JAL-2738 use GeneLocus extends DBRefEntry to hold chromosomal mappings
[jalview.git] / src / jalview / xml / binding / jalview / JalviewModel.java
1 //
2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
4 // Any modifications to this file will be lost upon recompilation of the source schema. 
5 // Generated on: 2018.12.20 at 11:47:26 AM GMT 
6 //
7
8
9 package jalview.xml.binding.jalview;
10
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
24
25
26 /**
27  * <p>Java class for JalviewModel complex type.
28  * 
29  * <p>The following schema fragment specifies the expected content contained within this class.
30  * 
31  * <pre>
32  * &lt;complexType name="JalviewModel">
33  *   &lt;complexContent>
34  *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
35  *       &lt;sequence>
36  *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
37  *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
38  *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
39  *         &lt;sequence>
40  *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
41  *             &lt;complexType>
42  *               &lt;complexContent>
43  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
44  *                   &lt;sequence>
45  *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
46  *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
47  *                       &lt;complexType>
48  *                         &lt;complexContent>
49  *                           &lt;extension base="{www.jalview.org}pdbentry">
50  *                             &lt;sequence>
51  *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
52  *                                 &lt;complexType>
53  *                                   &lt;simpleContent>
54  *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
55  *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
56  *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
57  *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
58  *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
59  *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
60  *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61  *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
62  *                                     &lt;/extension>
63  *                                   &lt;/simpleContent>
64  *                                 &lt;/complexType>
65  *                               &lt;/element>
66  *                             &lt;/sequence>
67  *                           &lt;/extension>
68  *                         &lt;/complexContent>
69  *                       &lt;/complexType>
70  *                     &lt;/element>
71  *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
72  *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
73  *                       &lt;complexType>
74  *                         &lt;complexContent>
75  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
76  *                             &lt;sequence>
77  *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
78  *                                 &lt;complexType>
79  *                                   &lt;complexContent>
80  *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
81  *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
82  *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
83  *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
84  *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
85  *                                     &lt;/restriction>
86  *                                   &lt;/complexContent>
87  *                                 &lt;/complexType>
88  *                               &lt;/element>
89  *                             &lt;/sequence>
90  *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
91  *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
92  *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
93  *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
94  *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
95  *                           &lt;/restriction>
96  *                         &lt;/complexContent>
97  *                       &lt;/complexType>
98  *                     &lt;/element>
99  *                   &lt;/sequence>
100  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
101  *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
102  *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103  *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
104  *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
105  *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
106  *                 &lt;/restriction>
107  *               &lt;/complexContent>
108  *             &lt;/complexType>
109  *           &lt;/element>
110  *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
111  *             &lt;complexType>
112  *               &lt;complexContent>
113  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
114  *                   &lt;sequence>
115  *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
116  *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
117  *                   &lt;/sequence>
118  *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
119  *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
120  *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
121  *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
122  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
123  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124  *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
125  *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
126  *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127  *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
129  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
130  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
131  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
132  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
133  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
135  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
137  *                 &lt;/restriction>
138  *               &lt;/complexContent>
139  *             &lt;/complexType>
140  *           &lt;/element>
141  *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
142  *             &lt;complexType>
143  *               &lt;complexContent>
144  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
145  *                   &lt;sequence>
146  *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147  *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
148  *                       &lt;complexType>
149  *                         &lt;complexContent>
150  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
151  *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152  *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
153  *                           &lt;/restriction>
154  *                         &lt;/complexContent>
155  *                       &lt;/complexType>
156  *                     &lt;/element>
157  *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
158  *                       &lt;complexType>
159  *                         &lt;complexContent>
160  *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
161  *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
