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[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     })
1969     public static class JSeq {
1970
1971         @XmlElement(namespace = "www.jalview.org")
1972         protected List<Feature> features;
1973         @XmlElement(namespace = "www.jalview.org")
1974         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1975         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1976         protected List<Integer> hiddenSequences;
1977         @XmlElement(namespace = "www.jalview.org")
1978         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1979         @XmlAttribute(name = "colour")
1980         protected Integer colour;
1981         @XmlAttribute(name = "start", required = true)
1982         protected int start;
1983         @XmlAttribute(name = "end", required = true)
1984         protected int end;
1985         @XmlAttribute(name = "id", required = true)
1986         protected String id;
1987         @XmlAttribute(name = "hidden")
1988         protected Boolean hidden;
1989         @XmlAttribute(name = "viewreference")
1990         protected Boolean viewreference;
1991
1992         /**
1993          * Gets the value of the features property.
1994          * 
1995          * &lt;p&gt;
1996          * This accessor method returns a reference to the live list,
1997          * not a snapshot. Therefore any modification you make to the
1998          * returned list will be present inside the JAXB object.
1999          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
2000          * 
2001          * &lt;p&gt;
2002          * For example, to add a new item, do as follows:
2003          * &lt;pre&gt;
2004          *    getFeatures().add(newItem);
2005          * &lt;/pre&gt;
2006          * 
2007          * 
2008          * &lt;p&gt;
2009          * Objects of the following type(s) are allowed in the list
2010          * {@link Feature }
2011          * 
2012          * 
2013          */
2014         public List<Feature> getFeatures() {
2015             if (features == null) {
2016                 features = new ArrayList<Feature>();
2017             }
2018             return this.features;
2019         }
2020
2021         /**
2022          * Gets the value of the pdbids property.
2023          * 
2024          * &lt;p&gt;
2025          * This accessor method returns a reference to the live list,
2026          * not a snapshot. Therefore any modification you make to the
2027          * returned list will be present inside the JAXB object.
2028          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
2029          * 
2030          * &lt;p&gt;
2031          * For example, to add a new item, do as follows:
2032          * &lt;pre&gt;
2033          *    getPdbids().add(newItem);
2034          * &lt;/pre&gt;
2035          * 
2036          * 
2037          * &lt;p&gt;
2038          * Objects of the following type(s) are allowed in the list
2039          * {@link JalviewModel.JSeq.Pdbids }
2040          * 
2041          * 
2042          */
2043         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2044             if (pdbids == null) {
2045                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2046             }
2047             return this.pdbids;
2048         }
2049
2050         /**
2051          * Gets the value of the hiddenSequences property.
2052          * 
2053          * &lt;p&gt;
2054          * This accessor method returns a reference to the live list,
2055          * not a snapshot. Therefore any modification you make to the
2056          * returned list will be present inside the JAXB object.
2057          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
2058          * 
2059          * &lt;p&gt;
2060          * For example, to add a new item, do as follows:
2061          * &lt;pre&gt;
2062          *    getHiddenSequences().add(newItem);
2063          * &lt;/pre&gt;
2064          * 
2065          * 
2066          * &lt;p&gt;
2067          * Objects of the following type(s) are allowed in the list
2068          * {@link Integer }
2069          * 
2070          * 
2071          */
2072         public List<Integer> getHiddenSequences() {
2073             if (hiddenSequences == null) {
2074                 hiddenSequences = new ArrayList<Integer>();
2075             }
2076             return this.hiddenSequences;
2077         }
2078
2079         /**
2080          * Gets the value of the rnaViewer property.
2081          * 
2082          * &lt;p&gt;
2083          * This accessor method returns a reference to the live list,
2084          * not a snapshot. Therefore any modification you make to the
2085          * returned list will be present inside the JAXB object.
2086          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
2087          * 
2088          * &lt;p&gt;
2089          * For example, to add a new item, do as follows:
2090          * &lt;pre&gt;
2091          *    getRnaViewer().add(newItem);
2092          * &lt;/pre&gt;
2093          * 
2094          * 
2095          * &lt;p&gt;
2096          * Objects of the following type(s) are allowed in the list
2097          * {@link JalviewModel.JSeq.RnaViewer }
2098          * 
2099          * 
2100          */
2101         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2102             if (rnaViewer == null) {
2103                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2104             }
2105             return this.rnaViewer;
2106         }
2107
2108         /**
2109          * Gets the value of the colour property.
2110          * 
2111          * @return
2112          *     possible object is
2113          *     {@link Integer }
2114          *     
2115          */
2116         public Integer getColour() {
2117             return colour;
2118         }
2119
2120         /**
2121          * Sets the value of the colour property.
2122          * 
2123          * @param value
2124          *     allowed object is
2125          *     {@link Integer }
2126          *     
2127          */
2128         public void setColour(Integer value) {
2129             this.colour = value;
2130         }
2131
2132         /**
2133          * Gets the value of the start property.
2134          * 
2135          */
2136         public int getStart() {
2137             return start;
2138         }
2139
2140         /**
2141          * Sets the value of the start property.
2142          * 
2143          */
2144         public void setStart(int value) {
2145             this.start = value;
2146         }
2147
2148         /**
2149          * Gets the value of the end property.
2150          * 
2151          */
2152         public int getEnd() {
2153             return end;
2154         }
2155
2156         /**
2157          * Sets the value of the end property.
2158          * 
2159          */
2160         public void setEnd(int value) {
2161             this.end = value;
2162         }
2163
2164         /**
2165          * Gets the value of the id property.
2166          * 
2167          * @return
2168          *     possible object is
2169          *     {@link String }
2170          *     
2171          */
2172         public String getId() {
2173             return id;
2174         }
2175
2176         /**
2177          * Sets the value of the id property.
2178          * 
2179          * @param value
2180          *     allowed object is
2181          *     {@link String }
2182          *     
2183          */
2184         public void setId(String value) {
2185             this.id = value;
2186         }
2187
2188         /**
2189          * Gets the value of the hidden property.
2190          * 
2191          * @return
2192          *     possible object is
2193          *     {@link Boolean }
2194          *     
2195          */
2196         public Boolean isHidden() {
2197             return hidden;
2198         }
2199
2200         /**
2201          * Sets the value of the hidden property.
2202          * 
2203          * @param value
2204          *     allowed object is
2205          *     {@link Boolean }
2206          *     
2207          */
2208         public void setHidden(Boolean value) {
2209             this.hidden = value;
2210         }
2211
2212         /**
2213          * Gets the value of the viewreference property.
2214          * 
2215          * @return
2216          *     possible object is
2217          *     {@link Boolean }
2218          *     
2219          */
2220         public Boolean isViewreference() {
2221             return viewreference;
2222         }
2223
2224         /**
2225          * Sets the value of the viewreference property.
2226          * 
2227          * @param value
2228          *     allowed object is
2229          *     {@link Boolean }
2230          *     
2231          */
2232         public void setViewreference(Boolean value) {
2233             this.viewreference = value;
2234         }
2235
2236
2237         /**
2238          * &lt;p&gt;Java class for anonymous complex type.
2239          * 
2240          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2241          * 
2242          * &lt;pre&gt;
2243          * &amp;lt;complexType&amp;gt;
2244          *   &amp;lt;complexContent&amp;gt;
2245          *     &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
2246          *       &amp;lt;sequence&amp;gt;
2247          *         &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
2248          *           &amp;lt;complexType&amp;gt;
2249          *             &amp;lt;simpleContent&amp;gt;
2250          *               &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2251          *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2252          *                 &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2253          *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2254          *                 &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2255          *                 &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
2256          *                 &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2257          *                 &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2258          *               &amp;lt;/extension&amp;gt;
2259          *             &amp;lt;/simpleContent&amp;gt;
2260          *           &amp;lt;/complexType&amp;gt;
2261          *         &amp;lt;/element&amp;gt;
2262          *       &amp;lt;/sequence&amp;gt;
2263          *     &amp;lt;/extension&amp;gt;
2264          *   &amp;lt;/complexContent&amp;gt;
2265          * &amp;lt;/complexType&amp;gt;
2266          * &lt;/pre&gt;
2267          * 
2268          * 
2269          */
2270         @XmlAccessorType(XmlAccessType.FIELD)
2271         @XmlType(name = "", propOrder = {
2272             "structureState"
2273         })
2274         public static class Pdbids
2275             extends Pdbentry
2276         {
2277
2278             @XmlElement(namespace = "www.jalview.org")
2279             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2280
2281             /**
2282              * Gets the value of the structureState property.
2283              * 
2284              * &lt;p&gt;
2285              * This accessor method returns a reference to the live list,
2286              * not a snapshot. Therefore any modification you make to the
2287              * returned list will be present inside the JAXB object.
2288              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
2289              * 
2290              * &lt;p&gt;
2291              * For example, to add a new item, do as follows:
2292              * &lt;pre&gt;
2293              *    getStructureState().add(newItem);
2294              * &lt;/pre&gt;
2295              * 
2296              * 
2297              * &lt;p&gt;
2298              * Objects of the following type(s) are allowed in the list
2299              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2300              * 
2301              * 
2302              */
2303             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2304                 if (structureState == null) {
2305                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2306                 }
2307                 return this.structureState;
2308             }
2309
2310
2311             /**
2312              * &lt;p&gt;Java class for anonymous complex type.
2313              * 
2314              * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2315              * 
2316              * &lt;pre&gt;
2317              * &amp;lt;complexType&amp;gt;
2318              *   &amp;lt;simpleContent&amp;gt;
2319              *     &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2320              *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2321              *       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2322              *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2323              *       &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2324              *       &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
2325              *       &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2326              *       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2327              *     &amp;lt;/extension&amp;gt;
2328              *   &amp;lt;/simpleContent&amp;gt;
2329              * &amp;lt;/complexType&amp;gt;
2330              * &lt;/pre&gt;
2331              * 
2332              * 
2333              */
2334             @XmlAccessorType(XmlAccessType.FIELD)
2335             @XmlType(name = "", propOrder = {
2336                 "value"
2337             })
2338             public static class StructureState {
2339
2340                 @XmlValue
2341                 protected String value;
2342                 @XmlAttribute(name = "visible")
2343                 protected Boolean visible;
2344                 @XmlAttribute(name = "viewId")
2345                 protected String viewId;
2346                 @XmlAttribute(name = "alignwithAlignPanel")
2347                 protected Boolean alignwithAlignPanel;
2348                 @XmlAttribute(name = "colourwithAlignPanel")
2349                 protected Boolean colourwithAlignPanel;
2350                 @XmlAttribute(name = "colourByJmol")
2351                 protected Boolean colourByJmol;
2352                 @XmlAttribute(name = "type")
2353                 protected String type;
2354                 @XmlAttribute(name = "width")
2355                 protected Integer width;
2356                 @XmlAttribute(name = "height")
2357                 protected Integer height;
2358                 @XmlAttribute(name = "xpos")
2359                 protected Integer xpos;
2360                 @XmlAttribute(name = "ypos")
2361                 protected Integer ypos;
2362
2363                 /**
2364                  * Gets the value of the value property.
2365                  * 
2366                  * @return
2367                  *     possible object is
2368                  *     {@link String }
2369                  *     
2370                  */
2371                 public String getValue() {
2372                     return value;
2373                 }
2374
2375                 /**
2376                  * Sets the value of the value property.
2377                  * 
2378                  * @param value
2379                  *     allowed object is
2380                  *     {@link String }
2381                  *     
2382                  */
2383                 public void setValue(String value) {
2384                     this.value = value;
2385                 }
2386
2387                 /**
2388                  * Gets the value of the visible property.
2389                  * 
2390                  * @return
2391                  *     possible object is
2392                  *     {@link Boolean }
2393                  *     
2394                  */
2395                 public Boolean isVisible() {
2396                     return visible;
2397                 }
2398
2399                 /**
2400                  * Sets the value of the visible property.
2401                  * 
2402                  * @param value
2403                  *     allowed object is
2404                  *     {@link Boolean }
2405                  *     
2406                  */
2407                 public void setVisible(Boolean value) {
2408                     this.visible = value;
2409                 }
2410
2411                 /**
2412                  * Gets the value of the viewId property.
2413                  * 
2414                  * @return
2415                  *     possible object is
2416                  *     {@link String }
2417                  *     
2418                  */
2419                 public String getViewId() {
2420                     return viewId;
2421                 }
2422
2423                 /**
2424                  * Sets the value of the viewId property.
2425                  * 
2426                  * @param value
2427                  *     allowed object is
2428                  *     {@link String }
2429                  *     
2430                  */
2431                 public void setViewId(String value) {
2432                     this.viewId = value;
2433                 }
2434
2435                 /**
2436                  * Gets the value of the alignwithAlignPanel property.
2437                  * 
2438                  * @return
2439                  *     possible object is
2440                  *     {@link Boolean }
2441                  *     
2442                  */
2443                 public boolean isAlignwithAlignPanel() {
2444                     if (alignwithAlignPanel == null) {
2445                         return true;
2446                     } else {
2447                         return alignwithAlignPanel;
2448                     }
2449                 }
2450
2451                 /**
2452                  * Sets the value of the alignwithAlignPanel property.
2453                  * 
2454                  * @param value
2455                  *     allowed object is
2456                  *     {@link Boolean }
2457                  *     
2458                  */
2459                 public void setAlignwithAlignPanel(Boolean value) {
2460                     this.alignwithAlignPanel = value;
2461                 }
2462
2463                 /**
2464                  * Gets the value of the colourwithAlignPanel property.
2465                  * 
2466                  * @return
2467                  *     possible object is
2468                  *     {@link Boolean }
2469                  *     
2470                  */
2471                 public boolean isColourwithAlignPanel() {
2472                     if (colourwithAlignPanel == null) {
2473                         return false;
2474                     } else {
2475                         return colourwithAlignPanel;
2476                     }
2477                 }
2478
2479                 /**
2480                  * Sets the value of the colourwithAlignPanel property.
