                 public void setColourwithAlignPanel(Boolean value) {
2515                     this.colourwithAlignPanel = value;
2516                 }
2517
2518                 /**
2519                  * Gets the value of the colourByJmol property.
2520                  * 
2521                  * @return
2522                  *     possible object is
2523                  *     {@link Boolean }
2524                  *     
2525                  */
2526                 public boolean isColourByJmol() {
2527                     if (colourByJmol == null) {
2528                         return true;
2529                     } else {
2530                         return colourByJmol;
2531                     }
2532                 }
2533
2534                 /**
2535                  * Sets the value of the colourByJmol property.
2536                  * 
2537                  * @param value
2538                  *     allowed object is
2539                  *     {@link Boolean }
2540                  *     
2541                  */
2542                 public void setColourByJmol(Boolean value) {
2543                     this.colourByJmol = value;
2544                 }
2545
2546                 /**
2547                  * Gets the value of the type property.
2548                  * 
2549                  * @return
2550                  *     possible object is
2551                  *     {@link String }
2552                  *     
2553                  */
2554                 public String getType() {
2555                     return type;
2556                 }
2557
2558                 /**
2559                  * Sets the value of the type property.
2560                  * 
2561                  * @param value
2562                  *     allowed object is
2563                  *     {@link String }
2564                  *     
2565                  */
2566                 public void setType(String value) {
2567                     this.type = value;
2568                 }
2569
2570                 /**
2571                  * Gets the value of the width property.
2572                  * 
2573                  * @return
2574                  *     possible object is
2575                  *     {@link Integer }
2576                  *     
2577                  */
2578                 public Integer getWidth() {
2579                     return width;
2580                 }
2581
2582                 /**
2583                  * Sets the value of the width property.
2584                  * 
2585                  * @param value
2586                  *     allowed object is
2587                  *     {@link Integer }
2588                  *     
2589                  */
2590                 public void setWidth(Integer value) {
2591                     this.width = value;
2592                 }
2593
2594                 /**
2595                  * Gets the value of the height property.
2596                  * 
2597                  * @return
2598                  *     possible object is
2599                  *     {@link Integer }
2600                  *     
2601                  */
2602                 public Integer getHeight() {
2603                     return height;
2604                 }
2605
2606                 /**
2607                  * Sets the value of the height property.
2608                  * 
2609                  * @param value
2610                  *     allowed object is
2611                  *     {@link Integer }
2612                  *     
2613                  */
2614                 public void setHeight(Integer value) {
2615                     this.height = value;
2616                 }
2617
2618                 /**
2619                  * Gets the value of the xpos property.
2620                  * 
2621                  * @return
2622                  *     possible object is
2623                  *     {@link Integer }
2624                  *     
2625                  */
2626                 public Integer getXpos() {
2627                     return xpos;
2628                 }
2629
2630                 /**
2631                  * Sets the value of the xpos property.
2632                  * 
2633                  * @param value
2634                  *     allowed object is
2635                  *     {@link Integer }
2636                  *     
2637                  */
2638                 public void setXpos(Integer value) {
2639                     this.xpos = value;
2640                 }
2641
2642                 /**
2643                  * Gets the value of the ypos property.
2644                  * 
2645                  * @return
2646                  *     possible object is
2647                  *     {@link Integer }
2648                  *     
2649                  */
2650                 public Integer getYpos() {
2651                     return ypos;
2652                 }
2653
2654                 /**
2655                  * Sets the value of the ypos property.
2656                  * 
2657                  * @param value
2658                  *     allowed object is
2659                  *     {@link Integer }
2660                  *     
2661                  */
2662                 public void setYpos(Integer value) {
2663                     this.ypos = value;
2664                 }
2665
2666             }
2667
2668         }
2669
2670
2671         /**
2672          * &lt;p&gt;Java class for anonymous complex type.
2673          * 
2674          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2675          * 
2676          * &lt;pre&gt;
2677          * &amp;lt;complexType&amp;gt;
2678          *   &amp;lt;complexContent&amp;gt;
2679          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2680          *       &amp;lt;sequence&amp;gt;
2681          *         &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
2682          *           &amp;lt;complexType&amp;gt;
2683          *             &amp;lt;complexContent&amp;gt;
2684          *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2685          *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2686          *                 &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2687          *                 &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2688          *                 &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2689          *               &amp;lt;/restriction&amp;gt;
2690          *             &amp;lt;/complexContent&amp;gt;
2691          *           &amp;lt;/complexType&amp;gt;
2692          *         &amp;lt;/element&amp;gt;
2693          *       &amp;lt;/sequence&amp;gt;
2694          *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2695          *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2696          *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2697          *       &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2698          *       &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2699          *     &amp;lt;/restriction&amp;gt;
2700          *   &amp;lt;/complexContent&amp;gt;
2701          * &amp;lt;/complexType&amp;gt;
2702          * &lt;/pre&gt;
2703          * 
2704          * 
2705          */
2706         @XmlAccessorType(XmlAccessType.FIELD)
2707         @XmlType(name = "", propOrder = {
2708             "secondaryStructure"
2709         })
2710         public static class RnaViewer {
2711
2712             @XmlElement(namespace = "www.jalview.org", required = true)
2713             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2714             @XmlAttribute(name = "title")
2715             protected String title;
2716             @XmlAttribute(name = "viewId")
2717             protected String viewId;
2718             @XmlAttribute(name = "dividerLocation")
2719             protected Integer dividerLocation;
2720             @XmlAttribute(name = "selectedRna")
2721             protected Integer selectedRna;
2722             @XmlAttribute(name = "width")
2723             protected Integer width;
2724             @XmlAttribute(name = "height")
2725             protected Integer height;
2726             @XmlAttribute(name = "xpos")
2727             protected Integer xpos;
2728             @XmlAttribute(name = "ypos")
2729             protected Integer ypos;
2730
2731             /**
2732              * Gets the value of the secondaryStructure property.
2733              * 
2734              * &lt;p&gt;
2735              * This accessor method returns a reference to the live list,
2736              * not a snapshot. Therefore any modification you make to the
2737              * returned list will be present inside the JAXB object.
2738              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure property.
2739              * 
2740              * &lt;p&gt;
2741              * For example, to add a new item, do as follows:
2742              * &lt;pre&gt;
2743              *    getSecondaryStructure().add(newItem);
2744              * &lt;/pre&gt;
2745              * 
2746              * 
2747              * &lt;p&gt;
2748              * Objects of the following type(s) are allowed in the list
2749              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2750              * 
2751              * 
2752              */
2753             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2754                 if (secondaryStructure == null) {
2755                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2756                 }
2757                 return this.secondaryStructure;
2758             }
2759
2760             /**
2761              * Gets the value of the title property.
2762              * 
2763              * @return
2764              *     possible object is
2765              *     {@link String }
2766              *     
2767              */
2768             public String getTitle() {
2769                 return title;
2770             }
2771
2772             /**
2773              * Sets the value of the title property.
2774              * 
2775              * @param value
2776              *     allowed object is
2777              *     {@link String }
2778              *     
2779              */
2780             public void setTitle(String value) {
2781                 this.title = value;
2782             }
2783
2784             /**
2785              * Gets the value of the viewId property.
2786              * 
2787              * @return
2788              *     possible object is
2789              *     {@link String }
2790              *     
2791              */
2792             public String getViewId() {
2793                 return viewId;
2794             }
2795
2796             /**
2797              * Sets the value of the viewId property.
2798              * 
2799              * @param value
2800              *     allowed object is
2801              *     {@link String }
2802              *     
2803              */
2804             public void setViewId(String value) {
2805                 this.viewId = value;
2806             }
2807
2808             /**
2809              * Gets the value of the dividerLocation property.
2810              * 
2811              * @return
2812              *     possible object is
2813              *     {@link Integer }
2814              *     
2815              */
2816             public Integer getDividerLocation() {
2817                 return dividerLocation;
2818             }
2819
2820             /**
2821              * Sets the value of the dividerLocation property.
2822              * 
2823              * @param value
2824              *     allowed object is
2825              *     {@link Integer }
2826              *     
2827              */
2828             public void setDividerLocation(Integer value) {
2829                 this.dividerLocation = value;
2830             }
2831
2832             /**
2833              * Gets the value of the selectedRna property.
2834              * 
2835              * @return
2836              *     possible object is
2837              *     {@link Integer }
2838              *     
2839              */
2840             public Integer getSelectedRna() {
2841                 return selectedRna;
2842             }
2843
2844             /**
2845              * Sets the value of the selectedRna property.
2846              * 
2847              * @param value
2848              *     allowed object is
2849              *     {@link Integer }
2850              *     
2851              */
2852             public void setSelectedRna(Integer value) {
2853                 this.selectedRna = value;
2854             }
2855
2856             /**
2857              * Gets the value of the width property.
2858              * 
2859              * @return
2860              *     possible object is
2861              *     {@link Integer }
2862              *     
2863              */
2864             public Integer getWidth() {
2865                 return width;
2866             }
2867
2868             /**
2869              * Sets the value of the width property.
2870              * 
2871              * @param value
2872              *     allowed object is
2873              *     {@link Integer }
2874              *     
2875              */
2876             public void setWidth(Integer value) {
2877                 this.width = value;
2878             }
2879
2880             /**
2881              * Gets the value of the height property.
2882              * 
2883              * @return
2884              *     possible object is
2885              *     {@link Integer }
2886              *     
2887              */
2888             public Integer getHeight() {
2889                 return height;
2890             }
2891
2892             /**
2893              * Sets the value of the height property.
2894              * 
2895              * @param value
2896              *     allowed object is
2897              *     {@link Integer }
2898              *     
2899              */
2900             public void setHeight(Integer value) {
2901                 this.height = value;
2902             }
2903
2904             /**
2905              * Gets the value of the xpos property.
2906              * 
2907              * @return
2908              *     possible object is
2909              *     {@link Integer }
2910              *     
2911              */
2912             public Integer getXpos() {
2913                 return xpos;
2914             }
2915
2916             /**
2917              * Sets the value of the xpos property.
2918              * 
2919              * @param value
2920              *     allowed object is
2921              *     {@link Integer }
2922              *     
2923              */
2924             public void setXpos(Integer value) {
2925                 this.xpos = value;
2926             }
2927
2928             /**
2929              * Gets the value of the ypos property.
2930              * 
2931              * @return
2932              *     possible object is
2933              *     {@link Integer }
2934              *     
2935              */
2936             public Integer getYpos() {
2937                 return ypos;
2938             }
2939
2940             /**
2941              * Sets the value of the ypos property.
2942              * 
2943              * @param value
2944              *     allowed object is
2945              *     {@link Integer }
2946              *     
2947              */
2948             public void setYpos(Integer value) {
2949                 this.ypos = value;
2950             }
2951
2952
2953             /**
2954              * &lt;p&gt;Java class for anonymous complex type.
2955              * 
2956              * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2957              * 
2958              * &lt;pre&gt;
2959              * &amp;lt;complexType&amp;gt;
2960              *   &amp;lt;complexContent&amp;gt;
2961              *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2962              *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2963              *       &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2964              *       &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2965              *       &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2966              *     &amp;lt;/restriction&amp;gt;
2967              *   &amp;lt;/complexContent&amp;gt;
2968              * &amp;lt;/complexType&amp;gt;
2969              * &lt;/pre&gt;
2970              * 
2971              * 
2972              */
2973             @XmlAccessorType(XmlAccessType.FIELD)
2974             @XmlType(name = "")
2975             public static class SecondaryStructure {
2976
2977                 @XmlAttribute(name = "title")
2978                 protected String title;
2979                 @XmlAttribute(name = "annotationId", required = true)
2980                 protected String annotationId;
2981                 @XmlAttribute(name = "gapped")
2982                 protected Boolean gapped;
2983                 @XmlAttribute(name = "viewerState")
2984                 protected String viewerState;
2985
2986                 /**
2987                  * Gets the value of the title property.
2988                  * 
2989                  * @return
2990                  *     possible object is
2991                  *     {@link String }
2992                  *     
2993                  */
2994                 public String getTitle() {
2995                     return title;
2996                 }
2997
2998                 /**
2999                  * Sets the value of the title property.