162  *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
163  *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
164  *                           &lt;/extension>
165  *                         &lt;/complexContent>
166  *                       &lt;/complexType>
167  *                     &lt;/element>
168  *                   &lt;/sequence>
169  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
170  *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
171  *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
172  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
173  *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
174  *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
175  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
176  *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
177  *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
178  *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
179  *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
180  *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
181  *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
182  *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
183  *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
184  *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185  *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186  *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
187  *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
188  *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
189  *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
190  *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
191  *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
192  *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
193  *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
194  *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
195  *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
196  *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
197  *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
198  *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
199  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
200  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
201  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
202  *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
203  *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
204  *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
205  *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
206  *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
207  *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
208  *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
209  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
210  *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
211  *                 &lt;/restriction>
212  *               &lt;/complexContent>
213  *             &lt;/complexType>
214  *           &lt;/element>
215  *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
216  *             &lt;complexType>
217  *               &lt;complexContent>
218  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
219  *                   &lt;sequence>
220  *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
221  *                   &lt;/sequence>
222  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
223  *                 &lt;/restriction>
224  *               &lt;/complexContent>
225  *             &lt;/complexType>
226  *           &lt;/element>
227  *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
228  *             &lt;complexType>
229  *               &lt;complexContent>
230  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
231  *                   &lt;sequence minOccurs="0">
232  *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
233  *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
234  *                   &lt;/sequence>
235  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
236  *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
237  *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
238  *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
239  *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
240  *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
241  *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
242  *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
243  *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
244  *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
245  *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
246  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
247  *                 &lt;/restriction>
248  *               &lt;/complexContent>
249  *             &lt;/complexType>
250  *           &lt;/element>
251  *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
252  *             &lt;complexType>
253  *               &lt;complexContent>
254  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
255  *                   &lt;sequence>
256  *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
257  *                       &lt;complexType>
258  *                         &lt;complexContent>
259  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
260  *                             &lt;attGroup ref="{www.jalview.org}position"/>
261  *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
262  *                           &lt;/restriction>
263  *                         &lt;/complexContent>
264  *                       &lt;/complexType>
265  *                     &lt;/element>
266  *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
267  *                       &lt;complexType>
268  *                         &lt;complexContent>
269  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
270  *                             &lt;attGroup ref="{www.jalview.org}position"/>
271  *                           &lt;/restriction>
272  *                         &lt;/complexContent>
273  *                       &lt;/complexType>
274  *                     &lt;/element>
275  *                     &lt;element name="seqPointMin">
276  *                       &lt;complexType>
277  *                         &lt;complexContent>
278  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
279  *                             &lt;attGroup ref="{www.jalview.org}position"/>
280  *                           &lt;/restriction>
281  *                         &lt;/complexContent>
282  *                       &lt;/complexType>
283  *                     &lt;/element>
284  *                     &lt;element name="seqPointMax">
285  *                       &lt;complexType>
286  *                         &lt;complexContent>
287  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
288  *                             &lt;attGroup ref="{www.jalview.org}position"/>
289  *                           &lt;/restriction>
290  *                         &lt;/complexContent>
291  *                       &lt;/complexType>
292  *                     &lt;/element>
293  *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
294  *                   &lt;/sequence>
295  *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
296  *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
297  *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
298  *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