2481                  * 
2482                  * @param value
2483                  *     allowed object is
2484                  *     {@link Boolean }
2485                  *     
2486                  */
2487                 public void setColourwithAlignPanel(Boolean value) {
2488                     this.colourwithAlignPanel = value;
2489                 }
2490
2491                 /**
2492                  * Gets the value of the colourByJmol property.
2493                  * 
2494                  * @return
2495                  *     possible object is
2496                  *     {@link Boolean }
2497                  *     
2498                  */
2499                 public boolean isColourByJmol() {
2500                     if (colourByJmol == null) {
2501                         return true;
2502                     } else {
2503                         return colourByJmol;
2504                     }
2505                 }
2506
2507                 /**
2508                  * Sets the value of the colourByJmol property.
2509                  * 
2510                  * @param value
2511                  *     allowed object is
2512                  *     {@link Boolean }
2513                  *     
2514                  */
2515                 public void setColourByJmol(Boolean value) {
2516                     this.colourByJmol = value;
2517                 }
2518
2519                 /**
2520                  * Gets the value of the type property.
2521                  * 
2522                  * @return
2523                  *     possible object is
2524                  *     {@link String }
2525                  *     
2526                  */
2527                 public String getType() {
2528                     return type;
2529                 }
2530
2531                 /**
2532                  * Sets the value of the type property.
2533                  * 
2534                  * @param value
2535                  *     allowed object is
2536                  *     {@link String }
2537                  *     
2538                  */
2539                 public void setType(String value) {
2540                     this.type = value;
2541                 }
2542
2543                 /**
2544                  * Gets the value of the width property.
2545                  * 
2546                  * @return
2547                  *     possible object is
2548                  *     {@link Integer }
2549                  *     
2550                  */
2551                 public Integer getWidth() {
2552                     return width;
2553                 }
2554
2555                 /**
2556                  * Sets the value of the width property.
2557                  * 
2558                  * @param value
2559                  *     allowed object is
2560                  *     {@link Integer }
2561                  *     
2562                  */
2563                 public void setWidth(Integer value) {
2564                     this.width = value;
2565                 }
2566
2567                 /**
2568                  * Gets the value of the height property.
2569                  * 
2570                  * @return
2571                  *     possible object is
2572                  *     {@link Integer }
2573                  *     
2574                  */
2575                 public Integer getHeight() {
2576                     return height;
2577                 }
2578
2579                 /**
2580                  * Sets the value of the height property.
2581                  * 
2582                  * @param value
2583                  *     allowed object is
2584                  *     {@link Integer }
2585                  *     
2586                  */
2587                 public void setHeight(Integer value) {
2588                     this.height = value;
2589                 }
2590
2591                 /**
2592                  * Gets the value of the xpos property.
2593                  * 
2594                  * @return
2595                  *     possible object is
2596                  *     {@link Integer }
2597                  *     
2598                  */
2599                 public Integer getXpos() {
2600                     return xpos;
2601                 }
2602
2603                 /**
2604                  * Sets the value of the xpos property.
2605                  * 
2606                  * @param value
2607                  *     allowed object is
2608                  *     {@link Integer }
2609                  *     
2610                  */
2611                 public void setXpos(Integer value) {
2612                     this.xpos = value;
2613                 }
2614
2615                 /**
2616                  * Gets the value of the ypos property.
2617                  * 
2618                  * @return
2619                  *     possible object is
2620                  *     {@link Integer }
2621                  *     
2622                  */
2623                 public Integer getYpos() {
2624                     return ypos;
2625                 }
2626
2627                 /**
2628                  * Sets the value of the ypos property.
2629                  * 
2630                  * @param value
2631                  *     allowed object is
2632                  *     {@link Integer }
2633                  *     
2634                  */
2635                 public void setYpos(Integer value) {
2636                     this.ypos = value;
2637                 }
2638
2639             }
2640
2641         }
2642
2643
2644         /**
2645          * &lt;p&gt;Java class for anonymous complex type.
2646          * 
2647          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2648          * 
2649          * &lt;pre&gt;
2650          * &amp;lt;complexType&amp;gt;
2651          *   &amp;lt;complexContent&amp;gt;
2652          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2653          *       &amp;lt;sequence&amp;gt;
2654          *         &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
2655          *           &amp;lt;complexType&amp;gt;
2656          *             &amp;lt;complexContent&amp;gt;
2657          *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2658          *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2659          *                 &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2660          *                 &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2661          *                 &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2662          *               &amp;lt;/restriction&amp;gt;
2663          *             &amp;lt;/complexContent&amp;gt;
2664          *           &amp;lt;/complexType&amp;gt;
2665          *         &amp;lt;/element&amp;gt;
2666          *       &amp;lt;/sequence&amp;gt;
2667          *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2668          *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2669          *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2670          *       &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2671          *       &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2672          *     &amp;lt;/restriction&amp;gt;
2673          *   &amp;lt;/complexContent&amp;gt;
2674          * &amp;lt;/complexType&amp;gt;
2675          * &lt;/pre&gt;
2676          * 
2677          * 
2678          */
2679         @XmlAccessorType(XmlAccessType.FIELD)
2680         @XmlType(name = "", propOrder = {
2681             "secondaryStructure"
2682         })
2683         public static class RnaViewer {
2684
2685             @XmlElement(namespace = "www.jalview.org", required = true)
2686             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2687             @XmlAttribute(name = "title")
2688             protected String title;
2689             @XmlAttribute(name = "viewId")
2690             protected String viewId;
2691             @XmlAttribute(name = "dividerLocation")
2692             protected Integer dividerLocation;
2693             @XmlAttribute(name = "selectedRna")
2694             protected Integer selectedRna;
2695             @XmlAttribute(name = "width")
2696             protected Integer width;
2697             @XmlAttribute(name = "height")
2698             protected Integer height;
2699             @XmlAttribute(name = "xpos")
2700             protected Integer xpos;
2701             @XmlAttribute(name = "ypos")
2702             protected Integer ypos;
2703
2704             /**
2705              * Gets the value of the secondaryStructure property.
2706              * 
2707              * &lt;p&gt;
2708              * This accessor method returns a reference to the live list,
2709              * not a snapshot. Therefore any modification you make to the
2710              * returned list will be present inside the JAXB object.
2711              * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure property.
2712              * 
2713              * &lt;p&gt;
2714              * For example, to add a new item, do as follows:
2715              * &lt;pre&gt;
2716              *    getSecondaryStructure().add(newItem);
2717              * &lt;/pre&gt;
2718              * 
2719              * 
2720              * &lt;p&gt;
2721              * Objects of the following type(s) are allowed in the list
2722              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2723              * 
2724              * 
2725              */
2726             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2727                 if (secondaryStructure == null) {
2728                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2729                 }
2730                 return this.secondaryStructure;
2731             }
2732
2733             /**
2734              * Gets the value of the title property.
2735              * 
2736              * @return
2737              *     possible object is
2738              *     {@link String }
2739              *     
2740              */
2741             public String getTitle() {
2742                 return title;
2743             }
2744
2745             /**
2746              * Sets the value of the title property.
2747              * 
2748              * @param value
2749              *     allowed object is
2750              *     {@link String }
2751              *     
2752              */
2753             public void setTitle(String value) {
2754                 this.title = value;
2755             }
2756
2757             /**
2758              * Gets the value of the viewId property.
2759              * 
2760              * @return
2761              *     possible object is
2762              *     {@link String }
2763              *     
2764              */
2765             public String getViewId() {
2766                 return viewId;
2767             }
2768
2769             /**
2770              * Sets the value of the viewId property.
2771              * 
2772              * @param value
2773              *     allowed object is
2774              *     {@link String }
2775              *     
2776              */
2777             public void setViewId(String value) {
2778                 this.viewId = value;
2779             }
2780
2781             /**
2782              * Gets the value of the dividerLocation property.
2783              * 
2784              * @return
2785              *     possible object is
2786              *     {@link Integer }
2787              *     
2788              */
2789             public Integer getDividerLocation() {
2790                 return dividerLocation;
2791             }
2792
2793             /**
2794              * Sets the value of the dividerLocation property.
2795              * 
2796              * @param value
2797              *     allowed object is
2798              *     {@link Integer }
2799              *     
2800              */
2801             public void setDividerLocation(Integer value) {
2802                 this.dividerLocation = value;
2803             }
2804
2805             /**
2806              * Gets the value of the selectedRna property.
2807              * 
2808              * @return
2809              *     possible object is
2810              *     {@link Integer }
2811              *     
2812              */
2813             public Integer getSelectedRna() {
2814                 return selectedRna;
2815             }
2816
2817             /**
2818              * Sets the value of the selectedRna property.
2819              * 
2820              * @param value
2821              *     allowed object is
2822              *     {@link Integer }
2823              *     
2824              */
2825             public void setSelectedRna(Integer value) {
2826                 this.selectedRna = value;
2827             }
2828
2829             /**
2830              * Gets the value of the width property.
2831              * 
2832              * @return
2833              *     possible object is
2834              *     {@link Integer }
2835              *     
2836              */
2837             public Integer getWidth() {
2838                 return width;
2839             }
2840
2841             /**
2842              * Sets the value of the width property.
2843              * 
2844              * @param value
2845              *     allowed object is
2846              *     {@link Integer }
2847              *     
2848              */
2849             public void setWidth(Integer value) {
2850                 this.width = value;
2851             }
2852
2853             /**
2854              * Gets the value of the height property.
2855              * 
2856              * @return
2857              *     possible object is
2858              *     {@link Integer }
2859              *     
2860              */
2861             public Integer getHeight() {
2862                 return height;
2863             }
2864
2865             /**
2866              * Sets the value of the height property.
2867              * 
2868              * @param value
2869              *     allowed object is
2870              *     {@link Integer }
2871              *     
2872              */
2873             public void setHeight(Integer value) {
2874                 this.height = value;
2875             }
2876
2877             /**
2878              * Gets the value of the xpos property.
2879              * 
2880              * @return
2881              *     possible object is
2882              *     {@link Integer }
2883              *     
2884              */
2885             public Integer getXpos() {
2886                 return xpos;
2887             }
2888
2889             /**
2890              * Sets the value of the xpos property.
2891              * 
2892              * @param value
2893              *     allowed object is
2894              *     {@link Integer }
2895              *     
2896              */
2897             public void setXpos(Integer value) {
2898                 this.xpos = value;
2899             }
2900
2901             /**
2902              * Gets the value of the ypos property.
2903              * 
2904              * @return
2905              *     possible object is
2906              *     {@link Integer }
2907              *     
2908              */
2909             public Integer getYpos() {
2910                 return ypos;
2911             }
2912
2913             /**
2914              * Sets the value of the ypos property.
2915              * 
2916              * @param value
2917              *     allowed object is
2918              *     {@link Integer }
2919              *     
2920              */
2921             public void setYpos(Integer value) {
2922                 this.ypos = value;
2923             }
2924
2925
2926             /**
2927              * &lt;p&gt;Java class for anonymous complex type.
2928              * 
2929              * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
2930              * 
2931              * &lt;pre&gt;
2932              * &amp;lt;complexType&amp;gt;
2933              *   &amp;lt;complexContent&amp;gt;
2934              *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2935              *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2936              *       &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2937              *       &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2938              *       &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2939              *     &amp;lt;/restriction&amp;gt;
2940              *   &amp;lt;/complexContent&amp;gt;
2941              * &amp;lt;/complexType&amp;gt;
2942              * &lt;/pre&gt;
2943              * 
2944              * 
2945              */
2946             @XmlAccessorType(XmlAccessType.FIELD)
2947             @XmlType(name = "")
2948             public static class SecondaryStructure {
2949
2950                 @XmlAttribute(name = "title")
2951                 protected String title;
2952                 @XmlAttribute(name = "annotationId", required = true)
2953                 protected String annotationId;
2954                 @XmlAttribute(name = "gapped")
2955                 protected Boolean gapped;
2956                 @XmlAttribute(name = "viewerState")
2957                 protected String viewerState;
2958
2959                 /**
2960                  * Gets the value of the title property.
2961                  * 
2962                  * @return
2963                  *     possible object is
2964                  *     {@link String }
2965                  *     
2966                  */
2967                 public String getTitle() {
2968                     return title;
2969                 }
2970
2971                 /**
2972                  * Sets the value of the title property.
2973                  * 
2974                  * @param value
2975                  *     allowed object is
2976                  *     {@link String }
2977                  *     
2978                  */
2979                 public void setTitle(String value) {
2980                     this.title = value;
2981                 }
2982
2983                 /**
2984                  * Gets the value of the annotationId property.
2985                  * 
2986                  * @return
2987                  *     possible object is
2988                  *     {@link String }
2989                  *     
2990                  */
2991                 public String getAnnotationId() {
2992                     return annotationId;
2993                 }
2994
2995                 /**
2996                  * Sets the value of the annotationId property.
2997                  * 
2998                  * @param value
2999                  *     allowed object is
3000                  *     {@link String }
3001                  *     
3002                  */
3003                 public void setAnnotationId(String value) {
3004                     this.annotationId = value;
3005                 }
3006
3007                 /**
3008                  * Gets the value of the gapped property.
3009                  * 
3010                  * @return
3011                  *     possible object is
3012                  *     {@link Boolean }
3013                  *     
3014                  */
3015                 public Boolean isGapped() {
3016                     return gapped;
3017                 }
3018
3019                 /**
3020                  * Sets the value of the gapped property.
3021                  * 
3022                  * @param value
3023                  *     allowed object is
3024                  *     {@link Boolean }
3025                  *     
3026                  */
3027                 public void setGapped(Boolean value) {
3028                     this.gapped = value;
3029                 }
3030
3031                 /**
3032                  * Gets the value of the viewerState property.
3033                  * 
3034                  * @return
3035                  *     possible object is
3036                  *     {@link String }
3037                  *     
3038                  */
3039                 public String getViewerState() {
3040                     return viewerState;
3041                 }
3042
3043                 /**
3044                  * Sets the value of the viewerState property.