3000                  * 
3001                  * @param value
3002                  *     allowed object is
3003                  *     {@link String }
3004                  *     
3005                  */
3006                 public void setTitle(String value) {
3007                     this.title = value;
3008                 }
3009
3010                 /**
3011                  * Gets the value of the annotationId property.
3012                  * 
3013                  * @return
3014                  *     possible object is
3015                  *     {@link String }
3016                  *     
3017                  */
3018                 public String getAnnotationId() {
3019                     return annotationId;
3020                 }
3021
3022                 /**
3023                  * Sets the value of the annotationId property.
3024                  * 
3025                  * @param value
3026                  *     allowed object is
3027                  *     {@link String }
3028                  *     
3029                  */
3030                 public void setAnnotationId(String value) {
3031                     this.annotationId = value;
3032                 }
3033
3034                 /**
3035                  * Gets the value of the gapped property.
3036                  * 
3037                  * @return
3038                  *     possible object is
3039                  *     {@link Boolean }
3040                  *     
3041                  */
3042                 public Boolean isGapped() {
3043                     return gapped;
3044                 }
3045
3046                 /**
3047                  * Sets the value of the gapped property.
3048                  * 
3049                  * @param value
3050                  *     allowed object is
3051                  *     {@link Boolean }
3052                  *     
3053                  */
3054                 public void setGapped(Boolean value) {
3055                     this.gapped = value;
3056                 }
3057
3058                 /**
3059                  * Gets the value of the viewerState property.
3060                  * 
3061                  * @return
3062                  *     possible object is
3063                  *     {@link String }
3064                  *     
3065                  */
3066                 public String getViewerState() {
3067                     return viewerState;
3068                 }
3069
3070                 /**
3071                  * Sets the value of the viewerState property.
3072                  * 
3073                  * @param value
3074                  *     allowed object is
3075                  *     {@link String }
3076                  *     
3077                  */
3078                 public void setViewerState(String value) {
3079                     this.viewerState = value;
3080                 }
3081
3082             }
3083
3084         }
3085
3086     }
3087
3088
3089     /**
3090      * &lt;p&gt;Java class for anonymous complex type.
3091      * 
3092      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3093      * 
3094      * &lt;pre&gt;
3095      * &amp;lt;complexType&amp;gt;
3096      *   &amp;lt;complexContent&amp;gt;
3097      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3098      *       &amp;lt;sequence&amp;gt;
3099      *         &amp;lt;element name="sequencePoint" maxOccurs="unbounded"&amp;gt;
3100      *           &amp;lt;complexType&amp;gt;
3101      *             &amp;lt;complexContent&amp;gt;
3102      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3103      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3104      *                 &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3105      *               &amp;lt;/restriction&amp;gt;
3106      *             &amp;lt;/complexContent&amp;gt;
3107      *           &amp;lt;/complexType&amp;gt;
3108      *         &amp;lt;/element&amp;gt;
3109      *         &amp;lt;element name="axis" maxOccurs="3" minOccurs="3"&amp;gt;
3110      *           &amp;lt;complexType&amp;gt;
3111      *             &amp;lt;complexContent&amp;gt;
3112      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3113      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3114      *               &amp;lt;/restriction&amp;gt;
3115      *             &amp;lt;/complexContent&amp;gt;
3116      *           &amp;lt;/complexType&amp;gt;
3117      *         &amp;lt;/element&amp;gt;
3118      *         &amp;lt;element name="seqPointMin"&amp;gt;
3119      *           &amp;lt;complexType&amp;gt;
3120      *             &amp;lt;complexContent&amp;gt;
3121      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3122      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3123      *               &amp;lt;/restriction&amp;gt;
3124      *             &amp;lt;/complexContent&amp;gt;
3125      *           &amp;lt;/complexType&amp;gt;
3126      *         &amp;lt;/element&amp;gt;
3127      *         &amp;lt;element name="seqPointMax"&amp;gt;
3128      *           &amp;lt;complexType&amp;gt;
3129      *             &amp;lt;complexContent&amp;gt;
3130      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3131      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3132      *               &amp;lt;/restriction&amp;gt;
3133      *             &amp;lt;/complexContent&amp;gt;
3134      *           &amp;lt;/complexType&amp;gt;
3135      *         &amp;lt;/element&amp;gt;
3136      *         &amp;lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&amp;gt;
3137      *       &amp;lt;/sequence&amp;gt;
3138      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
3139      *       &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
3140      *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3141      *       &amp;lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3142      *       &amp;lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3143      *       &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3144      *       &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3145      *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3146      *       &amp;lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
3147      *       &amp;lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3148      *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3149      *     &amp;lt;/restriction&amp;gt;
3150      *   &amp;lt;/complexContent&amp;gt;
3151      * &amp;lt;/complexType&amp;gt;
3152      * &lt;/pre&gt;
3153      * 
3154      * 
3155      */
3156     @XmlAccessorType(XmlAccessType.FIELD)
3157     @XmlType(name = "", propOrder = {
3158         "sequencePoint",
3159         "axis",
3160         "seqPointMin",
3161         "seqPointMax",
3162         "pcaData"
3163     })
3164     public static class PcaViewer {
3165
3166         @XmlElement(namespace = "www.jalview.org", required = true)
3167         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3168         @XmlElement(namespace = "www.jalview.org", required = true)
3169         protected List<JalviewModel.PcaViewer.Axis> axis;
3170         @XmlElement(namespace = "www.jalview.org", required = true)
3171         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3172         @XmlElement(namespace = "www.jalview.org", required = true)
3173         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3174         @XmlElement(namespace = "www.jalview.org", required = true)
3175         protected PcaDataType pcaData;
3176         @XmlAttribute(name = "title")
3177         protected String title;
3178         @XmlAttribute(name = "scoreModelName")
3179         protected String scoreModelName;
3180         @XmlAttribute(name = "xDim")
3181         protected Integer xDim;
3182         @XmlAttribute(name = "yDim")
3183         protected Integer yDim;
3184         @XmlAttribute(name = "zDim")
3185         protected Integer zDim;
3186         @XmlAttribute(name = "bgColour")
3187         protected Integer bgColour;
3188         @XmlAttribute(name = "scaleFactor")
3189         protected Float scaleFactor;
3190         @XmlAttribute(name = "showLabels")
3191         protected Boolean showLabels;
3192         @XmlAttribute(name = "linkToAllViews")
3193         protected Boolean linkToAllViews;
3194         @XmlAttribute(name = "width")
3195         protected Integer width;
3196         @XmlAttribute(name = "height")
3197         protected Integer height;
3198         @XmlAttribute(name = "xpos")
3199         protected Integer xpos;
3200         @XmlAttribute(name = "ypos")
3201         protected Integer ypos;
3202         @XmlAttribute(name = "includeGaps")
3203         protected Boolean includeGaps;
3204         @XmlAttribute(name = "matchGaps")
3205         protected Boolean matchGaps;
3206         @XmlAttribute(name = "includeGappedColumns")
3207         protected Boolean includeGappedColumns;
3208         @XmlAttribute(name = "denominateByShortestLength")
3209         protected Boolean denominateByShortestLength;
3210
3211         /**
3212          * Gets the value of the sequencePoint property.
3213          * 
3214          * &lt;p&gt;
3215          * This accessor method returns a reference to the live list,
3216          * not a snapshot. Therefore any modification you make to the
3217          * returned list will be present inside the JAXB object.
3218          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
3219          * 
3220          * &lt;p&gt;
3221          * For example, to add a new item, do as follows:
3222          * &lt;pre&gt;
3223          *    getSequencePoint().add(newItem);
3224          * &lt;/pre&gt;
3225          * 
3226          * 
3227          * &lt;p&gt;
3228          * Objects of the following type(s) are allowed in the list
3229          * {@link JalviewModel.PcaViewer.SequencePoint }
3230          * 
3231          * 
3232          */
3233         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3234             if (sequencePoint == null) {
3235                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3236             }
3237             return this.sequencePoint;
3238         }
3239
3240         /**
3241          * Gets the value of the axis property.
3242          * 
3243          * &lt;p&gt;
3244          * This accessor method returns a reference to the live list,
3245          * not a snapshot. Therefore any modification you make to the
3246          * returned list will be present inside the JAXB object.
3247          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
3248          * 
3249          * &lt;p&gt;
3250          * For example, to add a new item, do as follows:
3251          * &lt;pre&gt;
3252          *    getAxis().add(newItem);
3253          * &lt;/pre&gt;
3254          * 
3255          * 
3256          * &lt;p&gt;
3257          * Objects of the following type(s) are allowed in the list
3258          * {@link JalviewModel.PcaViewer.Axis }
3259          * 
3260          * 
3261          */
3262         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3263             if (axis == null) {
3264                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3265             }
3266             return this.axis;
3267         }
3268
3269         /**
3270          * Gets the value of the seqPointMin property.
3271          * 
3272          * @return
3273          *     possible object is
3274          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3275          *     
3276          */
3277         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3278             return seqPointMin;
3279         }
3280
3281         /**
3282          * Sets the value of the seqPointMin property.
3283          * 
3284          * @param value
3285          *     allowed object is
3286          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3287          *     
3288          */
3289         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3290             this.seqPointMin = value;
3291         }
3292
3293         /**
3294          * Gets the value of the seqPointMax property.
3295          * 
3296          * @return
3297          *     possible object is
3298          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3299          *     
3300          */
3301         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3302             return seqPointMax;
3303         }
3304
3305         /**
3306          * Sets the value of the seqPointMax property.
3307          * 
3308          * @param value
3309          *     allowed object is
3310          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3311          *     
3312          */
3313         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3314             this.seqPointMax = value;
3315         }
3316
3317         /**
3318          * Gets the value of the pcaData property.
3319          * 
3320          * @return
3321          *     possible object is
3322          *     {@link PcaDataType }
3323          *     
3324          */
3325         public PcaDataType getPcaData() {
3326             return pcaData;
3327         }
3328
3329         /**
3330          * Sets the value of the pcaData property.
3331          * 
3332          * @param value
3333          *     allowed object is
3334          *     {@link PcaDataType }
3335          *     
3336          */
3337         public void setPcaData(PcaDataType value) {
3338             this.pcaData = value;
3339         }
3340
3341         /**
3342          * Gets the value of the title property.
3343          * 
3344          * @return
3345          *     possible object is
3346          *     {@link String }
3347          *     
3348          */
3349         public String getTitle() {
3350             return title;
3351         }
3352
3353         /**
3354          * Sets the value of the title property.
3355          * 
3356          * @param value
3357          *     allowed object is
3358          *     {@link String }
3359          *     
3360          */
3361         public void setTitle(String value) {
3362             this.title = value;
3363         }
3364
3365         /**
3366          * Gets the value of the scoreModelName property.
3367          * 
3368          * @return
3369          *     possible object is
3370          *     {@link String }
3371          *     
3372          */
3373         public String getScoreModelName() {
3374             return scoreModelName;
3375         }
3376
3377         /**
3378          * Sets the value of the scoreModelName property.
3379          * 
3380          * @param value
3381          *     allowed object is
3382          *     {@link String }
3383          *     
3384          */
3385         public void setScoreModelName(String value) {
3386             this.scoreModelName = value;
3387         }
3388
3389         /**
3390          * Gets the value of the xDim property.
3391          * 
3392          * @return
3393          *     possible object is
3394          *     {@link Integer }
3395          *     
3396          */
3397         public Integer getXDim() {
3398             return xDim;
3399         }
3400
3401         /**
3402          * Sets the value of the xDim property.
3403          * 
3404          * @param value
3405          *     allowed object is
3406          *     {@link Integer }
3407          *     
3408          */
3409         public void setXDim(Integer value) {
3410             this.xDim = value;
3411         }
3412
3413         /**
3414          * Gets the value of the yDim property.
3415          * 
3416          * @return
3417          *     possible object is
3418          *     {@link Integer }
3419          *     
3420          */
3421         public Integer getYDim() {
3422             return yDim;
3423         }
3424
3425         /**
3426          * Sets the value of the yDim property.
3427          * 
3428          * @param value
3429          *     allowed object is
3430          *     {@link Integer }
3431          *     
3432          */
3433         public void setYDim(Integer value) {
3434             this.yDim = value;
3435         }
3436
3437         /**
3438          * Gets the value of the zDim property.