299  *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
300  *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
301  *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
302  *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
303  *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
304  *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
305  *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
306  *                 &lt;/restriction>
307  *               &lt;/complexContent>
308  *             &lt;/complexType>
309  *           &lt;/element>
310  *           &lt;element name="FeatureSettings" minOccurs="0">
311  *             &lt;complexType>
312  *               &lt;complexContent>
313  *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
314  *                   &lt;sequence>
315  *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
316  *                       &lt;complexType>
317  *                         &lt;complexContent>
318  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
319  *                             &lt;sequence>
320  *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
321  *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
322  *                             &lt;/sequence>
323  *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
324  *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
325  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
326  *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
327  *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
328  *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
329  *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
330  *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
331  *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
332  *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
333  *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
334  *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
335  *                           &lt;/restriction>
336  *                         &lt;/complexContent>
337  *                       &lt;/complexType>
338  *                     &lt;/element>
339  *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
340  *                       &lt;complexType>
341  *                         &lt;complexContent>
342  *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
343  *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
344  *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
345  *                           &lt;/restriction>
346  *                         &lt;/complexContent>
347  *                       &lt;/complexType>
348  *                     &lt;/element>
349  *                   &lt;/sequence>
350  *                 &lt;/restriction>
351  *               &lt;/complexContent>
352  *             &lt;/complexType>
353  *           &lt;/element>
354  *         &lt;/sequence>
355  *       &lt;/sequence>
356  *     &lt;/restriction>
357  *   &lt;/complexContent>
358  * &lt;/complexType>
359  * </pre>
360  * 
361  * 
362  */
363 @XmlAccessorType(XmlAccessType.FIELD)
364 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
365     "creationDate",
366     "version",
367     "vamsasModel",
368     "jSeq",
369     "jGroup",
370     "viewport",
371     "userColours",
372     "tree",
373     "pcaViewer",
374     "featureSettings"
375 })
376 public class JalviewModel {
377
378     @XmlElement(required = true)
379     @XmlSchemaType(name = "dateTime")
380     protected XMLGregorianCalendar creationDate;
381     @XmlElement(required = true)
382     protected String version;
383     @XmlElement(required = true)
384     protected VAMSAS vamsasModel;
385     @XmlElement(name = "JSeq")
386     protected List<JalviewModel.JSeq> jSeq;
387     @XmlElement(name = "JGroup")
388     protected List<JalviewModel.JGroup> jGroup;
389     @XmlElement(name = "Viewport")
390     protected List<JalviewModel.Viewport> viewport;
391     @XmlElement(name = "UserColours")
392     protected List<JalviewModel.UserColours> userColours;
393     protected List<JalviewModel.Tree> tree;
394     @XmlElement(name = "PcaViewer")
395     protected List<JalviewModel.PcaViewer> pcaViewer;
396     @XmlElement(name = "FeatureSettings")
397     protected JalviewModel.FeatureSettings featureSettings;
398
399     /**
400      * Gets the value of the creationDate property.
401      * 
402      * @return
403      *     possible object is
404      *     {@link XMLGregorianCalendar }
405      *     
406      */
407     public XMLGregorianCalendar getCreationDate() {
408         return creationDate;
409     }
410
411     /**
412      * Sets the value of the creationDate property.
413      * 
414      * @param value
415      *     allowed object is
416      *     {@link XMLGregorianCalendar }
417      *     
418      */
419     public void setCreationDate(XMLGregorianCalendar value) {
420         this.creationDate = value;
421     }
422
423     /**
424      * Gets the value of the version property.
425      * 
426      * @return
427      *     possible object is
428      *     {@link String }
429      *     
430      */
431     public String getVersion() {
432         return version;
433     }
434
435     /**
436      * Sets the value of the version property.
437      * 
438      * @param value
439      *     allowed object is
440      *     {@link String }
441      *     
442      */
443     public void setVersion(String value) {
444         this.version = value;
445     }
446
447     /**
448      * Gets the value of the vamsasModel property.
449      * 
450      * @return
451      *     possible object is
452      *     {@link VAMSAS }
453      *     
454      */
455     public VAMSAS getVamsasModel() {
456         return vamsasModel;
457     }
458
459     /**
460      * Sets the value of the vamsasModel property.
461      * 
462      * @param value
463      *     allowed object is
464      *     {@link VAMSAS }
465      *     
466      */
467     public void setVamsasModel(VAMSAS value) {
468         this.vamsasModel = value;
469     }
470
471     /**
472      * Gets the value of the jSeq property.
473      * 
474      * <p>
475      * This accessor method returns a reference to the live list,
476      * not a snapshot. Therefore any modification you make to the
477      * returned list will be present inside the JAXB object.
478      * This is why there is not a <CODE>set</CODE> method for the jSeq property.
479      * 
480      * <p>
481      * For example, to add a new item, do as follows:
482      * <pre>
483      *    getJSeq().add(newItem);
484      * </pre>
485      * 
486      * 
487      * <p>
488      * Objects of the following type(s) are allowed in the list
489      * {@link JalviewModel.JSeq }
490      * 
491      * 
492      */
493     public List<JalviewModel.JSeq> getJSeq() {
494         if (jSeq == null) {
495             jSeq = new ArrayList<JalviewModel.JSeq>();
496         }
497         return this.jSeq;
498     }
499
500     /**
501      * Gets the value of the jGroup property.
502      * 
503      * <p>
504      * This accessor method returns a reference to the live list,
505      * not a snapshot. Therefore any modification you make to the
506      * returned list will be present inside the JAXB object.
507      * This is why there is not a <CODE>set</CODE> method for the jGroup property.