3045                  * 
3046                  * @param value
3047                  *     allowed object is
3048                  *     {@link String }
3049                  *     
3050                  */
3051                 public void setViewerState(String value) {
3052                     this.viewerState = value;
3053                 }
3054
3055             }
3056
3057         }
3058
3059     }
3060
3061
3062     /**
3063      * &lt;p&gt;Java class for anonymous complex type.
3064      * 
3065      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3066      * 
3067      * &lt;pre&gt;
3068      * &amp;lt;complexType&amp;gt;
3069      *   &amp;lt;complexContent&amp;gt;
3070      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3071      *       &amp;lt;sequence&amp;gt;
3072      *         &amp;lt;element name="sequencePoint" maxOccurs="unbounded"&amp;gt;
3073      *           &amp;lt;complexType&amp;gt;
3074      *             &amp;lt;complexContent&amp;gt;
3075      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3076      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3077      *                 &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3078      *               &amp;lt;/restriction&amp;gt;
3079      *             &amp;lt;/complexContent&amp;gt;
3080      *           &amp;lt;/complexType&amp;gt;
3081      *         &amp;lt;/element&amp;gt;
3082      *         &amp;lt;element name="axis" maxOccurs="3" minOccurs="3"&amp;gt;
3083      *           &amp;lt;complexType&amp;gt;
3084      *             &amp;lt;complexContent&amp;gt;
3085      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3086      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3087      *               &amp;lt;/restriction&amp;gt;
3088      *             &amp;lt;/complexContent&amp;gt;
3089      *           &amp;lt;/complexType&amp;gt;
3090      *         &amp;lt;/element&amp;gt;
3091      *         &amp;lt;element name="seqPointMin"&amp;gt;
3092      *           &amp;lt;complexType&amp;gt;
3093      *             &amp;lt;complexContent&amp;gt;
3094      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3095      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3096      *               &amp;lt;/restriction&amp;gt;
3097      *             &amp;lt;/complexContent&amp;gt;
3098      *           &amp;lt;/complexType&amp;gt;
3099      *         &amp;lt;/element&amp;gt;
3100      *         &amp;lt;element name="seqPointMax"&amp;gt;
3101      *           &amp;lt;complexType&amp;gt;
3102      *             &amp;lt;complexContent&amp;gt;
3103      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3104      *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&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="pcaData" type="{www.jalview.org}PcaDataType"/&amp;gt;
3110      *       &amp;lt;/sequence&amp;gt;
3111      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
3112      *       &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
3113      *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3114      *       &amp;lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
3115      *       &amp;lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3116      *       &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3117      *       &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3118      *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3119      *       &amp;lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
3120      *       &amp;lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3121      *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3122      *     &amp;lt;/restriction&amp;gt;
3123      *   &amp;lt;/complexContent&amp;gt;
3124      * &amp;lt;/complexType&amp;gt;
3125      * &lt;/pre&gt;
3126      * 
3127      * 
3128      */
3129     @XmlAccessorType(XmlAccessType.FIELD)
3130     @XmlType(name = "", propOrder = {
3131         "sequencePoint",
3132         "axis",
3133         "seqPointMin",
3134         "seqPointMax",
3135         "pcaData"
3136     })
3137     public static class PcaViewer {
3138
3139         @XmlElement(namespace = "www.jalview.org", required = true)
3140         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3141         @XmlElement(namespace = "www.jalview.org", required = true)
3142         protected List<JalviewModel.PcaViewer.Axis> axis;
3143         @XmlElement(namespace = "www.jalview.org", required = true)
3144         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3145         @XmlElement(namespace = "www.jalview.org", required = true)
3146         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3147         @XmlElement(namespace = "www.jalview.org", required = true)
3148         protected PcaDataType pcaData;
3149         @XmlAttribute(name = "title")
3150         protected String title;
3151         @XmlAttribute(name = "scoreModelName")
3152         protected String scoreModelName;
3153         @XmlAttribute(name = "xDim")
3154         protected Integer xDim;
3155         @XmlAttribute(name = "yDim")
3156         protected Integer yDim;
3157         @XmlAttribute(name = "zDim")
3158         protected Integer zDim;
3159         @XmlAttribute(name = "bgColour")
3160         protected Integer bgColour;
3161         @XmlAttribute(name = "scaleFactor")
3162         protected Float scaleFactor;
3163         @XmlAttribute(name = "showLabels")
3164         protected Boolean showLabels;
3165         @XmlAttribute(name = "linkToAllViews")
3166         protected Boolean linkToAllViews;
3167         @XmlAttribute(name = "width")
3168         protected Integer width;
3169         @XmlAttribute(name = "height")
3170         protected Integer height;
3171         @XmlAttribute(name = "xpos")
3172         protected Integer xpos;
3173         @XmlAttribute(name = "ypos")
3174         protected Integer ypos;
3175         @XmlAttribute(name = "includeGaps")
3176         protected Boolean includeGaps;
3177         @XmlAttribute(name = "matchGaps")
3178         protected Boolean matchGaps;
3179         @XmlAttribute(name = "includeGappedColumns")
3180         protected Boolean includeGappedColumns;
3181         @XmlAttribute(name = "denominateByShortestLength")
3182         protected Boolean denominateByShortestLength;
3183
3184         /**
3185          * Gets the value of the sequencePoint property.
3186          * 
3187          * &lt;p&gt;
3188          * This accessor method returns a reference to the live list,
3189          * not a snapshot. Therefore any modification you make to the
3190          * returned list will be present inside the JAXB object.
3191          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
3192          * 
3193          * &lt;p&gt;
3194          * For example, to add a new item, do as follows:
3195          * &lt;pre&gt;
3196          *    getSequencePoint().add(newItem);
3197          * &lt;/pre&gt;
3198          * 
3199          * 
3200          * &lt;p&gt;
3201          * Objects of the following type(s) are allowed in the list
3202          * {@link JalviewModel.PcaViewer.SequencePoint }
3203          * 
3204          * 
3205          */
3206         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3207             if (sequencePoint == null) {
3208                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3209             }
3210             return this.sequencePoint;
3211         }
3212
3213         /**
3214          * Gets the value of the axis property.
3215          * 
3216          * &lt;p&gt;
3217          * This accessor method returns a reference to the live list,
3218          * not a snapshot. Therefore any modification you make to the
3219          * returned list will be present inside the JAXB object.
3220          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
3221          * 
3222          * &lt;p&gt;
3223          * For example, to add a new item, do as follows:
3224          * &lt;pre&gt;
3225          *    getAxis().add(newItem);
3226          * &lt;/pre&gt;
3227          * 
3228          * 
3229          * &lt;p&gt;
3230          * Objects of the following type(s) are allowed in the list
3231          * {@link JalviewModel.PcaViewer.Axis }
3232          * 
3233          * 
3234          */
3235         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3236             if (axis == null) {
3237                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3238             }
3239             return this.axis;
3240         }
3241
3242         /**
3243          * Gets the value of the seqPointMin property.
3244          * 
3245          * @return
3246          *     possible object is
3247          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3248          *     
3249          */
3250         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3251             return seqPointMin;
3252         }
3253
3254         /**
3255          * Sets the value of the seqPointMin property.
3256          * 
3257          * @param value
3258          *     allowed object is
3259          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3260          *     
3261          */
3262         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3263             this.seqPointMin = value;
3264         }
3265
3266         /**
3267          * Gets the value of the seqPointMax property.
3268          * 
3269          * @return
3270          *     possible object is
3271          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3272          *     
3273          */
3274         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3275             return seqPointMax;
3276         }
3277
3278         /**
3279          * Sets the value of the seqPointMax property.
3280          * 
3281          * @param value
3282          *     allowed object is
3283          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3284          *     
3285          */
3286         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3287             this.seqPointMax = value;
3288         }
3289
3290         /**
3291          * Gets the value of the pcaData property.
3292          * 
3293          * @return
3294          *     possible object is
3295          *     {@link PcaDataType }
3296          *     
3297          */
3298         public PcaDataType getPcaData() {
3299             return pcaData;
3300         }
3301
3302         /**
3303          * Sets the value of the pcaData property.
3304          * 
3305          * @param value
3306          *     allowed object is
3307          *     {@link PcaDataType }
3308          *     
3309          */
3310         public void setPcaData(PcaDataType value) {
3311             this.pcaData = value;
3312         }
3313
3314         /**
3315          * Gets the value of the title property.
3316          * 
3317          * @return
3318          *     possible object is
3319          *     {@link String }
3320          *     
3321          */
3322         public String getTitle() {
3323             return title;
3324         }
3325
3326         /**
3327          * Sets the value of the title property.
3328          * 
3329          * @param value
3330          *     allowed object is
3331          *     {@link String }
3332          *     
3333          */
3334         public void setTitle(String value) {
3335             this.title = value;
3336         }
3337
3338         /**
3339          * Gets the value of the scoreModelName property.
3340          * 
3341          * @return
3342          *     possible object is
3343          *     {@link String }
3344          *     
3345          */
3346         public String getScoreModelName() {
3347             return scoreModelName;
3348         }
3349
3350         /**
3351          * Sets the value of the scoreModelName property.
3352          * 
3353          * @param value
3354          *     allowed object is
3355          *     {@link String }
3356          *     
3357          */
3358         public void setScoreModelName(String value) {
3359             this.scoreModelName = value;
3360         }
3361
3362         /**
3363          * Gets the value of the xDim property.
3364          * 
3365          * @return
3366          *     possible object is
3367          *     {@link Integer }
3368          *     
3369          */
3370         public Integer getXDim() {
3371             return xDim;
3372         }
3373
3374         /**
3375          * Sets the value of the xDim property.
3376          * 
3377          * @param value
3378          *     allowed object is
3379          *     {@link Integer }
3380          *     
3381          */
3382         public void setXDim(Integer value) {
3383             this.xDim = value;
3384         }
3385
3386         /**
3387          * Gets the value of the yDim property.
3388          * 
3389          * @return
3390          *     possible object is
3391          *     {@link Integer }
3392          *     
3393          */
3394         public Integer getYDim() {
3395             return yDim;
3396         }
3397
3398         /**
3399          * Sets the value of the yDim property.
3400          * 
3401          * @param value
3402          *     allowed object is
3403          *     {@link Integer }
3404          *     
3405          */
3406         public void setYDim(Integer value) {
3407             this.yDim = value;
3408         }
3409
3410         /**
3411          * Gets the value of the zDim property.
3412          * 
3413          * @return
3414          *     possible object is
3415          *     {@link Integer }
3416          *     
3417          */
3418         public Integer getZDim() {
3419             return zDim;
3420         }
3421
3422         /**
3423          * Sets the value of the zDim property.
3424          * 
3425          * @param value
3426          *     allowed object is
3427          *     {@link Integer }
3428          *     
3429          */
3430         public void setZDim(Integer value) {
3431             this.zDim = value;
3432         }
3433
3434         /**
3435          * Gets the value of the bgColour property.
3436          * 
3437          * @return
3438          *     possible object is
3439          *     {@link Integer }
3440          *     
3441          */
3442         public Integer getBgColour() {
3443             return bgColour;
3444         }
3445
3446         /**
3447          * Sets the value of the bgColour property.
3448          * 
3449          * @param value
3450          *     allowed object is
3451          *     {@link Integer }
3452          *     
3453          */
3454         public void setBgColour(Integer value) {
3455             this.bgColour = value;
3456         }
3457
3458         /**
3459          * Gets the value of the scaleFactor property.
3460          * 
3461          * @return
3462          *     possible object is
3463          *     {@link Float }
3464          *     
3465          */
3466         public Float getScaleFactor() {
3467             return scaleFactor;
3468         }
3469
3470         /**
3471          * Sets the value of the scaleFactor property.
3472          * 
3473          * @param value
3474          *     allowed object is
3475          *     {@link Float }
3476          *     
3477          */
3478         public void setScaleFactor(Float value) {
3479             this.scaleFactor = value;
3480         }
3481
3482         /**
3483          * Gets the value of the showLabels property.
3484          * 
3485          * @return
3486          *     possible object is
3487          *     {@link Boolean }
3488          *     
3489          */
3490         public Boolean isShowLabels() {
3491             return showLabels;
3492         }
3493
3494         /**
3495          * Sets the value of the showLabels property.
3496          * 
3497          * @param value
3498          *     allowed object is
3499          *     {@link Boolean }
3500          *     
3501          */
3502         public void setShowLabels(Boolean value) {
3503             this.showLabels = value;
3504         }
3505
3506         /**
3507          * Gets the value of the linkToAllViews property.
3508          * 
3509          * @return
3510          *     possible object is
3511          *     {@link Boolean }
3512          *     
3513          */
3514         public Boolean isLinkToAllViews() {
3515             return linkToAllViews;
3516         }
3517
3518         /**
3519          * Sets the value of the linkToAllViews property.
3520          * 
3521          * @param value
3522          *     allowed object is
3523          *     {@link Boolean }
3524          *     
3525          */
3526         public void setLinkToAllViews(Boolean value) {
3527             this.linkToAllViews = value;
3528         }
3529
3530         /**
3531          * Gets the value of the width property.
3532          * 
3533          * @return
3534          *     possible object is
3535          *     {@link Integer }
3536          *     
3537          */
3538         public Integer getWidth() {
3539             return width;
3540         }
3541
3542         /**
3543          * Sets the value of the width property.
3544          * 
3545          * @param value
3546          *     allowed object is
3547          *     {@link Integer }
3548          *     
3549          */
3550         public void setWidth(Integer value) {
3551             this.width = value;
3552         }
3553
3554         /**
3555          * Gets the value of the height property.
3556          * 
3557          * @return
3558          *     possible object is
3559          *     {@link Integer }
3560          *     
3561          */
3562         public Integer getHeight() {
3563             return height;
3564         }
3565
3566         /**
3567          * Sets the value of the height property.
3568          * 
3569          * @param value
3570          *     allowed object is
3571          *     {@link Integer }
3572          *     
3573          */
3574         public void setHeight(Integer value) {
3575             this.height = value;
3576         }
3577
3578         /**
3579          * Gets the value of the xpos property.