3439          * 
3440          * @return
3441          *     possible object is
3442          *     {@link Integer }
3443          *     
3444          */
3445         public Integer getZDim() {
3446             return zDim;
3447         }
3448
3449         /**
3450          * Sets the value of the zDim property.
3451          * 
3452          * @param value
3453          *     allowed object is
3454          *     {@link Integer }
3455          *     
3456          */
3457         public void setZDim(Integer value) {
3458             this.zDim = value;
3459         }
3460
3461         /**
3462          * Gets the value of the bgColour property.
3463          * 
3464          * @return
3465          *     possible object is
3466          *     {@link Integer }
3467          *     
3468          */
3469         public Integer getBgColour() {
3470             return bgColour;
3471         }
3472
3473         /**
3474          * Sets the value of the bgColour property.
3475          * 
3476          * @param value
3477          *     allowed object is
3478          *     {@link Integer }
3479          *     
3480          */
3481         public void setBgColour(Integer value) {
3482             this.bgColour = value;
3483         }
3484
3485         /**
3486          * Gets the value of the scaleFactor property.
3487          * 
3488          * @return
3489          *     possible object is
3490          *     {@link Float }
3491          *     
3492          */
3493         public Float getScaleFactor() {
3494             return scaleFactor;
3495         }
3496
3497         /**
3498          * Sets the value of the scaleFactor property.
3499          * 
3500          * @param value
3501          *     allowed object is
3502          *     {@link Float }
3503          *     
3504          */
3505         public void setScaleFactor(Float value) {
3506             this.scaleFactor = value;
3507         }
3508
3509         /**
3510          * Gets the value of the showLabels property.
3511          * 
3512          * @return
3513          *     possible object is
3514          *     {@link Boolean }
3515          *     
3516          */
3517         public Boolean isShowLabels() {
3518             return showLabels;
3519         }
3520
3521         /**
3522          * Sets the value of the showLabels property.
3523          * 
3524          * @param value
3525          *     allowed object is
3526          *     {@link Boolean }
3527          *     
3528          */
3529         public void setShowLabels(Boolean value) {
3530             this.showLabels = value;
3531         }
3532
3533         /**
3534          * Gets the value of the linkToAllViews property.
3535          * 
3536          * @return
3537          *     possible object is
3538          *     {@link Boolean }
3539          *     
3540          */
3541         public Boolean isLinkToAllViews() {
3542             return linkToAllViews;
3543         }
3544
3545         /**
3546          * Sets the value of the linkToAllViews property.
3547          * 
3548          * @param value
3549          *     allowed object is
3550          *     {@link Boolean }
3551          *     
3552          */
3553         public void setLinkToAllViews(Boolean value) {
3554             this.linkToAllViews = value;
3555         }
3556
3557         /**
3558          * Gets the value of the width property.
3559          * 
3560          * @return
3561          *     possible object is
3562          *     {@link Integer }
3563          *     
3564          */
3565         public Integer getWidth() {
3566             return width;
3567         }
3568
3569         /**
3570          * Sets the value of the width property.
3571          * 
3572          * @param value
3573          *     allowed object is
3574          *     {@link Integer }
3575          *     
3576          */
3577         public void setWidth(Integer value) {
3578             this.width = value;
3579         }
3580
3581         /**
3582          * Gets the value of the height property.
3583          * 
3584          * @return
3585          *     possible object is
3586          *     {@link Integer }
3587          *     
3588          */
3589         public Integer getHeight() {
3590             return height;
3591         }
3592
3593         /**
3594          * Sets the value of the height property.
3595          * 
3596          * @param value
3597          *     allowed object is
3598          *     {@link Integer }
3599          *     
3600          */
3601         public void setHeight(Integer value) {
3602             this.height = value;
3603         }
3604
3605         /**
3606          * Gets the value of the xpos property.
3607          * 
3608          * @return
3609          *     possible object is
3610          *     {@link Integer }
3611          *     
3612          */
3613         public Integer getXpos() {
3614             return xpos;
3615         }
3616
3617         /**
3618          * Sets the value of the xpos property.
3619          * 
3620          * @param value
3621          *     allowed object is
3622          *     {@link Integer }
3623          *     
3624          */
3625         public void setXpos(Integer value) {
3626             this.xpos = value;
3627         }
3628
3629         /**
3630          * Gets the value of the ypos property.
3631          * 
3632          * @return
3633          *     possible object is
3634          *     {@link Integer }
3635          *     
3636          */
3637         public Integer getYpos() {
3638             return ypos;
3639         }
3640
3641         /**
3642          * Sets the value of the ypos property.
3643          * 
3644          * @param value
3645          *     allowed object is
3646          *     {@link Integer }
3647          *     
3648          */
3649         public void setYpos(Integer value) {
3650             this.ypos = value;
3651         }
3652
3653         /**
3654          * Gets the value of the includeGaps property.
3655          * 
3656          * @return
3657          *     possible object is
3658          *     {@link Boolean }
3659          *     
3660          */
3661         public Boolean isIncludeGaps() {
3662             return includeGaps;
3663         }
3664
3665         /**
3666          * Sets the value of the includeGaps property.
3667          * 
3668          * @param value
3669          *     allowed object is
3670          *     {@link Boolean }
3671          *     
3672          */
3673         public void setIncludeGaps(Boolean value) {
3674             this.includeGaps = value;
3675         }
3676
3677         /**
3678          * Gets the value of the matchGaps property.
3679          * 
3680          * @return
3681          *     possible object is
3682          *     {@link Boolean }
3683          *     
3684          */
3685         public Boolean isMatchGaps() {
3686             return matchGaps;
3687         }
3688
3689         /**
3690          * Sets the value of the matchGaps property.
3691          * 
3692          * @param value
3693          *     allowed object is
3694          *     {@link Boolean }
3695          *     
3696          */
3697         public void setMatchGaps(Boolean value) {
3698             this.matchGaps = value;
3699         }
3700
3701         /**
3702          * Gets the value of the includeGappedColumns property.
3703          * 
3704          * @return
3705          *     possible object is
3706          *     {@link Boolean }
3707          *     
3708          */
3709         public Boolean isIncludeGappedColumns() {
3710             return includeGappedColumns;
3711         }
3712
3713         /**
3714          * Sets the value of the includeGappedColumns property.
3715          * 
3716          * @param value
3717          *     allowed object is
3718          *     {@link Boolean }
3719          *     
3720          */
3721         public void setIncludeGappedColumns(Boolean value) {
3722             this.includeGappedColumns = value;
3723         }
3724
3725         /**
3726          * Gets the value of the denominateByShortestLength property.
3727          * 
3728          * @return
3729          *     possible object is
3730          *     {@link Boolean }
3731          *     
3732          */
3733         public Boolean isDenominateByShortestLength() {
3734             return denominateByShortestLength;
3735         }
3736
3737         /**
3738          * Sets the value of the denominateByShortestLength property.
3739          * 
3740          * @param value
3741          *     allowed object is
3742          *     {@link Boolean }
3743          *     
3744          */
3745         public void setDenominateByShortestLength(Boolean value) {
3746             this.denominateByShortestLength = value;
3747         }
3748
3749
3750         /**
3751          * &lt;p&gt;Java class for anonymous complex type.
3752          * 
3753          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3754          * 
3755          * &lt;pre&gt;
3756          * &amp;lt;complexType&amp;gt;
3757          *   &amp;lt;complexContent&amp;gt;
3758          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3759          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3760          *     &amp;lt;/restriction&amp;gt;
3761          *   &amp;lt;/complexContent&amp;gt;
3762          * &amp;lt;/complexType&amp;gt;
3763          * &lt;/pre&gt;
3764          * 
3765          * 
3766          */
3767         @XmlAccessorType(XmlAccessType.FIELD)
3768         @XmlType(name = "")
3769         public static class Axis {
3770
3771             @XmlAttribute(name = "xPos")
3772             protected Float xPos;
3773             @XmlAttribute(name = "yPos")
3774             protected Float yPos;
3775             @XmlAttribute(name = "zPos")
3776             protected Float zPos;
3777
3778             /**
3779              * Gets the value of the xPos property.
3780              * 
3781              * @return
3782              *     possible object is
3783              *     {@link Float }
3784              *     
3785              */
3786             public Float getXPos() {
3787                 return xPos;
3788             }
3789
3790             /**
3791              * Sets the value of the xPos property.
3792              * 
3793              * @param value
3794              *     allowed object is
3795              *     {@link Float }
3796              *     
3797              */
3798             public void setXPos(Float value) {
3799                 this.xPos = value;
3800             }
3801
3802             /**
3803              * Gets the value of the yPos property.
3804              * 
3805              * @return
3806              *     possible object is
3807              *     {@link Float }
3808              *     
3809              */
3810             public Float getYPos() {
3811                 return yPos;
3812             }
3813
3814             /**
3815              * Sets the value of the yPos property.
3816              * 
3817              * @param value
3818              *     allowed object is
3819              *     {@link Float }
3820              *     
3821              */
3822             public void setYPos(Float value) {
3823                 this.yPos = value;
3824             }
3825
3826             /**
3827              * Gets the value of the zPos property.
3828              * 
3829              * @return
3830              *     possible object is
3831              *     {@link Float }
3832              *     
3833              */
3834             public Float getZPos() {
3835                 return zPos;
3836             }
3837
3838             /**
3839              * Sets the value of the zPos property.
3840              * 
3841              * @param value
3842              *     allowed object is
3843              *     {@link Float }
3844              *     
3845              */
3846             public void setZPos(Float value) {
3847                 this.zPos = value;
3848             }
3849
3850         }
3851
3852
3853         /**
3854          * &lt;p&gt;Java class for anonymous complex type.
3855          * 
3856          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3857          * 
3858          * &lt;pre&gt;
3859          * &amp;lt;complexType&amp;gt;
3860          *   &amp;lt;complexContent&amp;gt;
3861          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3862          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3863          *     &amp;lt;/restriction&amp;gt;
3864          *   &amp;lt;/complexContent&amp;gt;
3865          * &amp;lt;/complexType&amp;gt;
3866          * &lt;/pre&gt;
3867          * 
3868          * 
3869          */
3870         @XmlAccessorType(XmlAccessType.FIELD)
3871         @XmlType(name = "")
3872         public static class SeqPointMax {
3873
3874             @XmlAttribute(name = "xPos")
3875             protected Float xPos;
3876             @XmlAttribute(name = "yPos")
3877             protected Float yPos;
3878             @XmlAttribute(name = "zPos")
3879             protected Float zPos;
3880
3881             /**
3882              * Gets the value of the xPos property.
3883              * 
3884              * @return
3885              *     possible object is
3886              *     {@link Float }
3887              *     
3888              */
3889             public Float getXPos() {
3890                 return xPos;
3891             }
3892
3893             /**
3894              * Sets the value of the xPos property.
3895              * 
3896              * @param value
3897              *     allowed object is
3898              *     {@link Float }
3899              *     
3900              */
3901             public void setXPos(Float value) {
3902                 this.xPos = value;
3903             }
3904
3905             /**
3906              * Gets the value of the yPos property.
3907              * 
3908              * @return
3909              *     possible object is
3910              *     {@link Float }
3911              *     
3912              */
3913             public Float getYPos() {
3914                 return yPos;
3915             }
3916
3917             /**
3918              * Sets the value of the yPos property.
3919              * 
3920              * @param value
3921              *     allowed object is
3922              *     {@link Float }
3923              *     
3924              */
3925             public void setYPos(Float value) {
3926                 this.yPos = value;
3927             }
3928
3929             /**
3930              * Gets the value of the zPos property.
3931              * 
3932              * @return
3933              *     possible object is
3934              *     {@link Float }
3935              *     
3936              */
3937             public Float getZPos() {
3938                 return zPos;
3939             }
3940
3941             /**
3942              * Sets the value of the zPos property.
3943              * 
3944              * @param value
3945              *     allowed object is
3946              *     {@link Float }
3947              *     
3948              */
3949             public void setZPos(Float value) {
3950                 this.zPos = value;
3951             }
3952
3953         }
3954
3955
3956         /**
3957          * &lt;p&gt;Java class for anonymous complex type.