508      * 
509      * <p>
510      * For example, to add a new item, do as follows:
511      * <pre>
512      *    getJGroup().add(newItem);
513      * </pre>
514      * 
515      * 
516      * <p>
517      * Objects of the following type(s) are allowed in the list
518      * {@link JalviewModel.JGroup }
519      * 
520      * 
521      */
522     public List<JalviewModel.JGroup> getJGroup() {
523         if (jGroup == null) {
524             jGroup = new ArrayList<JalviewModel.JGroup>();
525         }
526         return this.jGroup;
527     }
528
529     /**
530      * Gets the value of the viewport property.
531      * 
532      * <p>
533      * This accessor method returns a reference to the live list,
534      * not a snapshot. Therefore any modification you make to the
535      * returned list will be present inside the JAXB object.
536      * This is why there is not a <CODE>set</CODE> method for the viewport property.
537      * 
538      * <p>
539      * For example, to add a new item, do as follows:
540      * <pre>
541      *    getViewport().add(newItem);
542      * </pre>
543      * 
544      * 
545      * <p>
546      * Objects of the following type(s) are allowed in the list
547      * {@link JalviewModel.Viewport }
548      * 
549      * 
550      */
551     public List<JalviewModel.Viewport> getViewport() {
552         if (viewport == null) {
553             viewport = new ArrayList<JalviewModel.Viewport>();
554         }
555         return this.viewport;
556     }
557
558     /**
559      * Gets the value of the userColours property.
560      * 
561      * <p>
562      * This accessor method returns a reference to the live list,
563      * not a snapshot. Therefore any modification you make to the
564      * returned list will be present inside the JAXB object.
565      * This is why there is not a <CODE>set</CODE> method for the userColours property.
566      * 
567      * <p>
568      * For example, to add a new item, do as follows:
569      * <pre>
570      *    getUserColours().add(newItem);
571      * </pre>
572      * 
573      * 
574      * <p>
575      * Objects of the following type(s) are allowed in the list
576      * {@link JalviewModel.UserColours }
577      * 
578      * 
579      */
580     public List<JalviewModel.UserColours> getUserColours() {
581         if (userColours == null) {
582             userColours = new ArrayList<JalviewModel.UserColours>();
583         }
584         return this.userColours;
585     }
586
587     /**
588      * Gets the value of the tree property.
589      * 
590      * <p>
591      * This accessor method returns a reference to the live list,
592      * not a snapshot. Therefore any modification you make to the
593      * returned list will be present inside the JAXB object.
594      * This is why there is not a <CODE>set</CODE> method for the tree property.
595      * 
596      * <p>
597      * For example, to add a new item, do as follows:
598      * <pre>
599      *    getTree().add(newItem);
600      * </pre>
601      * 
602      * 
603      * <p>
604      * Objects of the following type(s) are allowed in the list
605      * {@link JalviewModel.Tree }
606      * 
607      * 
608      */
609     public List<JalviewModel.Tree> getTree() {
610         if (tree == null) {
611             tree = new ArrayList<JalviewModel.Tree>();
612         }
613         return this.tree;
614     }
615
616     /**
617      * Gets the value of the pcaViewer property.
618      * 
619      * <p>
620      * This accessor method returns a reference to the live list,
621      * not a snapshot. Therefore any modification you make to the
622      * returned list will be present inside the JAXB object.
623      * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
624      * 
625      * <p>
626      * For example, to add a new item, do as follows:
627      * <pre>
628      *    getPcaViewer().add(newItem);
629      * </pre>
630      * 
631      * 
632      * <p>
633      * Objects of the following type(s) are allowed in the list
634      * {@link JalviewModel.PcaViewer }
635      * 
636      * 
637      */
638     public List<JalviewModel.PcaViewer> getPcaViewer() {
639         if (pcaViewer == null) {
640             pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
641         }
642         return this.pcaViewer;
643     }
644
645     /**
646      * Gets the value of the featureSettings property.
647      * 
648      * @return
649      *     possible object is
650      *     {@link JalviewModel.FeatureSettings }
651      *     
652      */
653     public JalviewModel.FeatureSettings getFeatureSettings() {
654         return featureSettings;
655     }
656
657     /**
658      * Sets the value of the featureSettings property.
659      * 
660      * @param value
661      *     allowed object is
662      *     {@link JalviewModel.FeatureSettings }
663      *     
664      */
665     public void setFeatureSettings(JalviewModel.FeatureSettings value) {
666         this.featureSettings = value;
667     }
668
669
670     /**
671      * <p>Java class for anonymous complex type.