3580          * 
3581          * @return
3582          *     possible object is
3583          *     {@link Integer }
3584          *     
3585          */
3586         public Integer getXpos() {
3587             return xpos;
3588         }
3589
3590         /**
3591          * Sets the value of the xpos property.
3592          * 
3593          * @param value
3594          *     allowed object is
3595          *     {@link Integer }
3596          *     
3597          */
3598         public void setXpos(Integer value) {
3599             this.xpos = value;
3600         }
3601
3602         /**
3603          * Gets the value of the ypos property.
3604          * 
3605          * @return
3606          *     possible object is
3607          *     {@link Integer }
3608          *     
3609          */
3610         public Integer getYpos() {
3611             return ypos;
3612         }
3613
3614         /**
3615          * Sets the value of the ypos property.
3616          * 
3617          * @param value
3618          *     allowed object is
3619          *     {@link Integer }
3620          *     
3621          */
3622         public void setYpos(Integer value) {
3623             this.ypos = value;
3624         }
3625
3626         /**
3627          * Gets the value of the includeGaps property.
3628          * 
3629          * @return
3630          *     possible object is
3631          *     {@link Boolean }
3632          *     
3633          */
3634         public Boolean isIncludeGaps() {
3635             return includeGaps;
3636         }
3637
3638         /**
3639          * Sets the value of the includeGaps property.
3640          * 
3641          * @param value
3642          *     allowed object is
3643          *     {@link Boolean }
3644          *     
3645          */
3646         public void setIncludeGaps(Boolean value) {
3647             this.includeGaps = value;
3648         }
3649
3650         /**
3651          * Gets the value of the matchGaps property.
3652          * 
3653          * @return
3654          *     possible object is
3655          *     {@link Boolean }
3656          *     
3657          */
3658         public Boolean isMatchGaps() {
3659             return matchGaps;
3660         }
3661
3662         /**
3663          * Sets the value of the matchGaps property.
3664          * 
3665          * @param value
3666          *     allowed object is
3667          *     {@link Boolean }
3668          *     
3669          */
3670         public void setMatchGaps(Boolean value) {
3671             this.matchGaps = value;
3672         }
3673
3674         /**
3675          * Gets the value of the includeGappedColumns property.
3676          * 
3677          * @return
3678          *     possible object is
3679          *     {@link Boolean }
3680          *     
3681          */
3682         public Boolean isIncludeGappedColumns() {
3683             return includeGappedColumns;
3684         }
3685
3686         /**
3687          * Sets the value of the includeGappedColumns property.
3688          * 
3689          * @param value
3690          *     allowed object is
3691          *     {@link Boolean }
3692          *     
3693          */
3694         public void setIncludeGappedColumns(Boolean value) {
3695             this.includeGappedColumns = value;
3696         }
3697
3698         /**
3699          * Gets the value of the denominateByShortestLength property.
3700          * 
3701          * @return
3702          *     possible object is
3703          *     {@link Boolean }
3704          *     
3705          */
3706         public Boolean isDenominateByShortestLength() {
3707             return denominateByShortestLength;
3708         }
3709
3710         /**
3711          * Sets the value of the denominateByShortestLength property.
3712          * 
3713          * @param value
3714          *     allowed object is
3715          *     {@link Boolean }
3716          *     
3717          */
3718         public void setDenominateByShortestLength(Boolean value) {
3719             this.denominateByShortestLength = value;
3720         }
3721
3722
3723         /**
3724          * &lt;p&gt;Java class for anonymous complex type.
3725          * 
3726          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3727          * 
3728          * &lt;pre&gt;
3729          * &amp;lt;complexType&amp;gt;
3730          *   &amp;lt;complexContent&amp;gt;
3731          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3732          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3733          *     &amp;lt;/restriction&amp;gt;
3734          *   &amp;lt;/complexContent&amp;gt;
3735          * &amp;lt;/complexType&amp;gt;
3736          * &lt;/pre&gt;
3737          * 
3738          * 
3739          */
3740         @XmlAccessorType(XmlAccessType.FIELD)
3741         @XmlType(name = "")
3742         public static class Axis {
3743
3744             @XmlAttribute(name = "xPos")
3745             protected Float xPos;
3746             @XmlAttribute(name = "yPos")
3747             protected Float yPos;
3748             @XmlAttribute(name = "zPos")
3749             protected Float zPos;
3750
3751             /**
3752              * Gets the value of the xPos property.
3753              * 
3754              * @return
3755              *     possible object is
3756              *     {@link Float }
3757              *     
3758              */
3759             public Float getXPos() {
3760                 return xPos;
3761             }
3762
3763             /**
3764              * Sets the value of the xPos property.
3765              * 
3766              * @param value
3767              *     allowed object is
3768              *     {@link Float }
3769              *     
3770              */
3771             public void setXPos(Float value) {
3772                 this.xPos = value;
3773             }
3774
3775             /**
3776              * Gets the value of the yPos property.
3777              * 
3778              * @return
3779              *     possible object is
3780              *     {@link Float }
3781              *     
3782              */
3783             public Float getYPos() {
3784                 return yPos;
3785             }
3786
3787             /**
3788              * Sets the value of the yPos property.
3789              * 
3790              * @param value
3791              *     allowed object is
3792              *     {@link Float }
3793              *     
3794              */
3795             public void setYPos(Float value) {
3796                 this.yPos = value;
3797             }
3798
3799             /**
3800              * Gets the value of the zPos property.
3801              * 
3802              * @return
3803              *     possible object is
3804              *     {@link Float }
3805              *     
3806              */
3807             public Float getZPos() {
3808                 return zPos;
3809             }
3810
3811             /**
3812              * Sets the value of the zPos property.
3813              * 
3814              * @param value
3815              *     allowed object is
3816              *     {@link Float }
3817              *     
3818              */
3819             public void setZPos(Float value) {
3820                 this.zPos = value;
3821             }
3822
3823         }
3824
3825
3826         /**
3827          * &lt;p&gt;Java class for anonymous complex type.
3828          * 
3829          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3830          * 
3831          * &lt;pre&gt;
3832          * &amp;lt;complexType&amp;gt;
3833          *   &amp;lt;complexContent&amp;gt;
3834          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3835          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3836          *     &amp;lt;/restriction&amp;gt;
3837          *   &amp;lt;/complexContent&amp;gt;
3838          * &amp;lt;/complexType&amp;gt;
3839          * &lt;/pre&gt;
3840          * 
3841          * 
3842          */
3843         @XmlAccessorType(XmlAccessType.FIELD)
3844         @XmlType(name = "")
3845         public static class SeqPointMax {
3846
3847             @XmlAttribute(name = "xPos")
3848             protected Float xPos;
3849             @XmlAttribute(name = "yPos")
3850             protected Float yPos;
3851             @XmlAttribute(name = "zPos")
3852             protected Float zPos;
3853
3854             /**
3855              * Gets the value of the xPos property.
3856              * 
3857              * @return
3858              *     possible object is
3859              *     {@link Float }
3860              *     
3861              */
3862             public Float getXPos() {
3863                 return xPos;
3864             }
3865
3866             /**
3867              * Sets the value of the xPos property.
3868              * 
3869              * @param value
3870              *     allowed object is
3871              *     {@link Float }
3872              *     
3873              */
3874             public void setXPos(Float value) {
3875                 this.xPos = value;
3876             }
3877
3878             /**
3879              * Gets the value of the yPos property.
3880              * 
3881              * @return
3882              *     possible object is
3883              *     {@link Float }
3884              *     
3885              */
3886             public Float getYPos() {
3887                 return yPos;
3888             }
3889
3890             /**
3891              * Sets the value of the yPos property.
3892              * 
3893              * @param value
3894              *     allowed object is
3895              *     {@link Float }
3896              *     
3897              */
3898             public void setYPos(Float value) {
3899                 this.yPos = value;
3900             }
3901
3902             /**
3903              * Gets the value of the zPos property.
3904              * 
3905              * @return
3906              *     possible object is
3907              *     {@link Float }
3908              *     
3909              */
3910             public Float getZPos() {
3911                 return zPos;
3912             }
3913
3914             /**
3915              * Sets the value of the zPos property.
3916              * 
3917              * @param value
3918              *     allowed object is
3919              *     {@link Float }
3920              *     
3921              */
3922             public void setZPos(Float value) {
3923                 this.zPos = value;
3924             }
3925
3926         }
3927
3928
3929         /**
3930          * &lt;p&gt;Java class for anonymous complex type.
3931          * 
3932          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
3933          * 
3934          * &lt;pre&gt;
3935          * &amp;lt;complexType&amp;gt;
3936          *   &amp;lt;complexContent&amp;gt;
3937          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3938          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
3939          *     &amp;lt;/restriction&amp;gt;
3940          *   &amp;lt;/complexContent&amp;gt;
3941          * &amp;lt;/complexType&amp;gt;
3942          * &lt;/pre&gt;
3943          * 
3944          * 
3945          */
3946         @XmlAccessorType(XmlAccessType.FIELD)
3947         @XmlType(name = "")
3948         public static class SeqPointMin {
3949
3950             @XmlAttribute(name = "xPos")
3951             protected Float xPos;
3952             @XmlAttribute(name = "yPos")
3953             protected Float yPos;
3954             @XmlAttribute(name = "zPos")
3955             protected Float zPos;
3956
3957             /**
3958              * Gets the value of the xPos property.
3959              * 
3960              * @return
3961              *     possible object is
3962              *     {@link Float }
3963              *     
3964              */
3965             public Float getXPos() {
3966                 return xPos;
3967             }
3968
3969             /**
3970              * Sets the value of the xPos property.
3971              * 
3972              * @param value
3973              *     allowed object is
3974              *     {@link Float }
3975              *     
3976              */
3977             public void setXPos(Float value) {
3978                 this.xPos = value;
3979             }
3980
3981             /**
3982              * Gets the value of the yPos property.
3983              * 
3984              * @return
3985              *     possible object is
3986              *     {@link Float }
3987              *     
3988              */
3989             public Float getYPos() {
3990                 return yPos;
3991             }
3992
3993             /**
3994              * Sets the value of the yPos property.
3995              * 
3996              * @param value
3997              *     allowed object is
3998              *     {@link Float }
3999              *     
4000              */
4001             public void setYPos(Float value) {
4002                 this.yPos = value;
4003             }
4004
4005             /**
4006              * Gets the value of the zPos property.
4007              * 
4008              * @return
4009              *     possible object is
4010              *     {@link Float }
4011              *     
4012              */
4013             public Float getZPos() {
4014                 return zPos;
4015             }
4016
4017             /**
4018              * Sets the value of the zPos property.
4019              * 
4020              * @param value
4021              *     allowed object is
4022              *     {@link Float }
4023              *     
4024              */
4025             public void setZPos(Float value) {
4026                 this.zPos = value;
4027             }
4028
4029         }
4030
4031
4032         /**
4033          * &lt;p&gt;Java class for anonymous complex type.
4034          * 
4035          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4036          * 
4037          * &lt;pre&gt;
4038          * &amp;lt;complexType&amp;gt;
4039          *   &amp;lt;complexContent&amp;gt;
4040          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4041          *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
4042          *       &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4043          *     &amp;lt;/restriction&amp;gt;
4044          *   &amp;lt;/complexContent&amp;gt;
4045          * &amp;lt;/complexType&amp;gt;
4046          * &lt;/pre&gt;
4047          * 
4048          * 
4049          */
4050         @XmlAccessorType(XmlAccessType.FIELD)
4051         @XmlType(name = "")
4052         public static class SequencePoint {
4053
4054             @XmlAttribute(name = "sequenceRef")
4055             protected String sequenceRef;
4056             @XmlAttribute(name = "xPos")
4057             protected Float xPos;
4058             @XmlAttribute(name = "yPos")
4059             protected Float yPos;
4060             @XmlAttribute(name = "zPos")
4061             protected Float zPos;
4062
4063             /**
4064              * Gets the value of the sequenceRef property.
4065              * 
4066              * @return
4067              *     possible object is
4068              *     {@link String }
4069              *     
4070              */
4071             public String getSequenceRef() {
4072                 return sequenceRef;
4073             }
4074
4075             /**
4076              * Sets the value of the sequenceRef property.
4077              * 
4078              * @param value
4079              *     allowed object is
4080              *     {@link String }
4081              *     
4082              */
4083             public void setSequenceRef(String value) {
4084                 this.sequenceRef = value;
4085             }
4086
4087             /**
4088              * Gets the value of the xPos property.
4089              * 
4090              * @return
4091              *     possible object is
4092              *     {@link Float }
4093              *     
4094              */
4095             public Float getXPos() {
4096                 return xPos;
4097             }
4098
4099             /**
4100              * Sets the value of the xPos property.
4101              * 
4102              * @param value
4103              *     allowed object is
4104              *     {@link Float }
4105              *     
4106              */
4107             public void setXPos(Float value) {
4108                 this.xPos = value;
4109             }
4110
4111             /**
4112              * Gets the value of the yPos property.
4113              * 
4114              * @return
4115              *     possible object is
4116              *     {@link Float }
4117              *     
4118              */
4119             public Float getYPos() {
4120                 return yPos;
4121             }
4122
4123             /**
4124              * Sets the value of the yPos property.
4125              * 
4126              * @param value
4127              *     allowed object is
4128              *     {@link Float }
4129              *     
4130              */
4131             public void setYPos(Float value) {
4132                 this.yPos = value;
4133             }
4134
4135             /**
4136              * Gets the value of the zPos property.
4137              * 
4138              * @return
4139              *     possible object is
4140              *     {@link Float }
4141              *     
4142              */
4143             public Float getZPos() {
4144                 return zPos;
4145             }
4146
4147             /**
4148              * Sets the value of the zPos property.
4149              * 
4150              * @param value
4151              *     allowed object is
4152              *     {@link Float }
4153              *     
4154              */
4155             public void setZPos(Float value) {
4156                 this.zPos = value;
4157             }
4158
4159         }
4160
4161     }
4162
4163
4164     /**
4165      * &lt;p&gt;Java class for anonymous complex type.