3958          * 
3959          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3960          * 
3961          * &lt;pre&gt;
3962          * &amp;lt;complexType&amp;gt;
3963          *   &amp;lt;complexContent&amp;gt;
3964          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3965          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3966          *     &amp;lt;/restriction&amp;gt;
3967          *   &amp;lt;/complexContent&amp;gt;
3968          * &amp;lt;/complexType&amp;gt;
3969          * &lt;/pre&gt;
3970          * 
3971          * 
3972          */
3973         @XmlAccessorType(XmlAccessType.FIELD)
3974         @XmlType(name = "")
3975         public static class SeqPointMin {
3976
3977             @XmlAttribute(name = "xPos")
3978             protected Float xPos;
3979             @XmlAttribute(name = "yPos")
3980             protected Float yPos;
3981             @XmlAttribute(name = "zPos")
3982             protected Float zPos;
3983
3984             /**
3985              * Gets the value of the xPos property.
3986              * 
3987              * @return
3988              *     possible object is
3989              *     {@link Float }
3990              *     
3991              */
3992             public Float getXPos() {
3993                 return xPos;
3994             }
3995
3996             /**
3997              * Sets the value of the xPos property.
3998              * 
3999              * @param value
4000              *     allowed object is
4001              *     {@link Float }
4002              *     
4003              */
4004             public void setXPos(Float value) {
4005                 this.xPos = value;
4006             }
4007
4008             /**
4009              * Gets the value of the yPos property.
4010              * 
4011              * @return
4012              *     possible object is
4013              *     {@link Float }
4014              *     
4015              */
4016             public Float getYPos() {
4017                 return yPos;
4018             }
4019
4020             /**
4021              * Sets the value of the yPos property.
4022              * 
4023              * @param value
4024              *     allowed object is
4025              *     {@link Float }
4026              *     
4027              */
4028             public void setYPos(Float value) {
4029                 this.yPos = value;
4030             }
4031
4032             /**
4033              * Gets the value of the zPos property.
4034              * 
4035              * @return
4036              *     possible object is
4037              *     {@link Float }
4038              *     
4039              */
4040             public Float getZPos() {
4041                 return zPos;
4042             }
4043
4044             /**
4045              * Sets the value of the zPos property.
4046              * 
4047              * @param value
4048              *     allowed object is
4049              *     {@link Float }
4050              *     
4051              */
4052             public void setZPos(Float value) {
4053                 this.zPos = value;
4054             }
4055
4056         }
4057
4058
4059         /**
4060          * &lt;p&gt;Java class for anonymous complex type.
4061          * 
4062          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4063          * 
4064          * &lt;pre&gt;
4065          * &amp;lt;complexType&amp;gt;
4066          *   &amp;lt;complexContent&amp;gt;
4067          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4068          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
4069          *       &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4070          *     &amp;lt;/restriction&amp;gt;
4071          *   &amp;lt;/complexContent&amp;gt;
4072          * &amp;lt;/complexType&amp;gt;
4073          * &lt;/pre&gt;
4074          * 
4075          * 
4076          */
4077         @XmlAccessorType(XmlAccessType.FIELD)
4078         @XmlType(name = "")
4079         public static class SequencePoint {
4080
4081             @XmlAttribute(name = "sequenceRef")
4082             protected String sequenceRef;
4083             @XmlAttribute(name = "xPos")
4084             protected Float xPos;
4085             @XmlAttribute(name = "yPos")
4086             protected Float yPos;
4087             @XmlAttribute(name = "zPos")
4088             protected Float zPos;
4089
4090             /**
4091              * Gets the value of the sequenceRef property.
4092              * 
4093              * @return
4094              *     possible object is
4095              *     {@link String }
4096              *     
4097              */
4098             public String getSequenceRef() {
4099                 return sequenceRef;
4100             }
4101
4102             /**
4103              * Sets the value of the sequenceRef property.
4104              * 
4105              * @param value
4106              *     allowed object is
4107              *     {@link String }
4108              *     
4109              */
4110             public void setSequenceRef(String value) {
4111                 this.sequenceRef = value;
4112             }
4113
4114             /**
4115              * Gets the value of the xPos property.
4116              * 
4117              * @return
4118              *     possible object is
4119              *     {@link Float }
4120              *     
4121              */
4122             public Float getXPos() {
4123                 return xPos;
4124             }
4125
4126             /**
4127              * Sets the value of the xPos property.
4128              * 
4129              * @param value
4130              *     allowed object is
4131              *     {@link Float }
4132              *     
4133              */
4134             public void setXPos(Float value) {
4135                 this.xPos = value;
4136             }
4137
4138             /**
4139              * Gets the value of the yPos property.
4140              * 
4141              * @return
4142              *     possible object is
4143              *     {@link Float }
4144              *     
4145              */
4146             public Float getYPos() {
4147                 return yPos;
4148             }
4149
4150             /**
4151              * Sets the value of the yPos property.
4152              * 
4153              * @param value
4154              *     allowed object is
4155              *     {@link Float }
4156              *     
4157              */
4158             public void setYPos(Float value) {
4159                 this.yPos = value;
4160             }
4161
4162             /**
4163              * Gets the value of the zPos property.
4164              * 
4165              * @return
4166              *     possible object is
4167              *     {@link Float }
4168              *     
4169              */
4170             public Float getZPos() {
4171                 return zPos;
4172             }
4173
4174             /**
4175              * Sets the value of the zPos property.
4176              * 
4177              * @param value
4178              *     allowed object is
4179              *     {@link Float }
4180              *     
4181              */
4182             public void setZPos(Float value) {
4183                 this.zPos = value;
4184             }
4185
4186         }
4187
4188     }
4189
4190
4191     /**
4192      * &lt;p&gt;Java class for anonymous complex type.
4193      * 
4194      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4195      * 
4196      * &lt;pre&gt;
4197      * &amp;lt;complexType&amp;gt;
4198      *   &amp;lt;complexContent&amp;gt;
4199      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4200      *       &amp;lt;sequence minOccurs="0"&amp;gt;
4201      *         &amp;lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4202      *         &amp;lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4203      *       &amp;lt;/sequence&amp;gt;
4204      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
4205      *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4206      *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4207      *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4208      *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
4209      *       &amp;lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4210      *       &amp;lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4211      *       &amp;lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4212      *       &amp;lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4213      *       &amp;lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4214      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4215      *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4216      *     &amp;lt;/restriction&amp;gt;
4217      *   &amp;lt;/complexContent&amp;gt;
4218      * &amp;lt;/complexType&amp;gt;
4219      * &lt;/pre&gt;
4220      * 
4221      * 
4222      */
4223     @XmlAccessorType(XmlAccessType.FIELD)
4224     @XmlType(name = "", propOrder = {
4225         "title",
4226         "newick"
4227     })
4228     public static class Tree {
4229
4230         @XmlElement(namespace = "www.jalview.org")
4231         protected String title;
4232         @XmlElement(namespace = "www.jalview.org")
4233         protected String newick;
4234         @XmlAttribute(name = "fontName")
4235         protected String fontName;
4236         @XmlAttribute(name = "fontSize")
4237         protected Integer fontSize;
4238         @XmlAttribute(name = "fontStyle")
4239         protected Integer fontStyle;
4240         @XmlAttribute(name = "threshold")
4241         protected Float threshold;
4242         @XmlAttribute(name = "showBootstrap")
4243         protected Boolean showBootstrap;
4244         @XmlAttribute(name = "showDistances")
4245         protected Boolean showDistances;
4246         @XmlAttribute(name = "markUnlinked")
4247         protected Boolean markUnlinked;
4248         @XmlAttribute(name = "fitToWindow")
4249         protected Boolean fitToWindow;
4250         @XmlAttribute(name = "currentTree")
4251         protected Boolean currentTree;
4252         @XmlAttribute(name = "id")
4253         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4254         @XmlID
4255         @XmlSchemaType(name = "ID")
4256         protected String id;
4257         @XmlAttribute(name = "linkToAllViews")
4258         protected Boolean linkToAllViews;
4259         @XmlAttribute(name = "width")
4260         protected Integer width;
4261         @XmlAttribute(name = "height")
4262         protected Integer height;
4263         @XmlAttribute(name = "xpos")
4264         protected Integer xpos;
4265         @XmlAttribute(name = "ypos")
4266         protected Integer ypos;
4267
4268         /**
4269          * Gets the value of the title property.
4270          * 
4271          * @return
4272          *     possible object is
4273          *     {@link String }
4274          *     
4275          */
4276         public String getTitle() {
4277             return title;
4278         }
4279
4280         /**
4281          * Sets the value of the title property.
4282          * 
4283          * @param value
4284          *     allowed object is
4285          *     {@link String }
4286          *     
4287          */
4288         public void setTitle(String value) {
4289             this.title = value;
4290         }
4291
4292         /**
4293          * Gets the value of the newick property.
4294          * 
4295          * @return
4296          *     possible object is
4297          *     {@link String }
4298          *     
4299          */
4300         public String getNewick() {
4301             return newick;
4302         }
4303
4304         /**
4305          * Sets the value of the newick property.
4306          * 
4307          * @param value
4308          *     allowed object is
4309          *     {@link String }
4310          *     
4311          */
4312         public void setNewick(String value) {
4313             this.newick = value;
4314         }
4315
4316         /**
4317          * Gets the value of the fontName property.
4318          * 
4319          * @return
4320          *     possible object is
4321          *     {@link String }
4322          *     
4323          */
4324         public String getFontName() {
4325             return fontName;
4326         }
4327
4328         /**
4329          * Sets the value of the fontName property.
4330          * 
4331          * @param value
4332          *     allowed object is
4333          *     {@link String }
4334          *     
4335          */
4336         public void setFontName(String value) {
4337             this.fontName = value;
4338         }
4339
4340         /**
4341          * Gets the value of the fontSize property.
4342          * 
4343          * @return
4344          *     possible object is
4345          *     {@link Integer }
4346          *     
4347          */
4348         public Integer getFontSize() {
4349             return fontSize;
4350         }
4351
4352         /**
4353          * Sets the value of the fontSize property.
4354          * 
4355          * @param value
4356          *     allowed object is
4357          *     {@link Integer }
4358          *     
4359          */
4360         public void setFontSize(Integer value) {
4361             this.fontSize = value;
4362         }
4363
4364         /**
4365          * Gets the value of the fontStyle property.
4366          * 
4367          * @return
4368          *     possible object is
4369          *     {@link Integer }
4370          *     
4371          */
4372         public Integer getFontStyle() {
4373             return fontStyle;
4374         }
4375
4376         /**
4377          * Sets the value of the fontStyle property.
4378          * 
4379          * @param value
4380          *     allowed object is
4381          *     {@link Integer }
4382          *     
4383          */
4384         public void setFontStyle(Integer value) {
4385             this.fontStyle = value;
4386         }
4387
4388         /**
4389          * Gets the value of the threshold property.
4390          * 
4391          * @return
4392          *     possible object is
4393          *     {@link Float }
4394          *     
4395          */
4396         public Float getThreshold() {
4397             return threshold;
4398         }
4399
4400         /**
4401          * Sets the value of the threshold property.
4402          * 
4403          * @param value
4404          *     allowed object is
4405          *     {@link Float }
4406          *     
4407          */
4408         public void setThreshold(Float value) {
4409             this.threshold = value;
4410         }
4411
4412         /**
4413          * Gets the value of the showBootstrap property.
4414          * 
4415          * @return
4416          *     possible object is
4417          *     {@link Boolean }
4418          *     
4419          */
4420         public Boolean isShowBootstrap() {
4421             return showBootstrap;
4422         }
4423
4424         /**
4425          * Sets the value of the showBootstrap property.
4426          * 
4427          * @param value
4428          *     allowed object is
4429          *     {@link Boolean }
4430          *     
4431          */
4432         public void setShowBootstrap(Boolean value) {
4433             this.showBootstrap = value;
4434         }
4435
4436         /**
4437          * Gets the value of the showDistances property.
4438          * 
4439          * @return
4440          *     possible object is
4441          *     {@link Boolean }
4442          *     
4443          */
4444         public Boolean isShowDistances() {
4445             return showDistances;
4446         }
4447
4448         /**
4449          * Sets the value of the showDistances property.
4450          * 
4451          * @param value
4452          *     allowed object is
4453          *     {@link Boolean }
4454          *     
4455          */
4456         public void setShowDistances(Boolean value) {
4457             this.showDistances = value;
4458         }
4459
4460         /**
4461          * Gets the value of the markUnlinked property.