672      * 
673      * <p>The following schema fragment specifies the expected content contained within this class.
674      * 
675      * <pre>
676      * &lt;complexType>
677      *   &lt;complexContent>
678      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
679      *       &lt;sequence>
680      *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
681      *           &lt;complexType>
682      *             &lt;complexContent>
683      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
684      *                 &lt;sequence>
685      *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
686      *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
687      *                 &lt;/sequence>
688      *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
689      *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
690      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
691      *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
692      *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
693      *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
694      *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
695      *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
696      *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
697      *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
698      *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
699      *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
700      *               &lt;/restriction>
701      *             &lt;/complexContent>
702      *           &lt;/complexType>
703      *         &lt;/element>
704      *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
705      *           &lt;complexType>
706      *             &lt;complexContent>
707      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
708      *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
709      *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
710      *               &lt;/restriction>
711      *             &lt;/complexContent>
712      *           &lt;/complexType>
713      *         &lt;/element>
714      *       &lt;/sequence>
715      *     &lt;/restriction>
716      *   &lt;/complexContent>
717      * &lt;/complexType>
718      * </pre>
719      * 
720      * 
721      */
722     @XmlAccessorType(XmlAccessType.FIELD)
723     @XmlType(name = "", propOrder = {
724         "setting",
725         "group"
726     })
727     public static class FeatureSettings {
728
729         @XmlElement(namespace = "www.jalview.org")
730         protected List<JalviewModel.FeatureSettings.Setting> setting;
731         @XmlElement(namespace = "www.jalview.org")
732         protected List<JalviewModel.FeatureSettings.Group> group;
733
734         /**
735          * Gets the value of the setting property.
736          * 
737          * <p>
738          * This accessor method returns a reference to the live list,
739          * not a snapshot. Therefore any modification you make to the
740          * returned list will be present inside the JAXB object.
741          * This is why there is not a <CODE>set</CODE> method for the setting property.
742          * 
743          * <p>
744          * For example, to add a new item, do as follows:
745          * <pre>
746          *    getSetting().add(newItem);
747          * </pre>
748          * 
749          * 
750          * <p>
751          * Objects of the following type(s) are allowed in the list
752          * {@link JalviewModel.FeatureSettings.Setting }
753          * 
754          * 
755          */
756         public List<JalviewModel.FeatureSettings.Setting> getSetting() {
757             if (setting == null) {
758                 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
759             }
760             return this.setting;
761         }
762
763         /**
764          * Gets the value of the group property.
765          * 
766          * <p>
767          * This accessor method returns a reference to the live list,
768          * not a snapshot. Therefore any modification you make to the
769          * returned list will be present inside the JAXB object.
770          * This is why there is not a <CODE>set</CODE> method for the group property.
771          * 
772          * <p>
773          * For example, to add a new item, do as follows:
774          * <pre>
775          *    getGroup().add(newItem);
776          * </pre>
777          * 
778          * 
779          * <p>
780          * Objects of the following type(s) are allowed in the list
781          * {@link JalviewModel.FeatureSettings.Group }
782          * 
783          * 
784          */
785         public List<JalviewModel.FeatureSettings.Group> getGroup() {
786             if (group == null) {
787                 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
788             }
789             return this.group;
790         }
791
792
793         /**
794          * <p>Java class for anonymous complex type.
795          * 
796          * <p>The following schema fragment specifies the expected content contained within this class.
797          * 
798          * <pre>
799          * &lt;complexType>
800          *   &lt;complexContent>
801          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
802          *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
803          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
804          *     &lt;/restriction>
805          *   &lt;/complexContent>
806          * &lt;/complexType>
807          * </pre>
808          * 
809          * 
810          */
811         @XmlAccessorType(XmlAccessType.FIELD)
812         @XmlType(name = "")
813         public static class Group {
814
815             @XmlAttribute(name = "name", required = true)
816             protected String name;
817             @XmlAttribute(name = "display", required = true)
818             protected boolean display;
819
820             /**
821              * Gets the value of the name property.
822              * 
823              * @return
824              *     possible object is
825              *     {@link String }
826              *     
827              */
828             public String getName() {
829                 return name;
830             }
831
832             /**
833              * Sets the value of the name property.