4166      * 
4167      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4168      * 
4169      * &lt;pre&gt;
4170      * &amp;lt;complexType&amp;gt;
4171      *   &amp;lt;complexContent&amp;gt;
4172      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4173      *       &amp;lt;sequence minOccurs="0"&amp;gt;
4174      *         &amp;lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4175      *         &amp;lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4176      *       &amp;lt;/sequence&amp;gt;
4177      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
4178      *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4179      *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4180      *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4181      *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
4182      *       &amp;lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4183      *       &amp;lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4184      *       &amp;lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4185      *       &amp;lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4186      *       &amp;lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4187      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4188      *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4189      *     &amp;lt;/restriction&amp;gt;
4190      *   &amp;lt;/complexContent&amp;gt;
4191      * &amp;lt;/complexType&amp;gt;
4192      * &lt;/pre&gt;
4193      * 
4194      * 
4195      */
4196     @XmlAccessorType(XmlAccessType.FIELD)
4197     @XmlType(name = "", propOrder = {
4198         "title",
4199         "newick"
4200     })
4201     public static class Tree {
4202
4203         @XmlElement(namespace = "www.jalview.org")
4204         protected String title;
4205         @XmlElement(namespace = "www.jalview.org")
4206         protected String newick;
4207         @XmlAttribute(name = "fontName")
4208         protected String fontName;
4209         @XmlAttribute(name = "fontSize")
4210         protected Integer fontSize;
4211         @XmlAttribute(name = "fontStyle")
4212         protected Integer fontStyle;
4213         @XmlAttribute(name = "threshold")
4214         protected Float threshold;
4215         @XmlAttribute(name = "showBootstrap")
4216         protected Boolean showBootstrap;
4217         @XmlAttribute(name = "showDistances")
4218         protected Boolean showDistances;
4219         @XmlAttribute(name = "markUnlinked")
4220         protected Boolean markUnlinked;
4221         @XmlAttribute(name = "fitToWindow")
4222         protected Boolean fitToWindow;
4223         @XmlAttribute(name = "currentTree")
4224         protected Boolean currentTree;
4225         @XmlAttribute(name = "id")
4226         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4227         @XmlID
4228         @XmlSchemaType(name = "ID")
4229         protected String id;
4230         @XmlAttribute(name = "linkToAllViews")
4231         protected Boolean linkToAllViews;
4232         @XmlAttribute(name = "width")
4233         protected Integer width;
4234         @XmlAttribute(name = "height")
4235         protected Integer height;
4236         @XmlAttribute(name = "xpos")
4237         protected Integer xpos;
4238         @XmlAttribute(name = "ypos")
4239         protected Integer ypos;
4240
4241         /**
4242          * Gets the value of the title property.
4243          * 
4244          * @return
4245          *     possible object is
4246          *     {@link String }
4247          *     
4248          */
4249         public String getTitle() {
4250             return title;
4251         }
4252
4253         /**
4254          * Sets the value of the title property.
4255          * 
4256          * @param value
4257          *     allowed object is
4258          *     {@link String }
4259          *     
4260          */
4261         public void setTitle(String value) {
4262             this.title = value;
4263         }
4264
4265         /**
4266          * Gets the value of the newick property.
4267          * 
4268          * @return
4269          *     possible object is
4270          *     {@link String }
4271          *     
4272          */
4273         public String getNewick() {
4274             return newick;
4275         }
4276
4277         /**
4278          * Sets the value of the newick property.
4279          * 
4280          * @param value
4281          *     allowed object is
4282          *     {@link String }
4283          *     
4284          */
4285         public void setNewick(String value) {
4286             this.newick = value;
4287         }
4288
4289         /**
4290          * Gets the value of the fontName property.
4291          * 
4292          * @return
4293          *     possible object is
4294          *     {@link String }
4295          *     
4296          */
4297         public String getFontName() {
4298             return fontName;
4299         }
4300
4301         /**
4302          * Sets the value of the fontName property.
4303          * 
4304          * @param value
4305          *     allowed object is
4306          *     {@link String }
4307          *     
4308          */
4309         public void setFontName(String value) {
4310             this.fontName = value;
4311         }
4312
4313         /**
4314          * Gets the value of the fontSize property.
4315          * 
4316          * @return
4317          *     possible object is
4318          *     {@link Integer }
4319          *     
4320          */
4321         public Integer getFontSize() {
4322             return fontSize;
4323         }
4324
4325         /**
4326          * Sets the value of the fontSize property.
4327          * 
4328          * @param value
4329          *     allowed object is
4330          *     {@link Integer }
4331          *     
4332          */
4333         public void setFontSize(Integer value) {
4334             this.fontSize = value;
4335         }
4336
4337         /**
4338          * Gets the value of the fontStyle property.
4339          * 
4340          * @return
4341          *     possible object is
4342          *     {@link Integer }
4343          *     
4344          */
4345         public Integer getFontStyle() {
4346             return fontStyle;
4347         }
4348
4349         /**
4350          * Sets the value of the fontStyle property.
4351          * 
4352          * @param value
4353          *     allowed object is
4354          *     {@link Integer }
4355          *     
4356          */
4357         public void setFontStyle(Integer value) {
4358             this.fontStyle = value;
4359         }
4360
4361         /**
4362          * Gets the value of the threshold property.
4363          * 
4364          * @return
4365          *     possible object is
4366          *     {@link Float }
4367          *     
4368          */
4369         public Float getThreshold() {
4370             return threshold;
4371         }
4372
4373         /**
4374          * Sets the value of the threshold property.
4375          * 
4376          * @param value
4377          *     allowed object is
4378          *     {@link Float }
4379          *     
4380          */
4381         public void setThreshold(Float value) {
4382             this.threshold = value;
4383         }
4384
4385         /**
4386          * Gets the value of the showBootstrap property.
4387          * 
4388          * @return
4389          *     possible object is
4390          *     {@link Boolean }
4391          *     
4392          */
4393         public Boolean isShowBootstrap() {
4394             return showBootstrap;
4395         }
4396
4397         /**
4398          * Sets the value of the showBootstrap property.
4399          * 
4400          * @param value
4401          *     allowed object is
4402          *     {@link Boolean }
4403          *     
4404          */
4405         public void setShowBootstrap(Boolean value) {
4406             this.showBootstrap = value;
4407         }
4408
4409         /**
4410          * Gets the value of the showDistances property.
4411          * 
4412          * @return
4413          *     possible object is
4414          *     {@link Boolean }
4415          *     
4416          */
4417         public Boolean isShowDistances() {
4418             return showDistances;
4419         }
4420
4421         /**
4422          * Sets the value of the showDistances property.
4423          * 
4424          * @param value
4425          *     allowed object is
4426          *     {@link Boolean }
4427          *     
4428          */
4429         public void setShowDistances(Boolean value) {
4430             this.showDistances = value;
4431         }
4432
4433         /**
4434          * Gets the value of the markUnlinked property.
4435          * 
4436          * @return
4437          *     possible object is
4438          *     {@link Boolean }
4439          *     
4440          */
4441         public Boolean isMarkUnlinked() {
4442             return markUnlinked;
4443         }
4444
4445         /**
4446          * Sets the value of the markUnlinked property.
4447          * 
4448          * @param value
4449          *     allowed object is
4450          *     {@link Boolean }
4451          *     
4452          */
4453         public void setMarkUnlinked(Boolean value) {
4454             this.markUnlinked = value;
4455         }
4456
4457         /**
4458          * Gets the value of the fitToWindow property.
4459          * 
4460          * @return
4461          *     possible object is
4462          *     {@link Boolean }
4463          *     
4464          */
4465         public Boolean isFitToWindow() {
4466             return fitToWindow;
4467         }
4468
4469         /**
4470          * Sets the value of the fitToWindow property.
4471          * 
4472          * @param value
4473          *     allowed object is
4474          *     {@link Boolean }
4475          *     
4476          */
4477         public void setFitToWindow(Boolean value) {
4478             this.fitToWindow = value;
4479         }
4480
4481         /**
4482          * Gets the value of the currentTree property.
4483          * 
4484          * @return
4485          *     possible object is
4486          *     {@link Boolean }
4487          *     
4488          */
4489         public Boolean isCurrentTree() {
4490             return currentTree;
4491         }
4492
4493         /**
4494          * Sets the value of the currentTree property.
4495          * 
4496          * @param value
4497          *     allowed object is
4498          *     {@link Boolean }
4499          *     
4500          */
4501         public void setCurrentTree(Boolean value) {
4502             this.currentTree = value;
4503         }
4504
4505         /**
4506          * Gets the value of the id property.
4507          * 
4508          * @return
4509          *     possible object is
4510          *     {@link String }
4511          *     
4512          */
4513         public String getId() {
4514             return id;
4515         }
4516
4517         /**
4518          * Sets the value of the id property.
4519          * 
4520          * @param value
4521          *     allowed object is
4522          *     {@link String }
4523          *     
4524          */
4525         public void setId(String value) {
4526             this.id = value;
4527         }
4528
4529         /**
4530          * Gets the value of the linkToAllViews property.
4531          * 
4532          * @return
4533          *     possible object is
4534          *     {@link Boolean }
4535          *     
4536          */
4537         public boolean isLinkToAllViews() {
4538             if (linkToAllViews == null) {
4539                 return false;
4540             } else {
4541                 return linkToAllViews;
4542             }
4543         }
4544
4545         /**
4546          * Sets the value of the linkToAllViews property.
4547          * 
4548          * @param value
4549          *     allowed object is
4550          *     {@link Boolean }
4551          *     
4552          */
4553         public void setLinkToAllViews(Boolean value) {
4554             this.linkToAllViews = value;
4555         }
4556
4557         /**
4558          * Gets the value of the width property.
4559          * 
4560          * @return
4561          *     possible object is
4562          *     {@link Integer }
4563          *     
4564          */
4565         public Integer getWidth() {
4566             return width;
4567         }
4568
4569         /**
4570          * Sets the value of the width property.
4571          * 
4572          * @param value
4573          *     allowed object is
4574          *     {@link Integer }
4575          *     
4576          */
4577         public void setWidth(Integer value) {
4578             this.width = value;
4579         }
4580
4581         /**
4582          * Gets the value of the height property.
4583          * 
4584          * @return
4585          *     possible object is
4586          *     {@link Integer }
4587          *     
4588          */
4589         public Integer getHeight() {
4590             return height;
4591         }
4592
4593         /**
4594          * Sets the value of the height property.
4595          * 
4596          * @param value
4597          *     allowed object is
4598          *     {@link Integer }
4599          *     
4600          */
4601         public void setHeight(Integer value) {
4602             this.height = value;
4603         }
4604
4605         /**
4606          * Gets the value of the xpos property.
4607          * 
4608          * @return
4609          *     possible object is
4610          *     {@link Integer }
4611          *     
4612          */
4613         public Integer getXpos() {
4614             return xpos;
4615         }
4616
4617         /**
4618          * Sets the value of the xpos property.
4619          * 
4620          * @param value
4621          *     allowed object is
4622          *     {@link Integer }
4623          *     
4624          */
4625         public void setXpos(Integer value) {
4626             this.xpos = value;
4627         }
4628
4629         /**
4630          * Gets the value of the ypos property.
4631          * 
4632          * @return
4633          *     possible object is
4634          *     {@link Integer }
4635          *     
4636          */
4637         public Integer getYpos() {
4638             return ypos;
4639         }
4640
4641         /**
4642          * Sets the value of the ypos property.
4643          * 
4644          * @param value
4645          *     allowed object is
4646          *     {@link Integer }
4647          *     
4648          */
4649         public void setYpos(Integer value) {
4650             this.ypos = value;
4651         }
4652
4653     }
4654
4655
4656     /**
4657      * &lt;p&gt;Java class for anonymous complex type.
4658      * 
4659      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4660      * 
4661      * &lt;pre&gt;
4662      * &amp;lt;complexType&amp;gt;
4663      *   &amp;lt;complexContent&amp;gt;
4664      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4665      *       &amp;lt;sequence&amp;gt;
4666      *         &amp;lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
4667      *       &amp;lt;/sequence&amp;gt;
4668      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4669      *     &amp;lt;/restriction&amp;gt;
4670      *   &amp;lt;/complexContent&amp;gt;
4671      * &amp;lt;/complexType&amp;gt;
4672      * &lt;/pre&gt;
4673      * 
4674      * 
4675      */
4676     @XmlAccessorType(XmlAccessType.FIELD)
4677     @XmlType(name = "", propOrder = {
4678         "userColourScheme"
4679     })
4680     public static class UserColours {
4681
4682         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4683         protected JalviewUserColours userColourScheme;
4684         @XmlAttribute(name = "id")
4685         protected String id;
4686
4687         /**
4688          * Gets the value of the userColourScheme property.
4689          * 
4690          * @return
4691          *     possible object is
4692          *     {@link JalviewUserColours }
4693          *     
4694          */
4695         public JalviewUserColours getUserColourScheme() {
4696             return userColourScheme;
4697         }
4698
4699         /**
4700          * Sets the value of the userColourScheme property.
4701          * 
4702          * @param value
4703          *     allowed object is
4704          *     {@link JalviewUserColours }
4705          *     
4706          */
4707         public void setUserColourScheme(JalviewUserColours value) {
4708             this.userColourScheme = value;
4709         }
4710
4711         /**
4712          * Gets the value of the id property.
4713          * 
4714          * @return
4715          *     possible object is
4716          *     {@link String }
4717          *     
4718          */
4719         public String getId() {
4720             return id;
4721         }
4722
4723         /**
4724          * Sets the value of the id property.
4725          * 
4726          * @param value
4727          *     allowed object is
4728          *     {@link String }
4729          *     
4730          */
4731         public void setId(String value) {
4732             this.id = value;
4733         }
4734
4735     }
4736
4737
4738     /**
4739      * &lt;p&gt;Java class for anonymous complex type.