4462          * 
4463          * @return
4464          *     possible object is
4465          *     {@link Boolean }
4466          *     
4467          */
4468         public Boolean isMarkUnlinked() {
4469             return markUnlinked;
4470         }
4471
4472         /**
4473          * Sets the value of the markUnlinked property.
4474          * 
4475          * @param value
4476          *     allowed object is
4477          *     {@link Boolean }
4478          *     
4479          */
4480         public void setMarkUnlinked(Boolean value) {
4481             this.markUnlinked = value;
4482         }
4483
4484         /**
4485          * Gets the value of the fitToWindow property.
4486          * 
4487          * @return
4488          *     possible object is
4489          *     {@link Boolean }
4490          *     
4491          */
4492         public Boolean isFitToWindow() {
4493             return fitToWindow;
4494         }
4495
4496         /**
4497          * Sets the value of the fitToWindow property.
4498          * 
4499          * @param value
4500          *     allowed object is
4501          *     {@link Boolean }
4502          *     
4503          */
4504         public void setFitToWindow(Boolean value) {
4505             this.fitToWindow = value;
4506         }
4507
4508         /**
4509          * Gets the value of the currentTree property.
4510          * 
4511          * @return
4512          *     possible object is
4513          *     {@link Boolean }
4514          *     
4515          */
4516         public Boolean isCurrentTree() {
4517             return currentTree;
4518         }
4519
4520         /**
4521          * Sets the value of the currentTree property.
4522          * 
4523          * @param value
4524          *     allowed object is
4525          *     {@link Boolean }
4526          *     
4527          */
4528         public void setCurrentTree(Boolean value) {
4529             this.currentTree = value;
4530         }
4531
4532         /**
4533          * Gets the value of the id property.
4534          * 
4535          * @return
4536          *     possible object is
4537          *     {@link String }
4538          *     
4539          */
4540         public String getId() {
4541             return id;
4542         }
4543
4544         /**
4545          * Sets the value of the id property.
4546          * 
4547          * @param value
4548          *     allowed object is
4549          *     {@link String }
4550          *     
4551          */
4552         public void setId(String value) {
4553             this.id = value;
4554         }
4555
4556         /**
4557          * Gets the value of the linkToAllViews property.
4558          * 
4559          * @return
4560          *     possible object is
4561          *     {@link Boolean }
4562          *     
4563          */
4564         public boolean isLinkToAllViews() {
4565             if (linkToAllViews == null) {
4566                 return false;
4567             } else {
4568                 return linkToAllViews;
4569             }
4570         }
4571
4572         /**
4573          * Sets the value of the linkToAllViews property.
4574          * 
4575          * @param value
4576          *     allowed object is
4577          *     {@link Boolean }
4578          *     
4579          */
4580         public void setLinkToAllViews(Boolean value) {
4581             this.linkToAllViews = value;
4582         }
4583
4584         /**
4585          * Gets the value of the width property.
4586          * 
4587          * @return
4588          *     possible object is
4589          *     {@link Integer }
4590          *     
4591          */
4592         public Integer getWidth() {
4593             return width;
4594         }
4595
4596         /**
4597          * Sets the value of the width property.
4598          * 
4599          * @param value
4600          *     allowed object is
4601          *     {@link Integer }
4602          *     
4603          */
4604         public void setWidth(Integer value) {
4605             this.width = value;
4606         }
4607
4608         /**
4609          * Gets the value of the height property.
4610          * 
4611          * @return
4612          *     possible object is
4613          *     {@link Integer }
4614          *     
4615          */
4616         public Integer getHeight() {
4617             return height;
4618         }
4619
4620         /**
4621          * Sets the value of the height property.
4622          * 
4623          * @param value
4624          *     allowed object is
4625          *     {@link Integer }
4626          *     
4627          */
4628         public void setHeight(Integer value) {
4629             this.height = value;
4630         }
4631
4632         /**
4633          * Gets the value of the xpos property.
4634          * 
4635          * @return
4636          *     possible object is
4637          *     {@link Integer }
4638          *     
4639          */
4640         public Integer getXpos() {
4641             return xpos;
4642         }
4643
4644         /**
4645          * Sets the value of the xpos property.
4646          * 
4647          * @param value
4648          *     allowed object is
4649          *     {@link Integer }
4650          *     
4651          */
4652         public void setXpos(Integer value) {
4653             this.xpos = value;
4654         }
4655
4656         /**
4657          * Gets the value of the ypos property.
4658          * 
4659          * @return
4660          *     possible object is
4661          *     {@link Integer }
4662          *     
4663          */
4664         public Integer getYpos() {
4665             return ypos;
4666         }
4667
4668         /**
4669          * Sets the value of the ypos property.
4670          * 
4671          * @param value
4672          *     allowed object is
4673          *     {@link Integer }
4674          *     
4675          */
4676         public void setYpos(Integer value) {
4677             this.ypos = value;
4678         }
4679
4680     }
4681
4682
4683     /**
4684      * &lt;p&gt;Java class for anonymous complex type.
4685      * 
4686      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4687      * 
4688      * &lt;pre&gt;
4689      * &amp;lt;complexType&amp;gt;
4690      *   &amp;lt;complexContent&amp;gt;
4691      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4692      *       &amp;lt;sequence&amp;gt;
4693      *         &amp;lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
4694      *       &amp;lt;/sequence&amp;gt;
4695      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4696      *     &amp;lt;/restriction&amp;gt;
4697      *   &amp;lt;/complexContent&amp;gt;
4698      * &amp;lt;/complexType&amp;gt;
4699      * &lt;/pre&gt;
4700      * 
4701      * 
4702      */
4703     @XmlAccessorType(XmlAccessType.FIELD)
4704     @XmlType(name = "", propOrder = {
4705         "userColourScheme"
4706     })
4707     public static class UserColours {
4708
4709         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4710         protected JalviewUserColours userColourScheme;
4711         @XmlAttribute(name = "id")
4712         protected String id;
4713
4714         /**
4715          * Gets the value of the userColourScheme property.
4716          * 
4717          * @return
4718          *     possible object is
4719          *     {@link JalviewUserColours }
4720          *     
4721          */
4722         public JalviewUserColours getUserColourScheme() {
4723             return userColourScheme;
4724         }
4725
4726         /**
4727          * Sets the value of the userColourScheme property.
4728          * 
4729          * @param value
4730          *     allowed object is
4731          *     {@link JalviewUserColours }
4732          *     
4733          */
4734         public void setUserColourScheme(JalviewUserColours value) {
4735             this.userColourScheme = value;
4736         }
4737
4738         /**
4739          * Gets the value of the id property.
4740          * 
4741          * @return
4742          *     possible object is
4743          *     {@link String }
4744          *     
4745          */
4746         public String getId() {
4747             return id;
4748         }
4749
4750         /**
4751          * Sets the value of the id property.
4752          * 
4753          * @param value
4754          *     allowed object is
4755          *     {@link String }
4756          *     
4757          */
4758         public void setId(String value) {
4759             this.id = value;
4760         }
4761
4762     }
4763
4764
4765     /**
4766      * &lt;p&gt;Java class for anonymous complex type.
4767      * 
4768      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4769      * 
4770      * &lt;pre&gt;
4771      * &amp;lt;complexType&amp;gt;
4772      *   &amp;lt;complexContent&amp;gt;
4773      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4774      *       &amp;lt;sequence&amp;gt;
4775      *         &amp;lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
4776      *         &amp;lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4777      *           &amp;lt;complexType&amp;gt;
4778      *             &amp;lt;complexContent&amp;gt;
4779      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4780      *                 &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4781      *                 &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4782      *               &amp;lt;/restriction&amp;gt;
4783      *             &amp;lt;/complexContent&amp;gt;
4784      *           &amp;lt;/complexType&amp;gt;
4785      *         &amp;lt;/element&amp;gt;
4786      *         &amp;lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4787      *           &amp;lt;complexType&amp;gt;
4788      *             &amp;lt;complexContent&amp;gt;
4789      *               &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
4790      *                 &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4791      *                 &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4792      *                 &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4793      *               &amp;lt;/extension&amp;gt;
4794      *             &amp;lt;/complexContent&amp;gt;
4795      *           &amp;lt;/complexType&amp;gt;
4796      *         &amp;lt;/element&amp;gt;
4797      *       &amp;lt;/sequence&amp;gt;
4798      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
4799      *       &amp;lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4800      *       &amp;lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4801      *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4802      *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4803      *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4804      *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4805      *       &amp;lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4806      *       &amp;lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4807      *       &amp;lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4808      *       &amp;lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4809      *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4810      *       &amp;lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4811      *       &amp;lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4812      *       &amp;lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4813      *       &amp;lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4814      *       &amp;lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4815      *       &amp;lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4816      *       &amp;lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4817      *       &amp;lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4818      *       &amp;lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4819      *       &amp;lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4820      *       &amp;lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4821      *       &amp;lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4822      *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4823      *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4824      *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4825      *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4826      *       &amp;lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4827      *       &amp;lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4828      *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4829      *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4830      *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4831      *       &amp;lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4832      *       &amp;lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4833      *       &amp;lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4834      *       &amp;lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4835      *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4836      *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4837      *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4838      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4839      *       &amp;lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4840      *       &amp;lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4841      *       &amp;lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4842      *     &amp;lt;/restriction&amp;gt;
4843      *   &amp;lt;/complexContent&amp;gt;
4844      * &amp;lt;/complexType&amp;gt;
4845      * &lt;/pre&gt;
4846      * 
4847      * 
4848      */
4849     @XmlAccessorType(XmlAccessType.FIELD)
4850     @XmlType(name = "", propOrder = {
4851         "annotationColours",
4852         "hiddenColumns",
4853         "calcIdParam"
4854     })
4855     public static class Viewport {
4856
4857         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4858         protected AnnotationColourScheme annotationColours;
4859         @XmlElement(namespace = "www.jalview.org")
4860         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4861         @XmlElement(namespace = "www.jalview.org")
4862         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4863         @XmlAttribute(name = "conservationSelected")
4864         protected Boolean conservationSelected;
4865         @XmlAttribute(name = "pidSelected")
4866         protected Boolean pidSelected;
4867         @XmlAttribute(name = "bgColour")
4868         protected String bgColour;
4869         @XmlAttribute(name = "consThreshold")
4870         protected Integer consThreshold;
4871         @XmlAttribute(name = "pidThreshold")
4872         protected Integer pidThreshold;
4873         @XmlAttribute(name = "title")
4874         protected String title;
4875         @XmlAttribute(name = "showFullId")
4876         protected Boolean showFullId;
4877         @XmlAttribute(name = "rightAlignIds")
4878         protected Boolean rightAlignIds;
4879         @XmlAttribute(name = "showText")
4880         protected Boolean showText;
4881         @XmlAttribute(name = "showColourText")
4882         protected Boolean showColourText;
4883         @XmlAttribute(name = "showUnconserved")
4884         protected Boolean showUnconserved;
4885         @XmlAttribute(name = "showBoxes")
4886         protected Boolean showBoxes;
4887         @XmlAttribute(name = "wrapAlignment")
4888         protected Boolean wrapAlignment;
4889         @XmlAttribute(name = "renderGaps")
4890         protected Boolean renderGaps;
4891         @XmlAttribute(name = "showSequenceFeatures")
4892         protected Boolean showSequenceFeatures;
4893         @XmlAttribute(name = "showNPfeatureTooltip")
4894         protected Boolean showNPfeatureTooltip;
4895         @XmlAttribute(name = "showDbRefTooltip")
4896         protected Boolean showDbRefTooltip;
4897         @XmlAttribute(name = "followHighlight")
4898         protected Boolean followHighlight;
4899         @XmlAttribute(name = "followSelection")
4900         protected Boolean followSelection;
4901         @XmlAttribute(name = "showAnnotation")
4902         protected Boolean showAnnotation;
4903         @XmlAttribute(name = "centreColumnLabels")
4904         protected Boolean centreColumnLabels;
4905         @XmlAttribute(name = "showGroupConservation")
4906         protected Boolean showGroupConservation;
4907         @XmlAttribute(name = "showGroupConsensus")
4908         protected Boolean showGroupConsensus;
4909         @XmlAttribute(name = "showConsensusHistogram")
4910         protected Boolean showConsensusHistogram;
4911         @XmlAttribute(name = "showSequenceLogo")
4912         protected Boolean showSequenceLogo;
4913         @XmlAttribute(name = "normaliseSequenceLogo")
4914         protected Boolean normaliseSequenceLogo;
4915         @XmlAttribute(name = "ignoreGapsinConsensus")
4916         protected Boolean ignoreGapsinConsensus;
4917         @XmlAttribute(name = "startRes")
4918         protected Integer startRes;
4919         @XmlAttribute(name = "startSeq")
4920         protected Integer startSeq;
4921         @XmlAttribute(name = "fontName")
4922         protected String fontName;
4923         @XmlAttribute(name = "fontSize")
4924         protected Integer fontSize;
4925         @XmlAttribute(name = "fontStyle")
4926         protected Integer fontStyle;
4927         @XmlAttribute(name = "scaleProteinAsCdna")
4928         protected Boolean scaleProteinAsCdna;
4929         @XmlAttribute(name = "viewName")
4930         protected String viewName;
4931         @XmlAttribute(name = "sequenceSetId")
4932         protected String sequenceSetId;
4933         @XmlAttribute(name = "gatheredViews")
4934         protected Boolean gatheredViews;
4935         @XmlAttribute(name = "textCol1")
4936         protected Integer textCol1;
4937         @XmlAttribute(name = "textCol2")
4938         protected Integer textCol2;
4939         @XmlAttribute(name = "textColThreshold")
4940         protected Integer textColThreshold;
4941         @XmlAttribute(name = "id")
4942         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4943         @XmlID
4944         @XmlSchemaType(name = "ID")
4945         protected String id;
4946         @XmlAttribute(name = "complementId")
4947         protected String complementId;
4948         @XmlAttribute(name = "showComplementFeatures")
4949         protected Boolean showComplementFeatures;
4950         @XmlAttribute(name = "showComplementFeaturesOnTop")
4951         protected Boolean showComplementFeaturesOnTop;
4952         @XmlAttribute(name = "width")
4953         protected Integer width;
4954         @XmlAttribute(name = "height")
4955         protected Integer height;
4956         @XmlAttribute(name = "xpos")
4957         protected Integer xpos;
4958         @XmlAttribute(name = "ypos")
4959         protected Integer ypos;
4960
4961         /**
4962          * Gets the value of the annotationColours property.