834              * 
835              * @param value
836              *     allowed object is
837              *     {@link String }
838              *     
839              */
840             public void setName(String value) {
841                 this.name = value;
842             }
843
844             /**
845              * Gets the value of the display property.
846              * 
847              */
848             public boolean isDisplay() {
849                 return display;
850             }
851
852             /**
853              * Sets the value of the display property.
854              * 
855              */
856             public void setDisplay(boolean value) {
857                 this.display = value;
858             }
859
860         }
861
862
863         /**
864          * <p>Java class for anonymous complex type.
865          * 
866          * <p>The following schema fragment specifies the expected content contained within this class.
867          * 
868          * <pre>
869          * &lt;complexType>
870          *   &lt;complexContent>
871          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
872          *       &lt;sequence>
873          *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
874          *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
875          *       &lt;/sequence>
876          *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
877          *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
878          *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
879          *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
880          *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
881          *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
882          *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
883          *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
884          *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
885          *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
886          *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
887          *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
888          *     &lt;/restriction>
889          *   &lt;/complexContent>
890          * &lt;/complexType>
891          * </pre>
892          * 
893          * 
894          */
895         @XmlAccessorType(XmlAccessType.FIELD)
896         @XmlType(name = "", propOrder = {
897             "attributeName",
898             "matcherSet"
899         })
900         public static class Setting {
901
902             @XmlElement(namespace = "www.jalview.org")
903             protected List<String> attributeName;
904             @XmlElement(namespace = "www.jalview.org")
905             protected FeatureMatcherSet matcherSet;
906             @XmlAttribute(name = "type", required = true)
907             protected String type;
908             @XmlAttribute(name = "colour", required = true)
909             protected int colour;
910             @XmlAttribute(name = "display", required = true)
911             protected boolean display;
912             @XmlAttribute(name = "order")
913             protected Float order;
914             @XmlAttribute(name = "mincolour")
915             protected Integer mincolour;
916             @XmlAttribute(name = "noValueColour")
917             protected NoValueColour noValueColour;
918             @XmlAttribute(name = "threshold")
919             protected Float threshold;
920             @XmlAttribute(name = "threshstate")
921             protected Integer threshstate;
922             @XmlAttribute(name = "max")
923             protected Float max;
924             @XmlAttribute(name = "min")
925             protected Float min;
926             @XmlAttribute(name = "colourByLabel")
927             protected Boolean colourByLabel;
928             @XmlAttribute(name = "autoScale")
929             protected Boolean autoScale;
930
931             /**
932              * Gets the value of the attributeName property.
933              * 
934              * <p>
935              * This accessor method returns a reference to the live list,
936              * not a snapshot. Therefore any modification you make to the
937              * returned list will be present inside the JAXB object.
938              * This is why there is not a <CODE>set</CODE> method for the attributeName property.
939              * 
940              * <p>
941              * For example, to add a new item, do as follows:
942              * <pre>
943              *    getAttributeName().add(newItem);
944              * </pre>
945              * 
946              * 
947              * <p>
948              * Objects of the following type(s) are allowed in the list
949              * {@link String }
950              * 
951              * 
952              */
953             public List<String> getAttributeName() {
954                 if (attributeName == null) {
955                     attributeName = new ArrayList<String>();
956                 }
957                 return this.attributeName;
958             }
959
960             /**
961              * Gets the value of the matcherSet property.
962              * 
963              * @return
964              *     possible object is
965              *     {@link FeatureMatcherSet }
966              *     
967              */
968             public FeatureMatcherSet getMatcherSet() {
969                 return matcherSet;
970             }
971
972             /**
973              * Sets the value of the matcherSet property.
974              * 
975              * @param value
976              *     allowed object is
977              *     {@link FeatureMatcherSet }
978              *     
979              */
980             public void setMatcherSet(FeatureMatcherSet value) {
981                 this.matcherSet = value;
982             }
983
984             /**
985              * Gets the value of the type property.
986              * 
987              * @return
988              *     possible object is
989              *     {@link String }
990              *     
991              */
992             public String getType() {
993                 return type;
994             }
995
996             /**
997              * Sets the value of the type property.