4740      * 
4741      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
4742      * 
4743      * &lt;pre&gt;
4744      * &amp;lt;complexType&amp;gt;
4745      *   &amp;lt;complexContent&amp;gt;
4746      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4747      *       &amp;lt;sequence&amp;gt;
4748      *         &amp;lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
4749      *         &amp;lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4750      *           &amp;lt;complexType&amp;gt;
4751      *             &amp;lt;complexContent&amp;gt;
4752      *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4753      *                 &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4754      *                 &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4755      *               &amp;lt;/restriction&amp;gt;
4756      *             &amp;lt;/complexContent&amp;gt;
4757      *           &amp;lt;/complexType&amp;gt;
4758      *         &amp;lt;/element&amp;gt;
4759      *         &amp;lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4760      *           &amp;lt;complexType&amp;gt;
4761      *             &amp;lt;complexContent&amp;gt;
4762      *               &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
4763      *                 &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4764      *                 &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4765      *                 &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4766      *               &amp;lt;/extension&amp;gt;
4767      *             &amp;lt;/complexContent&amp;gt;
4768      *           &amp;lt;/complexType&amp;gt;
4769      *         &amp;lt;/element&amp;gt;
4770      *       &amp;lt;/sequence&amp;gt;
4771      *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
4772      *       &amp;lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4773      *       &amp;lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4774      *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4775      *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4776      *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4777      *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4778      *       &amp;lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4779      *       &amp;lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4780      *       &amp;lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4781      *       &amp;lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4782      *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4783      *       &amp;lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4784      *       &amp;lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4785      *       &amp;lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4786      *       &amp;lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4787      *       &amp;lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4788      *       &amp;lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4789      *       &amp;lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4790      *       &amp;lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4791      *       &amp;lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4792      *       &amp;lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4793      *       &amp;lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4794      *       &amp;lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4795      *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4796      *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4797      *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4798      *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4799      *       &amp;lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4800      *       &amp;lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4801      *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4802      *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4803      *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4804      *       &amp;lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4805      *       &amp;lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4806      *       &amp;lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4807      *       &amp;lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4808      *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4809      *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4810      *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4811      *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4812      *       &amp;lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4813      *       &amp;lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4814      *       &amp;lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4815      *     &amp;lt;/restriction&amp;gt;
4816      *   &amp;lt;/complexContent&amp;gt;
4817      * &amp;lt;/complexType&amp;gt;
4818      * &lt;/pre&gt;
4819      * 
4820      * 
4821      */
4822     @XmlAccessorType(XmlAccessType.FIELD)
4823     @XmlType(name = "", propOrder = {
4824         "annotationColours",
4825         "hiddenColumns",
4826         "calcIdParam"
4827     })
4828     public static class Viewport {
4829
4830         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4831         protected AnnotationColourScheme annotationColours;
4832         @XmlElement(namespace = "www.jalview.org")
4833         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4834         @XmlElement(namespace = "www.jalview.org")
4835         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4836         @XmlAttribute(name = "conservationSelected")
4837         protected Boolean conservationSelected;
4838         @XmlAttribute(name = "pidSelected")
4839         protected Boolean pidSelected;
4840         @XmlAttribute(name = "bgColour")
4841         protected String bgColour;
4842         @XmlAttribute(name = "consThreshold")
4843         protected Integer consThreshold;
4844         @XmlAttribute(name = "pidThreshold")
4845         protected Integer pidThreshold;
4846         @XmlAttribute(name = "title")
4847         protected String title;
4848         @XmlAttribute(name = "showFullId")
4849         protected Boolean showFullId;
4850         @XmlAttribute(name = "rightAlignIds")
4851         protected Boolean rightAlignIds;
4852         @XmlAttribute(name = "showText")
4853         protected Boolean showText;
4854         @XmlAttribute(name = "showColourText")
4855         protected Boolean showColourText;
4856         @XmlAttribute(name = "showUnconserved")
4857         protected Boolean showUnconserved;
4858         @XmlAttribute(name = "showBoxes")
4859         protected Boolean showBoxes;
4860         @XmlAttribute(name = "wrapAlignment")
4861         protected Boolean wrapAlignment;
4862         @XmlAttribute(name = "renderGaps")
4863         protected Boolean renderGaps;
4864         @XmlAttribute(name = "showSequenceFeatures")
4865         protected Boolean showSequenceFeatures;
4866         @XmlAttribute(name = "showNPfeatureTooltip")
4867         protected Boolean showNPfeatureTooltip;
4868         @XmlAttribute(name = "showDbRefTooltip")
4869         protected Boolean showDbRefTooltip;
4870         @XmlAttribute(name = "followHighlight")
4871         protected Boolean followHighlight;
4872         @XmlAttribute(name = "followSelection")
4873         protected Boolean followSelection;
4874         @XmlAttribute(name = "showAnnotation")
4875         protected Boolean showAnnotation;
4876         @XmlAttribute(name = "centreColumnLabels")
4877         protected Boolean centreColumnLabels;
4878         @XmlAttribute(name = "showGroupConservation")
4879         protected Boolean showGroupConservation;
4880         @XmlAttribute(name = "showGroupConsensus")
4881         protected Boolean showGroupConsensus;
4882         @XmlAttribute(name = "showConsensusHistogram")
4883         protected Boolean showConsensusHistogram;
4884         @XmlAttribute(name = "showSequenceLogo")
4885         protected Boolean showSequenceLogo;
4886         @XmlAttribute(name = "normaliseSequenceLogo")
4887         protected Boolean normaliseSequenceLogo;
4888         @XmlAttribute(name = "ignoreGapsinConsensus")
4889         protected Boolean ignoreGapsinConsensus;
4890         @XmlAttribute(name = "startRes")
4891         protected Integer startRes;
4892         @XmlAttribute(name = "startSeq")
4893         protected Integer startSeq;
4894         @XmlAttribute(name = "fontName")
4895         protected String fontName;
4896         @XmlAttribute(name = "fontSize")
4897         protected Integer fontSize;
4898         @XmlAttribute(name = "fontStyle")
4899         protected Integer fontStyle;
4900         @XmlAttribute(name = "scaleProteinAsCdna")
4901         protected Boolean scaleProteinAsCdna;
4902         @XmlAttribute(name = "viewName")
4903         protected String viewName;
4904         @XmlAttribute(name = "sequenceSetId")
4905         protected String sequenceSetId;
4906         @XmlAttribute(name = "gatheredViews")
4907         protected Boolean gatheredViews;
4908         @XmlAttribute(name = "textCol1")
4909         protected Integer textCol1;
4910         @XmlAttribute(name = "textCol2")
4911         protected Integer textCol2;
4912         @XmlAttribute(name = "textColThreshold")
4913         protected Integer textColThreshold;
4914         @XmlAttribute(name = "id")
4915         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4916         @XmlID
4917         @XmlSchemaType(name = "ID")
4918         protected String id;
4919         @XmlAttribute(name = "complementId")
4920         protected String complementId;
4921         @XmlAttribute(name = "showComplementFeatures")
4922         protected Boolean showComplementFeatures;
4923         @XmlAttribute(name = "showComplementFeaturesOnTop")
4924         protected Boolean showComplementFeaturesOnTop;
4925         @XmlAttribute(name = "width")
4926         protected Integer width;
4927         @XmlAttribute(name = "height")
4928         protected Integer height;
4929         @XmlAttribute(name = "xpos")
4930         protected Integer xpos;
4931         @XmlAttribute(name = "ypos")
4932         protected Integer ypos;
4933
4934         /**
4935          * Gets the value of the annotationColours property.
4936          * 
4937          * @return
4938          *     possible object is
4939          *     {@link AnnotationColourScheme }
4940          *     
4941          */
4942         public AnnotationColourScheme getAnnotationColours() {
4943             return annotationColours;
4944         }
4945
4946         /**
4947          * Sets the value of the annotationColours property.
4948          * 
4949          * @param value
4950          *     allowed object is
4951          *     {@link AnnotationColourScheme }
4952          *     
4953          */
4954         public void setAnnotationColours(AnnotationColourScheme value) {
4955             this.annotationColours = value;
4956         }
4957
4958         /**
4959          * Gets the value of the hiddenColumns property.
4960          * 
4961          * &lt;p&gt;
4962          * This accessor method returns a reference to the live list,
4963          * not a snapshot. Therefore any modification you make to the
4964          * returned list will be present inside the JAXB object.
4965          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
4966          * 
4967          * &lt;p&gt;
4968          * For example, to add a new item, do as follows:
4969          * &lt;pre&gt;
4970          *    getHiddenColumns().add(newItem);
4971          * &lt;/pre&gt;
4972          * 
4973          * 
4974          * &lt;p&gt;
4975          * Objects of the following type(s) are allowed in the list
4976          * {@link JalviewModel.Viewport.HiddenColumns }
4977          * 
4978          * 
4979          */
4980         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
4981             if (hiddenColumns == null) {
4982                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
4983             }
4984             return this.hiddenColumns;
4985         }
4986
4987         /**
4988          * Gets the value of the calcIdParam property.
4989          * 
4990          * &lt;p&gt;
4991          * This accessor method returns a reference to the live list,
4992          * not a snapshot. Therefore any modification you make to the
4993          * returned list will be present inside the JAXB object.
4994          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
4995          * 
4996          * &lt;p&gt;
4997          * For example, to add a new item, do as follows:
4998          * &lt;pre&gt;
4999          *    getCalcIdParam().add(newItem);
5000          * &lt;/pre&gt;
5001          * 
5002          * 
5003          * &lt;p&gt;
5004          * Objects of the following type(s) are allowed in the list
5005          * {@link JalviewModel.Viewport.CalcIdParam }
5006          * 
5007          * 
5008          */
5009         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5010             if (calcIdParam == null) {
5011                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5012             }
5013             return this.calcIdParam;
5014         }
5015
5016         /**
5017          * Gets the value of the conservationSelected property.
5018          * 
5019          * @return
5020          *     possible object is
5021          *     {@link Boolean }
5022          *     
5023          */
5024         public Boolean isConservationSelected() {
5025             return conservationSelected;
5026         }
5027
5028         /**
5029          * Sets the value of the conservationSelected property.
5030          * 
5031          * @param value
5032          *     allowed object is
5033          *     {@link Boolean }
5034          *     
5035          */
5036         public void setConservationSelected(Boolean value) {
5037             this.conservationSelected = value;
5038         }
5039
5040         /**
5041          * Gets the value of the pidSelected property.
5042          * 
5043          * @return
5044          *     possible object is
5045          *     {@link Boolean }
5046          *     
5047          */
5048         public Boolean isPidSelected() {
5049             return pidSelected;
5050         }
5051
5052         /**
5053          * Sets the value of the pidSelected property.
5054          * 
5055          * @param value
5056          *     allowed object is
5057          *     {@link Boolean }
5058          *     
5059          */
5060         public void setPidSelected(Boolean value) {
5061             this.pidSelected = value;
5062         }
5063
5064         /**
5065          * Gets the value of the bgColour property.
5066          * 
5067          * @return
5068          *     possible object is
5069          *     {@link String }
5070          *     
5071          */
5072         public String getBgColour() {
5073             return bgColour;
5074         }
5075
5076         /**
5077          * Sets the value of the bgColour property.
5078          * 
5079          * @param value
5080          *     allowed object is
5081          *     {@link String }
5082          *     
5083          */
5084         public void setBgColour(String value) {
5085             this.bgColour = value;
5086         }
5087
5088         /**
5089          * Gets the value of the consThreshold property.
5090          * 
5091          * @return
5092          *     possible object is
5093          *     {@link Integer }
5094          *     
5095          */
5096         public Integer getConsThreshold() {
5097             return consThreshold;
5098         }
5099
5100         /**
5101          * Sets the value of the consThreshold property.
5102          * 
5103          * @param value
5104          *     allowed object is
5105          *     {@link Integer }
5106          *     
5107          */
5108         public void setConsThreshold(Integer value) {
5109             this.consThreshold = value;
5110         }
5111
5112         /**
5113          * Gets the value of the pidThreshold property.
5114          * 
5115          * @return
5116          *     possible object is
5117          *     {@link Integer }
5118          *     
5119          */
5120         public Integer getPidThreshold() {
5121             return pidThreshold;
5122         }
5123
5124         /**
5125          * Sets the value of the pidThreshold property.
5126          * 
5127          * @param value
5128          *     allowed object is
5129          *     {@link Integer }
5130          *     
5131          */
5132         public void setPidThreshold(Integer value) {
5133             this.pidThreshold = value;
5134         }
5135
5136         /**
5137          * Gets the value of the title property.
5138          * 
5139          * @return
5140          *     possible object is
5141          *     {@link String }
5142          *     
5143          */
5144         public String getTitle() {
5145             return title;
5146         }
5147
5148         /**
5149          * Sets the value of the title property.
5150          * 
5151          * @param value
5152          *     allowed object is
5153          *     {@link String }
5154          *     
5155          */
5156         public void setTitle(String value) {
5157             this.title = value;
5158         }
5159
5160         /**
5161          * Gets the value of the showFullId property.
5162          * 
5163          * @return
5164          *     possible object is
5165          *     {@link Boolean }
5166          *     
5167          */
5168         public Boolean isShowFullId() {
5169             return showFullId;
5170         }
5171
5172         /**
5173          * Sets the value of the showFullId property.
5174          * 
5175          * @param value
5176          *     allowed object is
5177          *     {@link Boolean }
5178          *     
5179          */
5180         public void setShowFullId(Boolean value) {
5181             this.showFullId = value;
5182         }
5183
5184         /**
5185          * Gets the value of the rightAlignIds property.
5186          * 
5187          * @return
5188          *     possible object is
5189          *     {@link Boolean }
5190          *     
5191          */
5192         public Boolean isRightAlignIds() {
5193             return rightAlignIds;
5194         }
5195
5196         /**
5197          * Sets the value of the rightAlignIds property.