4963          * 
4964          * @return
4965          *     possible object is
4966          *     {@link AnnotationColourScheme }
4967          *     
4968          */
4969         public AnnotationColourScheme getAnnotationColours() {
4970             return annotationColours;
4971         }
4972
4973         /**
4974          * Sets the value of the annotationColours property.
4975          * 
4976          * @param value
4977          *     allowed object is
4978          *     {@link AnnotationColourScheme }
4979          *     
4980          */
4981         public void setAnnotationColours(AnnotationColourScheme value) {
4982             this.annotationColours = value;
4983         }
4984
4985         /**
4986          * Gets the value of the hiddenColumns property.
4987          * 
4988          * &lt;p&gt;
4989          * This accessor method returns a reference to the live list,
4990          * not a snapshot. Therefore any modification you make to the
4991          * returned list will be present inside the JAXB object.
4992          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
4993          * 
4994          * &lt;p&gt;
4995          * For example, to add a new item, do as follows:
4996          * &lt;pre&gt;
4997          *    getHiddenColumns().add(newItem);
4998          * &lt;/pre&gt;
4999          * 
5000          * 
5001          * &lt;p&gt;
5002          * Objects of the following type(s) are allowed in the list
5003          * {@link JalviewModel.Viewport.HiddenColumns }
5004          * 
5005          * 
5006          */
5007         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5008             if (hiddenColumns == null) {
5009                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5010             }
5011             return this.hiddenColumns;
5012         }
5013
5014         /**
5015          * Gets the value of the calcIdParam property.
5016          * 
5017          * &lt;p&gt;
5018          * This accessor method returns a reference to the live list,
5019          * not a snapshot. Therefore any modification you make to the
5020          * returned list will be present inside the JAXB object.
5021          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
5022          * 
5023          * &lt;p&gt;
5024          * For example, to add a new item, do as follows:
5025          * &lt;pre&gt;
5026          *    getCalcIdParam().add(newItem);
5027          * &lt;/pre&gt;
5028          * 
5029          * 
5030          * &lt;p&gt;
5031          * Objects of the following type(s) are allowed in the list
5032          * {@link JalviewModel.Viewport.CalcIdParam }
5033          * 
5034          * 
5035          */
5036         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5037             if (calcIdParam == null) {
5038                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5039             }
5040             return this.calcIdParam;
5041         }
5042
5043         /**
5044          * Gets the value of the conservationSelected property.
5045          * 
5046          * @return
5047          *     possible object is
5048          *     {@link Boolean }
5049          *     
5050          */
5051         public Boolean isConservationSelected() {
5052             return conservationSelected;
5053         }
5054
5055         /**
5056          * Sets the value of the conservationSelected property.
5057          * 
5058          * @param value
5059          *     allowed object is
5060          *     {@link Boolean }
5061          *     
5062          */
5063         public void setConservationSelected(Boolean value) {
5064             this.conservationSelected = value;
5065         }
5066
5067         /**
5068          * Gets the value of the pidSelected property.
5069          * 
5070          * @return
5071          *     possible object is
5072          *     {@link Boolean }
5073          *     
5074          */
5075         public Boolean isPidSelected() {
5076             return pidSelected;
5077         }
5078
5079         /**
5080          * Sets the value of the pidSelected property.
5081          * 
5082          * @param value
5083          *     allowed object is
5084          *     {@link Boolean }
5085          *     
5086          */
5087         public void setPidSelected(Boolean value) {
5088             this.pidSelected = value;
5089         }
5090
5091         /**
5092          * Gets the value of the bgColour property.
5093          * 
5094          * @return
5095          *     possible object is
5096          *     {@link String }
5097          *     
5098          */
5099         public String getBgColour() {
5100             return bgColour;
5101         }
5102
5103         /**
5104          * Sets the value of the bgColour property.
5105          * 
5106          * @param value
5107          *     allowed object is
5108          *     {@link String }
5109          *     
5110          */
5111         public void setBgColour(String value) {
5112             this.bgColour = value;
5113         }
5114
5115         /**
5116          * Gets the value of the consThreshold property.
5117          * 
5118          * @return
5119          *     possible object is
5120          *     {@link Integer }
5121          *     
5122          */
5123         public Integer getConsThreshold() {
5124             return consThreshold;
5125         }
5126
5127         /**
5128          * Sets the value of the consThreshold property.
5129          * 
5130          * @param value
5131          *     allowed object is
5132          *     {@link Integer }
5133          *     
5134          */
5135         public void setConsThreshold(Integer value) {
5136             this.consThreshold = value;
5137         }
5138
5139         /**
5140          * Gets the value of the pidThreshold property.
5141          * 
5142          * @return
5143          *     possible object is
5144          *     {@link Integer }
5145          *     
5146          */
5147         public Integer getPidThreshold() {
5148             return pidThreshold;
5149         }
5150
5151         /**
5152          * Sets the value of the pidThreshold property.
5153          * 
5154          * @param value
5155          *     allowed object is
5156          *     {@link Integer }
5157          *     
5158          */
5159         public void setPidThreshold(Integer value) {
5160             this.pidThreshold = value;
5161         }
5162
5163         /**
5164          * Gets the value of the title property.
5165          * 
5166          * @return
5167          *     possible object is
5168          *     {@link String }
5169          *     
5170          */
5171         public String getTitle() {
5172             return title;
5173         }
5174
5175         /**
5176          * Sets the value of the title property.
5177          * 
5178          * @param value
5179          *     allowed object is
5180          *     {@link String }
5181          *     
5182          */
5183         public void setTitle(String value) {
5184             this.title = value;
5185         }
5186
5187         /**
5188          * Gets the value of the showFullId property.
5189          * 
5190          * @return
5191          *     possible object is
5192          *     {@link Boolean }
5193          *     
5194          */
5195         public Boolean isShowFullId() {
5196             return showFullId;
5197         }
5198
5199         /**
5200          * Sets the value of the showFullId property.
5201          * 
5202          * @param value
5203          *     allowed object is
5204          *     {@link Boolean }
5205          *     
5206          */
5207         public void setShowFullId(Boolean value) {
5208             this.showFullId = value;
5209         }
5210
5211         /**
5212          * Gets the value of the rightAlignIds property.
5213          * 
5214          * @return
5215          *     possible object is
5216          *     {@link Boolean }
5217          *     
5218          */
5219         public Boolean isRightAlignIds() {
5220             return rightAlignIds;
5221         }
5222
5223         /**
5224          * Sets the value of the rightAlignIds property.
5225          * 
5226          * @param value
5227          *     allowed object is
5228          *     {@link Boolean }
5229          *     
5230          */
5231         public void setRightAlignIds(Boolean value) {
5232             this.rightAlignIds = value;
5233         }
5234
5235         /**
5236          * Gets the value of the showText property.
5237          * 
5238          * @return
5239          *     possible object is
5240          *     {@link Boolean }
5241          *     
5242          */
5243         public Boolean isShowText() {
5244             return showText;
5245         }
5246
5247         /**
5248          * Sets the value of the showText property.
5249          * 
5250          * @param value
5251          *     allowed object is
5252          *     {@link Boolean }
5253          *     
5254          */
5255         public void setShowText(Boolean value) {
5256             this.showText = value;
5257         }
5258
5259         /**
5260          * Gets the value of the showColourText property.
5261          * 
5262          * @return
5263          *     possible object is
5264          *     {@link Boolean }
5265          *     
5266          */
5267         public Boolean isShowColourText() {
5268             return showColourText;
5269         }
5270
5271         /**
5272          * Sets the value of the showColourText property.
5273          * 
5274          * @param value
5275          *     allowed object is
5276          *     {@link Boolean }
5277          *     
5278          */
5279         public void setShowColourText(Boolean value) {
5280             this.showColourText = value;
5281         }
5282
5283         /**
5284          * Gets the value of the showUnconserved property.
5285          * 
5286          * @return
5287          *     possible object is
5288          *     {@link Boolean }
5289          *     
5290          */
5291         public boolean isShowUnconserved() {
5292             if (showUnconserved == null) {
5293                 return false;
5294             } else {
5295                 return showUnconserved;
5296             }
5297         }
5298
5299         /**
5300          * Sets the value of the showUnconserved property.
5301          * 
5302          * @param value
5303          *     allowed object is
5304          *     {@link Boolean }
5305          *     
5306          */
5307         public void setShowUnconserved(Boolean value) {
5308             this.showUnconserved = value;
5309         }
5310
5311         /**
5312          * Gets the value of the showBoxes property.
5313          * 
5314          * @return
5315          *     possible object is
5316          *     {@link Boolean }
5317          *     
5318          */
5319         public Boolean isShowBoxes() {
5320             return showBoxes;
5321         }
5322
5323         /**
5324          * Sets the value of the showBoxes property.
5325          * 
5326          * @param value
5327          *     allowed object is
5328          *     {@link Boolean }
5329          *     
5330          */
5331         public void setShowBoxes(Boolean value) {
5332             this.showBoxes = value;
5333         }
5334
5335         /**
5336          * Gets the value of the wrapAlignment property.
5337          * 
5338          * @return
5339          *     possible object is
5340          *     {@link Boolean }
5341          *     
5342          */
5343         public Boolean isWrapAlignment() {
5344             return wrapAlignment;
5345         }
5346
5347         /**
5348          * Sets the value of the wrapAlignment property.
5349          * 
5350          * @param value
5351          *     allowed object is
5352          *     {@link Boolean }
5353          *     
5354          */
5355         public void setWrapAlignment(Boolean value) {
5356             this.wrapAlignment = value;
5357         }
5358
5359         /**
5360          * Gets the value of the renderGaps property.
5361          * 
5362          * @return
5363          *     possible object is
5364          *     {@link Boolean }
5365          *     
5366          */
5367         public Boolean isRenderGaps() {
5368             return renderGaps;
5369         }
5370
5371         /**
5372          * Sets the value of the renderGaps property.
5373          * 
5374          * @param value
5375          *     allowed object is
5376          *     {@link Boolean }
5377          *     
5378          */
5379         public void setRenderGaps(Boolean value) {
5380             this.renderGaps = value;
5381         }
5382
5383         /**
5384          * Gets the value of the showSequenceFeatures property.