998              * 
999              * @param value
1000              *     allowed object is
1001              *     {@link String }
1002              *     
1003              */
1004             public void setType(String value) {
1005                 this.type = value;
1006             }
1007
1008             /**
1009              * Gets the value of the colour property.
1010              * 
1011              */
1012             public int getColour() {
1013                 return colour;
1014             }
1015
1016             /**
1017              * Sets the value of the colour property.
1018              * 
1019              */
1020             public void setColour(int value) {
1021                 this.colour = value;
1022             }
1023
1024             /**
1025              * Gets the value of the display property.
1026              * 
1027              */
1028             public boolean isDisplay() {
1029                 return display;
1030             }
1031
1032             /**
1033              * Sets the value of the display property.
1034              * 
1035              */
1036             public void setDisplay(boolean value) {
1037                 this.display = value;
1038             }
1039
1040             /**
1041              * Gets the value of the order property.
1042              * 
1043              * @return
1044              *     possible object is
1045              *     {@link Float }
1046              *     
1047              */
1048             public Float getOrder() {
1049                 return order;
1050             }
1051
1052             /**
1053              * Sets the value of the order property.
1054              * 
1055              * @param value
1056              *     allowed object is
1057              *     {@link Float }
1058              *     
1059              */
1060             public void setOrder(Float value) {
1061                 this.order = value;
1062             }
1063
1064             /**
1065              * Gets the value of the mincolour property.
1066              * 
1067              * @return
1068              *     possible object is
1069              *     {@link Integer }
1070              *     
1071              */
1072             public Integer getMincolour() {
1073                 return mincolour;
1074             }
1075
1076             /**
1077              * Sets the value of the mincolour property.
1078              * 
1079              * @param value
1080              *     allowed object is
1081              *     {@link Integer }
1082              *     
1083              */
1084             public void setMincolour(Integer value) {
1085                 this.mincolour = value;
1086             }
1087
1088             /**
1089              * Gets the value of the noValueColour property.
1090              * 
1091              * @return
1092              *     possible object is
1093              *     {@link NoValueColour }
1094              *     
1095              */
1096             public NoValueColour getNoValueColour() {
1097                 if (noValueColour == null) {
1098                     return NoValueColour.MIN;
1099                 } else {
1100                     return noValueColour;
1101                 }
1102             }
1103
1104             /**
1105              * Sets the value of the noValueColour property.
1106              * 
1107              * @param value
1108              *     allowed object is
1109              *     {@link NoValueColour }
1110              *     
1111              */
1112             public void setNoValueColour(NoValueColour value) {
1113                 this.noValueColour = value;
1114             }
1115
1116             /**
1117              * Gets the value of the threshold property.
1118              * 
1119              * @return
1120              *     possible object is
1121              *     {@link Float }
1122              *     
1123              */
1124             public Float getThreshold() {
1125                 return threshold;
1126             }
1127
1128             /**
1129              * Sets the value of the threshold property.
1130              * 
1131              * @param value
1132              *     allowed object is
1133              *     {@link Float }
1134              *     
1135              */
1136             public void setThreshold(Float value) {
1137                 this.threshold = value;
1138             }
1139
1140             /**
1141              * Gets the value of the threshstate property.
1142              * 
1143              * @return
1144              *     possible object is
1145              *     {@link Integer }
1146              *     
1147              */
1148             public Integer getThreshstate() {
1149                 return threshstate;
1150             }
1151
1152             /**
1153              * Sets the value of the threshstate property.
1154              * 
1155              * @param value
1156              *     allowed object is
1157              *     {@link Integer }
1158              *     
1159              */
1160             public void setThreshstate(Integer value) {
1161                 this.threshstate = value;
1162             }
1163
1164             /**
1165              * Gets the value of the max property.
1166              * 
1167              * @return
1168              *     possible object is
1169              *     {@link Float }
1170              *     
1171              */
1172             public Float getMax() {
1173                 return max;
1174             }
1175
1176             /**
1177              * Sets the value of the max property.
1178              * 
1179              * @param value
1180              *     allowed object is
1181              *     {@link Float }
1182              *     
1183              */
1184             public void setMax(Float value) {
1185                 this.max = value;
1186             }
1187
1188             /**
1189              * Gets the value of the min property.