5198          * 
5199          * @param value
5200          *     allowed object is
5201          *     {@link Boolean }
5202          *     
5203          */
5204         public void setRightAlignIds(Boolean value) {
5205             this.rightAlignIds = value;
5206         }
5207
5208         /**
5209          * Gets the value of the showText property.
5210          * 
5211          * @return
5212          *     possible object is
5213          *     {@link Boolean }
5214          *     
5215          */
5216         public Boolean isShowText() {
5217             return showText;
5218         }
5219
5220         /**
5221          * Sets the value of the showText property.
5222          * 
5223          * @param value
5224          *     allowed object is
5225          *     {@link Boolean }
5226          *     
5227          */
5228         public void setShowText(Boolean value) {
5229             this.showText = value;
5230         }
5231
5232         /**
5233          * Gets the value of the showColourText property.
5234          * 
5235          * @return
5236          *     possible object is
5237          *     {@link Boolean }
5238          *     
5239          */
5240         public Boolean isShowColourText() {
5241             return showColourText;
5242         }
5243
5244         /**
5245          * Sets the value of the showColourText property.
5246          * 
5247          * @param value
5248          *     allowed object is
5249          *     {@link Boolean }
5250          *     
5251          */
5252         public void setShowColourText(Boolean value) {
5253             this.showColourText = value;
5254         }
5255
5256         /**
5257          * Gets the value of the showUnconserved property.
5258          * 
5259          * @return
5260          *     possible object is
5261          *     {@link Boolean }
5262          *     
5263          */
5264         public boolean isShowUnconserved() {
5265             if (showUnconserved == null) {
5266                 return false;
5267             } else {
5268                 return showUnconserved;
5269             }
5270         }
5271
5272         /**
5273          * Sets the value of the showUnconserved property.
5274          * 
5275          * @param value
5276          *     allowed object is
5277          *     {@link Boolean }
5278          *     
5279          */
5280         public void setShowUnconserved(Boolean value) {
5281             this.showUnconserved = value;
5282         }
5283
5284         /**
5285          * Gets the value of the showBoxes property.
5286          * 
5287          * @return
5288          *     possible object is
5289          *     {@link Boolean }
5290          *     
5291          */
5292         public Boolean isShowBoxes() {
5293             return showBoxes;
5294         }
5295
5296         /**
5297          * Sets the value of the showBoxes property.
5298          * 
5299          * @param value
5300          *     allowed object is
5301          *     {@link Boolean }
5302          *     
5303          */
5304         public void setShowBoxes(Boolean value) {
5305             this.showBoxes = value;
5306         }
5307
5308         /**
5309          * Gets the value of the wrapAlignment property.
5310          * 
5311          * @return
5312          *     possible object is
5313          *     {@link Boolean }
5314          *     
5315          */
5316         public Boolean isWrapAlignment() {
5317             return wrapAlignment;
5318         }
5319
5320         /**
5321          * Sets the value of the wrapAlignment property.
5322          * 
5323          * @param value
5324          *     allowed object is
5325          *     {@link Boolean }
5326          *     
5327          */
5328         public void setWrapAlignment(Boolean value) {
5329             this.wrapAlignment = value;
5330         }
5331
5332         /**
5333          * Gets the value of the renderGaps property.
5334          * 
5335          * @return
5336          *     possible object is
5337          *     {@link Boolean }
5338          *     
5339          */
5340         public Boolean isRenderGaps() {
5341             return renderGaps;
5342         }
5343
5344         /**
5345          * Sets the value of the renderGaps property.
5346          * 
5347          * @param value
5348          *     allowed object is
5349          *     {@link Boolean }
5350          *     
5351          */
5352         public void setRenderGaps(Boolean value) {
5353             this.renderGaps = value;
5354         }
5355
5356         /**
5357          * Gets the value of the showSequenceFeatures property.
5358          * 
5359          * @return
5360          *     possible object is
5361          *     {@link Boolean }
5362          *     
5363          */
5364         public Boolean isShowSequenceFeatures() {
5365             return showSequenceFeatures;
5366         }
5367
5368         /**
5369          * Sets the value of the showSequenceFeatures property.
5370          * 
5371          * @param value
5372          *     allowed object is
5373          *     {@link Boolean }
5374          *     
5375          */
5376         public void setShowSequenceFeatures(Boolean value) {
5377             this.showSequenceFeatures = value;
5378         }
5379
5380         /**
5381          * Gets the value of the showNPfeatureTooltip property.
5382          * 
5383          * @return
5384          *     possible object is
5385          *     {@link Boolean }
5386          *     
5387          */
5388         public Boolean isShowNPfeatureTooltip() {
5389             return showNPfeatureTooltip;
5390         }
5391
5392         /**
5393          * Sets the value of the showNPfeatureTooltip property.
5394          * 
5395          * @param value
5396          *     allowed object is
5397          *     {@link Boolean }
5398          *     
5399          */
5400         public void setShowNPfeatureTooltip(Boolean value) {
5401             this.showNPfeatureTooltip = value;
5402         }
5403
5404         /**
5405          * Gets the value of the showDbRefTooltip property.
5406          * 
5407          * @return
5408          *     possible object is
5409          *     {@link Boolean }
5410          *     
5411          */
5412         public Boolean isShowDbRefTooltip() {
5413             return showDbRefTooltip;
5414         }
5415
5416         /**
5417          * Sets the value of the showDbRefTooltip property.
5418          * 
5419          * @param value
5420          *     allowed object is
5421          *     {@link Boolean }
5422          *     
5423          */
5424         public void setShowDbRefTooltip(Boolean value) {
5425             this.showDbRefTooltip = value;
5426         }
5427
5428         /**
5429          * Gets the value of the followHighlight property.
5430          * 
5431          * @return
5432          *     possible object is
5433          *     {@link Boolean }
5434          *     
5435          */
5436         public boolean isFollowHighlight() {
5437             if (followHighlight == null) {
5438                 return true;
5439             } else {
5440                 return followHighlight;
5441             }
5442         }
5443
5444         /**
5445          * Sets the value of the followHighlight property.
5446          * 
5447          * @param value
5448          *     allowed object is
5449          *     {@link Boolean }
5450          *     
5451          */
5452         public void setFollowHighlight(Boolean value) {
5453             this.followHighlight = value;
5454         }
5455
5456         /**
5457          * Gets the value of the followSelection property.
5458          * 
5459          * @return
5460          *     possible object is
5461          *     {@link Boolean }
5462          *     
5463          */
5464         public boolean isFollowSelection() {
5465             if (followSelection == null) {
5466                 return true;
5467             } else {
5468                 return followSelection;
5469             }
5470         }
5471
5472         /**
5473          * Sets the value of the followSelection property.
5474          * 
5475          * @param value
5476          *     allowed object is
5477          *     {@link Boolean }
5478          *     
5479          */
5480         public void setFollowSelection(Boolean value) {
5481             this.followSelection = value;
5482         }
5483
5484         /**
5485          * Gets the value of the showAnnotation property.
5486          * 
5487          * @return
5488          *     possible object is
5489          *     {@link Boolean }
5490          *     
5491          */
5492         public Boolean isShowAnnotation() {
5493             return showAnnotation;
5494         }
5495
5496         /**
5497          * Sets the value of the showAnnotation property.
5498          * 
5499          * @param value
5500          *     allowed object is
5501          *     {@link Boolean }
5502          *     
5503          */
5504         public void setShowAnnotation(Boolean value) {
5505             this.showAnnotation = value;
5506         }
5507
5508         /**
5509          * Gets the value of the centreColumnLabels property.
5510          * 
5511          * @return
5512          *     possible object is
5513          *     {@link Boolean }
5514          *     
5515          */
5516         public boolean isCentreColumnLabels() {
5517             if (centreColumnLabels == null) {
5518                 return false;
5519             } else {
5520                 return centreColumnLabels;
5521             }
5522         }
5523
5524         /**
5525          * Sets the value of the centreColumnLabels property.
5526          * 
5527          * @param value
5528          *     allowed object is
5529          *     {@link Boolean }
5530          *     
5531          */
5532         public void setCentreColumnLabels(Boolean value) {
5533             this.centreColumnLabels = value;
5534         }
5535
5536         /**
5537          * Gets the value of the showGroupConservation property.
5538          * 
5539          * @return
5540          *     possible object is
5541          *     {@link Boolean }
5542          *     
5543          */
5544         public boolean isShowGroupConservation() {
5545             if (showGroupConservation == null) {
5546                 return false;
5547             } else {
5548                 return showGroupConservation;
5549             }
5550         }
5551
5552         /**
5553          * Sets the value of the showGroupConservation property.
5554          * 
5555          * @param value
5556          *     allowed object is
5557          *     {@link Boolean }
5558          *     
5559          */
5560         public void setShowGroupConservation(Boolean value) {
5561             this.showGroupConservation = value;
5562         }
5563
5564         /**
5565          * Gets the value of the showGroupConsensus property.
5566          * 
5567          * @return
5568          *     possible object is
5569          *     {@link Boolean }
5570          *     
5571          */
5572         public boolean isShowGroupConsensus() {
5573             if (showGroupConsensus == null) {
5574                 return false;
5575             } else {
5576                 return showGroupConsensus;
5577             }
5578         }
5579
5580         /**
5581          * Sets the value of the showGroupConsensus property.
5582          * 
5583          * @param value
5584          *     allowed object is
5585          *     {@link Boolean }
5586          *     
5587          */
5588         public void setShowGroupConsensus(Boolean value) {
5589             this.showGroupConsensus = value;
5590         }
5591
5592         /**
5593          * Gets the value of the showConsensusHistogram property.
5594          * 
5595          * @return
5596          *     possible object is
5597          *     {@link Boolean }
5598          *     
5599          */
5600         public boolean isShowConsensusHistogram() {
5601             if (showConsensusHistogram == null) {
5602                 return true;
5603             } else {
5604                 return showConsensusHistogram;
5605             }
5606         }
5607
5608         /**
5609          * Sets the value of the showConsensusHistogram property.
5610          * 
5611          * @param value
5612          *     allowed object is
5613          *     {@link Boolean }
5614          *     
5615          */
5616         public void setShowConsensusHistogram(Boolean value) {
5617             this.showConsensusHistogram = value;
5618         }
5619
5620         /**
5621          * Gets the value of the showSequenceLogo property.
5622          * 
5623          * @return
5624          *     possible object is
5625          *     {@link Boolean }
5626          *     
5627          */
5628         public boolean isShowSequenceLogo() {
5629             if (showSequenceLogo == null) {
5630                 return false;
5631             } else {
5632                 return showSequenceLogo;
5633             }
5634         }
5635
5636         /**
5637          * Sets the value of the showSequenceLogo property.
5638          * 
5639          * @param value
5640          *     allowed object is
5641          *     {@link Boolean }
5642          *     
5643          */
5644         public void setShowSequenceLogo(Boolean value) {
5645             this.showSequenceLogo = value;
5646         }
5647
5648         /**
5649          * Gets the value of the normaliseSequenceLogo property.
5650          * 
5651          * @return
5652          *     possible object is
5653          *     {@link Boolean }
5654          *     
5655          */
5656         public boolean isNormaliseSequenceLogo() {
5657             if (normaliseSequenceLogo == null) {
5658                 return false;
5659             } else {
5660                 return normaliseSequenceLogo;
5661             }
5662         }
5663
5664         /**
5665          * Sets the value of the normaliseSequenceLogo property.
5666          * 
5667          * @param value
5668          *     allowed object is
5669          *     {@link Boolean }
5670          *     
5671          */
5672         public void setNormaliseSequenceLogo(Boolean value) {
5673             this.normaliseSequenceLogo = value;
5674         }
5675
5676         /**
5677          * Gets the value of the ignoreGapsinConsensus property.
5678          * 
5679          * @return
5680          *     possible object is
5681          *     {@link Boolean }
5682          *     
5683          */
5684         public boolean isIgnoreGapsinConsensus() {
5685             if (ignoreGapsinConsensus == null) {
5686                 return true;
5687             } else {
5688                 return ignoreGapsinConsensus;
5689             }
5690         }
5691
5692         /**
5693          * Sets the value of the ignoreGapsinConsensus property.
5694          * 
5695          * @param value
5696          *     allowed object is
5697          *     {@link Boolean }
5698          *     
5699          */
5700         public void setIgnoreGapsinConsensus(Boolean value) {
5701             this.ignoreGapsinConsensus = value;
5702         }
5703
5704         /**
5705          * Gets the value of the startRes property.
5706          * 
5707          * @return
5708          *     possible object is
5709          *     {@link Integer }
5710          *     
5711          */
5712         public Integer getStartRes() {
5713             return startRes;
5714         }
5715
5716         /**
5717          * Sets the value of the startRes property.
5718          * 
5719          * @param value
5720          *     allowed object is
5721          *     {@link Integer }
5722          *     
5723          */
5724         public void setStartRes(Integer value) {
5725             this.startRes = value;
5726         }
5727
5728         /**
5729          * Gets the value of the startSeq property.
5730          * 
5731          * @return
5732          *     possible object is
5733          *     {@link Integer }
5734          *     
5735          */
5736         public Integer getStartSeq() {
5737             return startSeq;
5738         }
5739
5740         /**
5741          * Sets the value of the startSeq property.
5742          * 
5743          * @param value
5744          *     allowed object is
5745          *     {@link Integer }
5746          *     
5747          */
5748         public void setStartSeq(Integer value) {
5749             this.startSeq = value;
5750         }
5751
5752         /**
5753          * Gets the value of the fontName property.
5754          * 
5755          * @return
5756          *     possible object is
5757          *     {@link String }
5758          *     
5759          */
5760         public String getFontName() {
5761             return fontName;
5762         }
5763
5764         /**
5765          * Sets the value of the fontName property.
5766          * 
5767          * @param value
5768          *     allowed object is
5769          *     {@link String }
5770          *     
5771          */
5772         public void setFontName(String value) {
5773             this.fontName = value;
5774         }
5775
5776         /**
5777          * Gets the value of the fontSize property.