5385          * 
5386          * @return
5387          *     possible object is
5388          *     {@link Boolean }
5389          *     
5390          */
5391         public Boolean isShowSequenceFeatures() {
5392             return showSequenceFeatures;
5393         }
5394
5395         /**
5396          * Sets the value of the showSequenceFeatures property.
5397          * 
5398          * @param value
5399          *     allowed object is
5400          *     {@link Boolean }
5401          *     
5402          */
5403         public void setShowSequenceFeatures(Boolean value) {
5404             this.showSequenceFeatures = value;
5405         }
5406
5407         /**
5408          * Gets the value of the showNPfeatureTooltip property.
5409          * 
5410          * @return
5411          *     possible object is
5412          *     {@link Boolean }
5413          *     
5414          */
5415         public Boolean isShowNPfeatureTooltip() {
5416             return showNPfeatureTooltip;
5417         }
5418
5419         /**
5420          * Sets the value of the showNPfeatureTooltip property.
5421          * 
5422          * @param value
5423          *     allowed object is
5424          *     {@link Boolean }
5425          *     
5426          */
5427         public void setShowNPfeatureTooltip(Boolean value) {
5428             this.showNPfeatureTooltip = value;
5429         }
5430
5431         /**
5432          * Gets the value of the showDbRefTooltip property.
5433          * 
5434          * @return
5435          *     possible object is
5436          *     {@link Boolean }
5437          *     
5438          */
5439         public Boolean isShowDbRefTooltip() {
5440             return showDbRefTooltip;
5441         }
5442
5443         /**
5444          * Sets the value of the showDbRefTooltip property.
5445          * 
5446          * @param value
5447          *     allowed object is
5448          *     {@link Boolean }
5449          *     
5450          */
5451         public void setShowDbRefTooltip(Boolean value) {
5452             this.showDbRefTooltip = value;
5453         }
5454
5455         /**
5456          * Gets the value of the followHighlight property.
5457          * 
5458          * @return
5459          *     possible object is
5460          *     {@link Boolean }
5461          *     
5462          */
5463         public boolean isFollowHighlight() {
5464             if (followHighlight == null) {
5465                 return true;
5466             } else {
5467                 return followHighlight;
5468             }
5469         }
5470
5471         /**
5472          * Sets the value of the followHighlight property.
5473          * 
5474          * @param value
5475          *     allowed object is
5476          *     {@link Boolean }
5477          *     
5478          */
5479         public void setFollowHighlight(Boolean value) {
5480             this.followHighlight = value;
5481         }
5482
5483         /**
5484          * Gets the value of the followSelection property.
5485          * 
5486          * @return
5487          *     possible object is
5488          *     {@link Boolean }
5489          *     
5490          */
5491         public boolean isFollowSelection() {
5492             if (followSelection == null) {
5493                 return true;
5494             } else {
5495                 return followSelection;
5496             }
5497         }
5498
5499         /**
5500          * Sets the value of the followSelection property.
5501          * 
5502          * @param value
5503          *     allowed object is
5504          *     {@link Boolean }
5505          *     
5506          */
5507         public void setFollowSelection(Boolean value) {
5508             this.followSelection = value;
5509         }
5510
5511         /**
5512          * Gets the value of the showAnnotation property.
5513          * 
5514          * @return
5515          *     possible object is
5516          *     {@link Boolean }
5517          *     
5518          */
5519         public Boolean isShowAnnotation() {
5520             return showAnnotation;
5521         }
5522
5523         /**
5524          * Sets the value of the showAnnotation property.
5525          * 
5526          * @param value
5527          *     allowed object is
5528          *     {@link Boolean }
5529          *     
5530          */
5531         public void setShowAnnotation(Boolean value) {
5532             this.showAnnotation = value;
5533         }
5534
5535         /**
5536          * Gets the value of the centreColumnLabels property.
5537          * 
5538          * @return
5539          *     possible object is
5540          *     {@link Boolean }
5541          *     
5542          */
5543         public boolean isCentreColumnLabels() {
5544             if (centreColumnLabels == null) {
5545                 return false;
5546             } else {
5547                 return centreColumnLabels;
5548             }
5549         }
5550
5551         /**
5552          * Sets the value of the centreColumnLabels property.
5553          * 
5554          * @param value
5555          *     allowed object is
5556          *     {@link Boolean }
5557          *     
5558          */
5559         public void setCentreColumnLabels(Boolean value) {
5560             this.centreColumnLabels = value;
5561         }
5562
5563         /**
5564          * Gets the value of the showGroupConservation property.
5565          * 
5566          * @return
5567          *     possible object is
5568          *     {@link Boolean }
5569          *     
5570          */
5571         public boolean isShowGroupConservation() {
5572             if (showGroupConservation == null) {
5573                 return false;
5574             } else {
5575                 return showGroupConservation;
5576             }
5577         }
5578
5579         /**
5580          * Sets the value of the showGroupConservation property.
5581          * 
5582          * @param value
5583          *     allowed object is
5584          *     {@link Boolean }
5585          *     
5586          */
5587         public void setShowGroupConservation(Boolean value) {
5588             this.showGroupConservation = value;
5589         }
5590
5591         /**
5592          * Gets the value of the showGroupConsensus property.
5593          * 
5594          * @return
5595          *     possible object is
5596          *     {@link Boolean }
5597          *     
5598          */
5599         public boolean isShowGroupConsensus() {
5600             if (showGroupConsensus == null) {
5601                 return false;
5602             } else {
5603                 return showGroupConsensus;
5604             }
5605         }
5606
5607         /**
5608          * Sets the value of the showGroupConsensus property.
5609          * 
5610          * @param value
5611          *     allowed object is
5612          *     {@link Boolean }
5613          *     
5614          */
5615         public void setShowGroupConsensus(Boolean value) {
5616             this.showGroupConsensus = value;
5617         }
5618
5619         /**
5620          * Gets the value of the showConsensusHistogram property.
5621          * 
5622          * @return
5623          *     possible object is
5624          *     {@link Boolean }
5625          *     
5626          */
5627         public boolean isShowConsensusHistogram() {
5628             if (showConsensusHistogram == null) {
5629                 return true;
5630             } else {
5631                 return showConsensusHistogram;
5632             }
5633         }
5634
5635         /**
5636          * Sets the value of the showConsensusHistogram property.
5637          * 
5638          * @param value
5639          *     allowed object is
5640          *     {@link Boolean }
5641          *     
5642          */
5643         public void setShowConsensusHistogram(Boolean value) {
5644             this.showConsensusHistogram = value;
5645         }
5646
5647         /**
5648          * Gets the value of the showSequenceLogo property.
5649          * 
5650          * @return
5651          *     possible object is
5652          *     {@link Boolean }
5653          *     
5654          */
5655         public boolean isShowSequenceLogo() {
5656             if (showSequenceLogo == null) {
5657                 return false;
5658             } else {
5659                 return showSequenceLogo;
5660             }
5661         }
5662
5663         /**
5664          * Sets the value of the showSequenceLogo property.
5665          * 
5666          * @param value
5667          *     allowed object is
5668          *     {@link Boolean }
5669          *     
5670          */
5671         public void setShowSequenceLogo(Boolean value) {
5672             this.showSequenceLogo = value;
5673         }
5674
5675         /**
5676          * Gets the value of the normaliseSequenceLogo property.
5677          * 
5678          * @return
5679          *     possible object is
5680          *     {@link Boolean }
5681          *     
5682          */
5683         public boolean isNormaliseSequenceLogo() {
5684             if (normaliseSequenceLogo == null) {
5685                 return false;
5686             } else {
5687                 return normaliseSequenceLogo;
5688             }
5689         }
5690
5691         /**
5692          * Sets the value of the normaliseSequenceLogo property.
5693          * 
5694          * @param value
5695          *     allowed object is
5696          *     {@link Boolean }
5697          *     
5698          */
5699         public void setNormaliseSequenceLogo(Boolean value) {
5700             this.normaliseSequenceLogo = value;
5701         }
5702
5703         /**
5704          * Gets the value of the ignoreGapsinConsensus property.
5705          * 
5706          * @return
5707          *     possible object is
5708          *     {@link Boolean }
5709          *     
5710          */
5711         public boolean isIgnoreGapsinConsensus() {
5712             if (ignoreGapsinConsensus == null) {
5713                 return true;
5714             } else {
5715                 return ignoreGapsinConsensus;
5716             }
5717         }
5718
5719         /**
5720          * Sets the value of the ignoreGapsinConsensus property.
5721          * 
5722          * @param value
5723          *     allowed object is
5724          *     {@link Boolean }
5725          *     
5726          */
5727         public void setIgnoreGapsinConsensus(Boolean value) {
5728             this.ignoreGapsinConsensus = value;
5729         }
5730
5731         /**
5732          * Gets the value of the startRes property.
5733          * 
5734          * @return
5735          *     possible object is
5736          *     {@link Integer }
5737          *     
5738          */
5739         public Integer getStartRes() {
5740             return startRes;
5741         }
5742
5743         /**
5744          * Sets the value of the startRes property.
5745          * 
5746          * @param value
5747          *     allowed object is
5748          *     {@link Integer }
5749          *     
5750          */
5751         public void setStartRes(Integer value) {
5752             this.startRes = value;
5753         }
5754
5755         /**
5756          * Gets the value of the startSeq property.
5757          * 
5758          * @return
5759          *     possible object is
5760          *     {@link Integer }
5761          *     
5762          */
5763         public Integer getStartSeq() {
5764             return startSeq;
5765         }
5766
5767         /**
5768          * Sets the value of the startSeq property.
5769          * 
5770          * @param value
5771          *     allowed object is
5772          *     {@link Integer }
5773          *     
5774          */
5775         public void setStartSeq(Integer value) {
5776             this.startSeq = value;
5777         }
5778
5779         /**
5780          * Gets the value of the fontName property.
5781          * 
5782          * @return
5783          *     possible object is
5784          *     {@link String }
5785          *     
5786          */
5787         public String getFontName() {
5788             return fontName;
5789         }
5790
5791         /**
5792          * Sets the value of the fontName property.
5793          * 
5794          * @param value
5795          *     allowed object is
5796          *     {@link String }
5797          *     
5798          */
5799         public void setFontName(String value) {
5800             this.fontName = value;
5801         }
5802
5803         /**
5804          * Gets the value of the fontSize property.
5805          * 
5806          * @return
5807          *     possible object is
5808          *     {@link Integer }
5809          *     
5810          */
5811         public Integer getFontSize() {
5812             return fontSize;
5813         }
5814
5815         /**
5816          * Sets the value of the fontSize property.
5817          * 
5818          * @param value
5819          *     allowed object is
5820          *     {@link Integer }
5821          *     
5822          */
5823         public void setFontSize(Integer value) {
5824             this.fontSize = value;
5825         }
5826
5827         /**
5828          * Gets the value of the fontStyle property.
5829          * 
5830          * @return
5831          *     possible object is
5832          *     {@link Integer }
5833          *     
5834          */
5835         public Integer getFontStyle() {
5836             return fontStyle;
5837         }
5838
5839         /**
5840          * Sets the value of the fontStyle property.
5841          * 
5842          * @param value
5843          *     allowed object is
5844          *     {@link Integer }
5845          *     
5846          */
5847         public void setFontStyle(Integer value) {
5848             this.fontStyle = value;
5849         }
5850
5851         /**
5852          * Gets the value of the scaleProteinAsCdna property.
5853          * 
5854          * @return
5855          *     possible object is
5856          *     {@link Boolean }
5857          *     
5858          */
5859         public boolean isScaleProteinAsCdna() {
5860             if (scaleProteinAsCdna == null) {
5861                 return true;
5862             } else {
5863                 return scaleProteinAsCdna;
5864             }
5865         }
5866
5867         /**
5868          * Sets the value of the scaleProteinAsCdna property.
5869          * 
5870          * @param value
5871          *     allowed object is
5872          *     {@link Boolean }
5873          *     
5874          */
5875         public void setScaleProteinAsCdna(Boolean value) {
5876             this.scaleProteinAsCdna = value;
5877         }
5878
5879         /**
5880          * Gets the value of the viewName property.