5778          * 
5779          * @return
5780          *     possible object is
5781          *     {@link Integer }
5782          *     
5783          */
5784         public Integer getFontSize() {
5785             return fontSize;
5786         }
5787
5788         /**
5789          * Sets the value of the fontSize property.
5790          * 
5791          * @param value
5792          *     allowed object is
5793          *     {@link Integer }
5794          *     
5795          */
5796         public void setFontSize(Integer value) {
5797             this.fontSize = value;
5798         }
5799
5800         /**
5801          * Gets the value of the fontStyle property.
5802          * 
5803          * @return
5804          *     possible object is
5805          *     {@link Integer }
5806          *     
5807          */
5808         public Integer getFontStyle() {
5809             return fontStyle;
5810         }
5811
5812         /**
5813          * Sets the value of the fontStyle property.
5814          * 
5815          * @param value
5816          *     allowed object is
5817          *     {@link Integer }
5818          *     
5819          */
5820         public void setFontStyle(Integer value) {
5821             this.fontStyle = value;
5822         }
5823
5824         /**
5825          * Gets the value of the scaleProteinAsCdna property.
5826          * 
5827          * @return
5828          *     possible object is
5829          *     {@link Boolean }
5830          *     
5831          */
5832         public boolean isScaleProteinAsCdna() {
5833             if (scaleProteinAsCdna == null) {
5834                 return true;
5835             } else {
5836                 return scaleProteinAsCdna;
5837             }
5838         }
5839
5840         /**
5841          * Sets the value of the scaleProteinAsCdna property.
5842          * 
5843          * @param value
5844          *     allowed object is
5845          *     {@link Boolean }
5846          *     
5847          */
5848         public void setScaleProteinAsCdna(Boolean value) {
5849             this.scaleProteinAsCdna = value;
5850         }
5851
5852         /**
5853          * Gets the value of the viewName property.
5854          * 
5855          * @return
5856          *     possible object is
5857          *     {@link String }
5858          *     
5859          */
5860         public String getViewName() {
5861             return viewName;
5862         }
5863
5864         /**
5865          * Sets the value of the viewName property.
5866          * 
5867          * @param value
5868          *     allowed object is
5869          *     {@link String }
5870          *     
5871          */
5872         public void setViewName(String value) {
5873             this.viewName = value;
5874         }
5875
5876         /**
5877          * Gets the value of the sequenceSetId property.
5878          * 
5879          * @return
5880          *     possible object is
5881          *     {@link String }
5882          *     
5883          */
5884         public String getSequenceSetId() {
5885             return sequenceSetId;
5886         }
5887
5888         /**
5889          * Sets the value of the sequenceSetId property.
5890          * 
5891          * @param value
5892          *     allowed object is
5893          *     {@link String }
5894          *     
5895          */
5896         public void setSequenceSetId(String value) {
5897             this.sequenceSetId = value;
5898         }
5899
5900         /**
5901          * Gets the value of the gatheredViews property.
5902          * 
5903          * @return
5904          *     possible object is
5905          *     {@link Boolean }
5906          *     
5907          */
5908         public Boolean isGatheredViews() {
5909             return gatheredViews;
5910         }
5911
5912         /**
5913          * Sets the value of the gatheredViews property.
5914          * 
5915          * @param value
5916          *     allowed object is
5917          *     {@link Boolean }
5918          *     
5919          */
5920         public void setGatheredViews(Boolean value) {
5921             this.gatheredViews = value;
5922         }
5923
5924         /**
5925          * Gets the value of the textCol1 property.
5926          * 
5927          * @return
5928          *     possible object is
5929          *     {@link Integer }
5930          *     
5931          */
5932         public Integer getTextCol1() {
5933             return textCol1;
5934         }
5935
5936         /**
5937          * Sets the value of the textCol1 property.
5938          * 
5939          * @param value
5940          *     allowed object is
5941          *     {@link Integer }
5942          *     
5943          */
5944         public void setTextCol1(Integer value) {
5945             this.textCol1 = value;
5946         }
5947
5948         /**
5949          * Gets the value of the textCol2 property.
5950          * 
5951          * @return
5952          *     possible object is
5953          *     {@link Integer }
5954          *     
5955          */
5956         public Integer getTextCol2() {
5957             return textCol2;
5958         }
5959
5960         /**
5961          * Sets the value of the textCol2 property.
5962          * 
5963          * @param value
5964          *     allowed object is
5965          *     {@link Integer }
5966          *     
5967          */
5968         public void setTextCol2(Integer value) {
5969             this.textCol2 = value;
5970         }
5971
5972         /**
5973          * Gets the value of the textColThreshold property.
5974          * 
5975          * @return
5976          *     possible object is
5977          *     {@link Integer }
5978          *     
5979          */
5980         public Integer getTextColThreshold() {
5981             return textColThreshold;
5982         }
5983
5984         /**
5985          * Sets the value of the textColThreshold property.
5986          * 
5987          * @param value
5988          *     allowed object is
5989          *     {@link Integer }
5990          *     
5991          */
5992         public void setTextColThreshold(Integer value) {
5993             this.textColThreshold = value;
5994         }
5995
5996         /**
5997          * Gets the value of the id property.
5998          * 
5999          * @return
6000          *     possible object is
6001          *     {@link String }
6002          *     
6003          */
6004         public String getId() {
6005             return id;
6006         }
6007
6008         /**
6009          * Sets the value of the id property.
6010          * 
6011          * @param value
6012          *     allowed object is
6013          *     {@link String }
6014          *     
6015          */
6016         public void setId(String value) {
6017             this.id = value;
6018         }
6019
6020         /**
6021          * Gets the value of the complementId property.
6022          * 
6023          * @return
6024          *     possible object is
6025          *     {@link String }
6026          *     
6027          */
6028         public String getComplementId() {
6029             return complementId;
6030         }
6031
6032         /**
6033          * Sets the value of the complementId property.
6034          * 
6035          * @param value
6036          *     allowed object is
6037          *     {@link String }
6038          *     
6039          */
6040         public void setComplementId(String value) {
6041             this.complementId = value;
6042         }
6043
6044         /**
6045          * Gets the value of the showComplementFeatures property.
6046          * 
6047          * @return
6048          *     possible object is
6049          *     {@link Boolean }
6050          *     
6051          */
6052         public boolean isShowComplementFeatures() {
6053             if (showComplementFeatures == null) {
6054                 return false;
6055             } else {
6056                 return showComplementFeatures;
6057             }
6058         }
6059
6060         /**
6061          * Sets the value of the showComplementFeatures property.
6062          * 
6063          * @param value
6064          *     allowed object is
6065          *     {@link Boolean }
6066          *     
6067          */
6068         public void setShowComplementFeatures(Boolean value) {
6069             this.showComplementFeatures = value;
6070         }
6071
6072         /**
6073          * Gets the value of the showComplementFeaturesOnTop property.
6074          * 
6075          * @return
6076          *     possible object is
6077          *     {@link Boolean }
6078          *     
6079          */
6080         public boolean isShowComplementFeaturesOnTop() {
6081             if (showComplementFeaturesOnTop == null) {
6082                 return false;
6083             } else {
6084                 return showComplementFeaturesOnTop;
6085             }
6086         }
6087
6088         /**
6089          * Sets the value of the showComplementFeaturesOnTop property.
6090          * 
6091          * @param value
6092          *     allowed object is
6093          *     {@link Boolean }
6094          *     
6095          */
6096         public void setShowComplementFeaturesOnTop(Boolean value) {
6097             this.showComplementFeaturesOnTop = value;
6098         }
6099
6100         /**
6101          * Gets the value of the width property.
6102          * 
6103          * @return
6104          *     possible object is
6105          *     {@link Integer }
6106          *     
6107          */
6108         public Integer getWidth() {
6109             return width;
6110         }
6111
6112         /**
6113          * Sets the value of the width property.
6114          * 
6115          * @param value
6116          *     allowed object is
6117          *     {@link Integer }
6118          *     
6119          */
6120         public void setWidth(Integer value) {
6121             this.width = value;
6122         }
6123
6124         /**
6125          * Gets the value of the height property.
6126          * 
6127          * @return
6128          *     possible object is
6129          *     {@link Integer }
6130          *     
6131          */
6132         public Integer getHeight() {
6133             return height;
6134         }
6135
6136         /**
6137          * Sets the value of the height property.
6138          * 
6139          * @param value
6140          *     allowed object is
6141          *     {@link Integer }
6142          *     
6143          */
6144         public void setHeight(Integer value) {
6145             this.height = value;
6146         }
6147
6148         /**
6149          * Gets the value of the xpos property.
6150          * 
6151          * @return
6152          *     possible object is
6153          *     {@link Integer }
6154          *     
6155          */
6156         public Integer getXpos() {
6157             return xpos;
6158         }
6159
6160         /**
6161          * Sets the value of the xpos property.
6162          * 
6163          * @param value
6164          *     allowed object is
6165          *     {@link Integer }
6166          *     
6167          */
6168         public void setXpos(Integer value) {
6169             this.xpos = value;
6170         }
6171
6172         /**
6173          * Gets the value of the ypos property.
6174          * 
6175          * @return
6176          *     possible object is
6177          *     {@link Integer }
6178          *     
6179          */
6180         public Integer getYpos() {
6181             return ypos;
6182         }
6183
6184         /**
6185          * Sets the value of the ypos property.
6186          * 
6187          * @param value
6188          *     allowed object is
6189          *     {@link Integer }
6190          *     
6191          */
6192         public void setYpos(Integer value) {
6193             this.ypos = value;
6194         }
6195
6196
6197         /**
6198          * &lt;p&gt;Java class for anonymous complex type.
6199          * 
6200          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
6201          * 
6202          * &lt;pre&gt;
6203          * &amp;lt;complexType&amp;gt;
6204          *   &amp;lt;complexContent&amp;gt;
6205          *     &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
6206          *       &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6207          *       &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
6208          *       &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
6209          *     &amp;lt;/extension&amp;gt;
6210          *   &amp;lt;/complexContent&amp;gt;
6211          * &amp;lt;/complexType&amp;gt;
6212          * &lt;/pre&gt;
6213          * 
6214          * 
6215          */
6216         @XmlAccessorType(XmlAccessType.FIELD)
6217         @XmlType(name = "")
6218         public static class CalcIdParam
6219             extends WebServiceParameterSet
6220         {
6221
6222             @XmlAttribute(name = "calcId", required = true)
6223             protected String calcId;
6224             @XmlAttribute(name = "needsUpdate")
6225             protected Boolean needsUpdate;
6226             @XmlAttribute(name = "autoUpdate", required = true)
6227             protected boolean autoUpdate;
6228
6229             /**
6230              * Gets the value of the calcId property.
6231              * 
6232              * @return
6233              *     possible object is
6234              *     {@link String }
6235              *     
6236              */
6237             public String getCalcId() {
6238                 return calcId;
6239             }
6240
6241             /**
6242              * Sets the value of the calcId property.
6243              * 
6244              * @param value
6245              *     allowed object is
6246              *     {@link String }
6247              *     
6248              */
6249             public void setCalcId(String value) {
6250                 this.calcId = value;
6251             }
6252
6253             /**
6254              * Gets the value of the needsUpdate property.
6255              * 
6256              * @return
6257              *     possible object is
6258              *     {@link Boolean }
6259              *     
6260              */
6261             public boolean isNeedsUpdate() {
6262                 if (needsUpdate == null) {
6263                     return false;
6264                 } else {
6265                     return needsUpdate;
6266                 }
6267             }
6268
6269             /**
6270              * Sets the value of the needsUpdate property.
6271              * 
6272              * @param value
6273              *     allowed object is
6274              *     {@link Boolean }
6275              *     
6276              */
6277             public void setNeedsUpdate(Boolean value) {
6278                 this.needsUpdate = value;
6279             }
6280
6281             /**
6282              * Gets the value of the autoUpdate property.
6283              * 
6284              */
6285             public boolean isAutoUpdate() {
6286                 return autoUpdate;
6287             }
6288
6289             /**
6290              * Sets the value of the autoUpdate property.
6291              * 
6292              */
6293             public void setAutoUpdate(boolean value) {
6294                 this.autoUpdate = value;
6295             }
6296
6297         }
6298
6299
6300         /**
6301          * &lt;p&gt;Java class for anonymous complex type.
6302          * 
6303          * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
6304          * 
6305          * &lt;pre&gt;
6306          * &amp;lt;complexType&amp;gt;
6307          *   &amp;lt;complexContent&amp;gt;
6308          *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
6309          *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6310          *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6311          *     &amp;lt;/restriction&amp;gt;
6312          *   &amp;lt;/complexContent&amp;gt;
6313          * &amp;lt;/complexType&amp;gt;
6314          * &lt;/pre&gt;
6315          * 
6316          * 
6317          */
6318         @XmlAccessorType(XmlAccessType.FIELD)
6319         @XmlType(name = "")
6320         public static class HiddenColumns {
6321
6322             @XmlAttribute(name = "start")
6323             protected Integer start;
6324             @XmlAttribute(name = "end")
6325             protected Integer end;
6326
6327             /**
6328              * Gets the value of the start property.
6329              * 
6330              * @return
6331              *     possible object is
6332              *     {@link Integer }
6333              *     
6334              */
6335             public Integer getStart() {
6336                 return start;
6337             }
6338
6339             /**
6340              * Sets the value of the start property.
6341              * 
6342              * @param value
6343              *     allowed object is
6344              *     {@link Integer }
6345              *     
6346              */
6347             public void setStart(Integer value) {
6348                 this.start = value;
6349             }
6350
6351             /**
6352              * Gets the value of the end property.
6353              * 
6354              * @return
6355              *     possible object is
6356              *     {@link Integer }
6357              *     
6358              */
6359             public Integer getEnd() {
6360                 return end;
6361             }
6362
6363             /**
6364              * Sets the value of the end property.
6365              * 
6366              * @param value
6367              *     allowed object is
6368              *     {@link Integer }
6369              *     
6370              */
6371             public void setEnd(Integer value) {
6372                 this.end = value;
6373             }
6374
6375         }
6376
6377     }
6378
6379 }