5881          * 
5882          * @return
5883          *     possible object is
5884          *     {@link String }
5885          *     
5886          */
5887         public String getViewName() {
5888             return viewName;
5889         }
5890
5891         /**
5892          * Sets the value of the viewName property.
5893          * 
5894          * @param value
5895          *     allowed object is
5896          *     {@link String }
5897          *     
5898          */
5899         public void setViewName(String value) {
5900             this.viewName = value;
5901         }
5902
5903         /**
5904          * Gets the value of the sequenceSetId property.
5905          * 
5906          * @return
5907          *     possible object is
5908          *     {@link String }
5909          *     
5910          */
5911         public String getSequenceSetId() {
5912             return sequenceSetId;
5913         }
5914
5915         /**
5916          * Sets the value of the sequenceSetId property.
5917          * 
5918          * @param value
5919          *     allowed object is
5920          *     {@link String }
5921          *     
5922          */
5923         public void setSequenceSetId(String value) {
5924             this.sequenceSetId = value;
5925         }
5926
5927         /**
5928          * Gets the value of the gatheredViews property.
5929          * 
5930          * @return
5931          *     possible object is
5932          *     {@link Boolean }
5933          *     
5934          */
5935         public Boolean isGatheredViews() {
5936             return gatheredViews;
5937         }
5938
5939         /**
5940          * Sets the value of the gatheredViews property.
5941          * 
5942          * @param value
5943          *     allowed object is
5944          *     {@link Boolean }
5945          *     
5946          */
5947         public void setGatheredViews(Boolean value) {
5948             this.gatheredViews = value;
5949         }
5950
5951         /**
5952          * Gets the value of the textCol1 property.
5953          * 
5954          * @return
5955          *     possible object is
5956          *     {@link Integer }
5957          *     
5958          */
5959         public Integer getTextCol1() {
5960             return textCol1;
5961         }
5962
5963         /**
5964          * Sets the value of the textCol1 property.
5965          * 
5966          * @param value
5967          *     allowed object is
5968          *     {@link Integer }
5969          *     
5970          */
5971         public void setTextCol1(Integer value) {
5972             this.textCol1 = value;
5973         }
5974
5975         /**
5976          * Gets the value of the textCol2 property.
5977          * 
5978          * @return
5979          *     possible object is
5980          *     {@link Integer }
5981          *     
5982          */
5983         public Integer getTextCol2() {
5984             return textCol2;
5985         }
5986
5987         /**
5988          * Sets the value of the textCol2 property.
5989          * 
5990          * @param value
5991          *     allowed object is
5992          *     {@link Integer }
5993          *     
5994          */
5995         public void setTextCol2(Integer value) {
5996             this.textCol2 = value;
5997         }
5998
5999         /**
6000          * Gets the value of the textColThreshold property.
6001          * 
6002          * @return
6003          *     possible object is
6004          *     {@link Integer }
6005          *     
6006          */
6007         public Integer getTextColThreshold() {
6008             return textColThreshold;
6009         }
6010
6011         /**
6012          * Sets the value of the textColThreshold property.
6013          * 
6014          * @param value
6015          *     allowed object is
6016          *     {@link Integer }
6017          *     
6018          */
6019         public void setTextColThreshold(Integer value) {
6020             this.textColThreshold = value;
6021         }
6022
6023         /**
6024          * Gets the value of the id property.
6025          * 
6026          * @return
6027          *     possible object is
6028          *     {@link String }
6029          *     
6030          */
6031         public String getId() {
6032             return id;
6033         }
6034
6035         /**
6036          * Sets the value of the id property.
6037          * 
6038          * @param value
6039          *     allowed object is
6040          *     {@link String }
6041          *     
6042          */
6043         public void setId(String value) {
6044             this.id = value;
6045         }
6046
6047         /**
6048          * Gets the value of the complementId property.
6049          * 
6050          * @return
6051          *     possible object is
6052          *     {@link String }
6053          *     
6054          */
6055         public String getComplementId() {
6056             return complementId;
6057         }
6058
6059         /**
6060          * Sets the value of the complementId property.
6061          * 
6062          * @param value
6063          *     allowed object is
6064          *     {@link String }
6065          *     
6066          */
6067         public void setComplementId(String value) {
6068             this.complementId = value;
6069         }
6070
6071         /**
6072          * Gets the value of the showComplementFeatures property.
6073          * 
6074          * @return
6075          *     possible object is
6076          *     {@link Boolean }
6077          *     
6078          */
6079         public boolean isShowComplementFeatures() {
6080             if (showComplementFeatures == null) {
6081                 return false;
6082             } else {
6083                 return showComplementFeatures;
6084             }
6085         }
6086
6087         /**
6088          * Sets the value of the showComplementFeatures property.
6089          * 
6090          * @param value
6091          *     allowed object is
6092          *     {@link Boolean }
6093          *     
6094          */
6095         public void setShowComplementFeatures(Boolean value) {
6096             this.showComplementFeatures = value;
6097         }
6098
6099         /**
6100          * Gets the value of the showComplementFeaturesOnTop property.
6101          * 
6102          * @return
6103          *     possible object is
6104          *     {@link Boolean }
6105          *     
6106          */
6107         public boolean isShowComplementFeaturesOnTop() {
6108             if (showComplementFeaturesOnTop == null) {
6109                 return false;
6110             } else {
6111                 return showComplementFeaturesOnTop;
6112             }
6113         }
6114
6115         /**
6116          * Sets the value of the showComplementFeaturesOnTop property.
6117          * 
6118          * @param value
6119          *     allowed object is
6120          *     {@link Boolean }
6121          *     
6122          */
6123         public void setShowComplementFeaturesOnTop(Boolean value) {
6124             this.showComplementFeaturesOnTop = value;
6125         }
6126
6127         /**
6128          * Gets the value of the width property.
6129          * 
6130          * @return
6131          *     possible object is
6132          *     {@link Integer }
6133          *     
6134          */
6135         public Integer getWidth() {
6136             return width;
6137         }
6138
6139         /**
6140          * Sets the value of the width property.
6141          * 
6142          * @param value
6143          *     allowed object is
6144          *     {@link Integer }
6145          *     
6146          */
6147         public void setWidth(Integer value) {
6148             this.width = value;
6149         }
6150
6151         /**
6152          * Gets the value of the height property.
6153          * 
6154          * @return
6155          *     possible object is
6156          *     {@link Integer }
6157          *     
6158          */
6159         public Integer getHeight() {
6160             return height;
6161         }
6162
6163         /**
6164          * Sets the value of the height property.
6165          * 
6166          * @param value
6167          *     allowed object is
6168          *     {@link Integer }
6169          *     
6170          */
6171         public void setHeight(Integer value) {
6172             this.height = value;
6173         }
6174
6175         /**
6176          * Gets the value of the xpos property.
6177          * 
6178          * @return
6179          *     possible object is
6180          *     {@link Integer }
6181          *     
6182          */
6183         public Integer getXpos() {
6184             return xpos;
6185         }
6186
6187         /**
6188          * Sets the value of the xpos property.
6189          * 
6190          * @param value
6191          *     allowed object is
6192          *     {@link Integer }
6193          *     
6194          */
6195         public void setXpos(Integer value) {
6196             this.xpos = value;
6197         }
6198
6199         /**
6200          * Gets the value of the ypos property.
6201          * 
6202          * @return
6203          *     possible object is
6204          *     {@link Integer }
6205          *     
6206          */
6207         public Integer getYpos() {
6208             return ypos;
6209         }
6210
6211         /**
6212          * Sets the value of the ypos property.
6213          * 
6214          * @param value
6215          *     allowed object is
6216          *     {@link Integer }
6217          *     
6218          */
6219         public void setYpos(Integer value) {
6220             this.ypos = value;
6221         }
6222
6223
6224         /**
6225          * &lt;p&gt;Java class for anonymous complex type.
6226          * 
6227          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
6228          * 
6229          * &lt;pre&gt;
6230          * &amp;lt;complexType&amp;gt;
6231          *   &amp;lt;complexContent&amp;gt;
6232          *     &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
6233          *       &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6234          *       &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
6235          *       &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
6236          *     &amp;lt;/extension&amp;gt;
6237          *   &amp;lt;/complexContent&amp;gt;
6238          * &amp;lt;/complexType&amp;gt;
6239          * &lt;/pre&gt;
6240          * 
6241          * 
6242          */
6243         @XmlAccessorType(XmlAccessType.FIELD)
6244         @XmlType(name = "")
6245         public static class CalcIdParam
6246             extends WebServiceParameterSet
6247         {
6248
6249             @XmlAttribute(name = "calcId", required = true)
6250             protected String calcId;
6251             @XmlAttribute(name = "needsUpdate")
6252             protected Boolean needsUpdate;
6253             @XmlAttribute(name = "autoUpdate", required = true)
6254             protected boolean autoUpdate;
6255
6256             /**
6257              * Gets the value of the calcId property.
6258              * 
6259              * @return
6260              *     possible object is
6261              *     {@link String }
6262              *     
6263              */
6264             public String getCalcId() {
6265                 return calcId;
6266             }
6267
6268             /**
6269              * Sets the value of the calcId property.
6270              * 
6271              * @param value
6272              *     allowed object is
6273              *     {@link String }
6274              *     
6275              */
6276             public void setCalcId(String value) {
6277                 this.calcId = value;
6278             }
6279
6280             /**
6281              * Gets the value of the needsUpdate property.
6282              * 
6283              * @return
6284              *     possible object is
6285              *     {@link Boolean }
6286              *     
6287              */
6288             public boolean isNeedsUpdate() {
6289                 if (needsUpdate == null) {
6290                     return false;
6291                 } else {
6292                     return needsUpdate;
6293                 }
6294             }
6295
6296             /**
6297              * Sets the value of the needsUpdate property.
6298              * 
6299              * @param value
6300              *     allowed object is
6301              *     {@link Boolean }
6302              *     
6303              */
6304             public void setNeedsUpdate(Boolean value) {
6305                 this.needsUpdate = value;
6306             }
6307
6308             /**
6309              * Gets the value of the autoUpdate property.
6310              * 
6311              */
6312             public boolean isAutoUpdate() {
6313                 return autoUpdate;
6314             }
6315
6316             /**
6317              * Sets the value of the autoUpdate property.
6318              * 
6319              */
6320             public void setAutoUpdate(boolean value) {
6321                 this.autoUpdate = value;
6322             }
6323
6324         }
6325
6326
6327         /**
6328          * &lt;p&gt;Java class for anonymous complex type.
6329          * 
6330          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
6331          * 
6332          * &lt;pre&gt;
6333          * &amp;lt;complexType&amp;gt;
6334          *   &amp;lt;complexContent&amp;gt;
6335          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
6336          *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6337          *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6338          *     &amp;lt;/restriction&amp;gt;
6339          *   &amp;lt;/complexContent&amp;gt;
6340          * &amp;lt;/complexType&amp;gt;
6341          * &lt;/pre&gt;
6342          * 
6343          * 
6344          */
6345         @XmlAccessorType(XmlAccessType.FIELD)
6346         @XmlType(name = "")
6347         public static class HiddenColumns {
6348
6349             @XmlAttribute(name = "start")
6350             protected Integer start;
6351             @XmlAttribute(name = "end")
6352             protected Integer end;
6353
6354             /**
6355              * Gets the value of the start property.
6356              * 
6357              * @return
6358              *     possible object is
6359              *     {@link Integer }
6360              *     
6361              */
6362             public Integer getStart() {
6363                 return start;
6364             }
6365
6366             /**
6367              * Sets the value of the start property.
6368              * 
6369              * @param value
6370              *     allowed object is
6371              *     {@link Integer }
6372              *     
6373              */
6374             public void setStart(Integer value) {
6375                 this.start = value;
6376             }
6377
6378             /**
6379              * Gets the value of the end property.
6380              * 
6381              * @return
6382              *     possible object is
6383              *     {@link Integer }
6384              *     
6385              */
6386             public Integer getEnd() {
6387                 return end;
6388             }
6389
6390             /**
6391              * Sets the value of the end property.
6392              * 
6393              * @param value
6394              *     allowed object is
6395              *     {@link Integer }
6396              *     
6397              */
6398             public void setEnd(Integer value) {
6399                 this.end = value;
6400             }
6401
6402         }
6403
6404     }
6405
6406 }