1190              * 
1191              * @return
1192              *     possible object is
1193              *     {@link Float }
1194              *     
1195              */
1196             public Float getMin() {
1197                 return min;
1198             }
1199
1200             /**
1201              * Sets the value of the min property.
1202              * 
1203              * @param value
1204              *     allowed object is
1205              *     {@link Float }
1206              *     
1207              */
1208             public void setMin(Float value) {
1209                 this.min = value;
1210             }
1211
1212             /**
1213              * Gets the value of the colourByLabel property.
1214              * 
1215              * @return
1216              *     possible object is
1217              *     {@link Boolean }
1218              *     
1219              */
1220             public Boolean isColourByLabel() {
1221                 return colourByLabel;
1222             }
1223
1224             /**
1225              * Sets the value of the colourByLabel property.
1226              * 
1227              * @param value
1228              *     allowed object is
1229              *     {@link Boolean }
1230              *     
1231              */
1232             public void setColourByLabel(Boolean value) {
1233                 this.colourByLabel = value;
1234             }
1235
1236             /**
1237              * Gets the value of the autoScale property.
1238              * 
1239              * @return
1240              *     possible object is
1241              *     {@link Boolean }
1242              *     
1243              */
1244             public Boolean isAutoScale() {
1245                 return autoScale;
1246             }
1247
1248             /**
1249              * Sets the value of the autoScale property.
1250              * 
1251              * @param value
1252              *     allowed object is
1253              *     {@link Boolean }
1254              *     
1255              */
1256             public void setAutoScale(Boolean value) {
1257                 this.autoScale = value;
1258             }
1259
1260         }
1261
1262     }
1263
1264
1265     /**
1266      * <p>Java class for anonymous complex type.
1267      * 
1268      * <p>The following schema fragment specifies the expected content contained within this class.
1269      * 
1270      * <pre>
1271      * &lt;complexType>
1272      *   &lt;complexContent>
1273      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1274      *       &lt;sequence>
1275      *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1276      *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1277      *       &lt;/sequence>
1278      *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1279      *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1280      *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1281      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1282      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1283      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1284      *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1285      *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1286      *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1287      *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1288      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1289      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1290      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1291      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1292      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1293      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1294      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1295      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1296      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1297      *     &lt;/restriction>
1298      *   &lt;/complexContent>
1299      * &lt;/complexType>
1300      * </pre>
1301      * 
1302      * 
1303      */
1304     @XmlAccessorType(XmlAccessType.FIELD)
1305     @XmlType(name = "", propOrder = {
1306         "seq",
1307         "annotationColours"
1308     })
1309     public static class JGroup {
1310
1311         @XmlElement(namespace = "www.jalview.org", required = true)
1312         protected List<String> seq;
1313         @XmlElement(namespace = "www.jalview.org")
1314         protected AnnotationColourScheme annotationColours;
1315         @XmlAttribute(name = "start")
1316         protected Integer start;
1317         @XmlAttribute(name = "end")
1318         protected Integer end;
1319         @XmlAttribute(name = "name")
1320         protected String name;
1321         @XmlAttribute(name = "colour")
1322         protected String colour;
1323         @XmlAttribute(name = "consThreshold")
1324         protected Integer consThreshold;
1325         @XmlAttribute(name = "pidThreshold")
1326         protected Integer pidThreshold;
1327         @XmlAttribute(name = "outlineColour")
1328         protected Integer outlineColour;
1329         @XmlAttribute(name = "displayBoxes")
1330         protected Boolean displayBoxes;
1331         @XmlAttribute(name = "displayText")
1332         protected Boolean displayText;
1333         @XmlAttribute(name = "colourText")
1334         protected Boolean colourText;
1335         @XmlAttribute(name = "textCol1")
1336         protected Integer textCol1;
1337         @XmlAttribute(name = "textCol2")
1338         protected Integer textCol2;
1339         @XmlAttribute(name = "textColThreshold")
1340         protected Integer textColThreshold;
1341         @XmlAttribute(name = "showUnconserved")
1342         protected Boolean showUnconserved;
1343         @XmlAttribute(name = "ignoreGapsinConsensus")
1344         protected Boolean ignoreGapsinConsensus;
1345         @XmlAttribute(name = "showConsensusHistogram")
1346         protected Boolean showConsensusHistogram;
1347         @XmlAttribute(name = "showSequenceLogo")
1348         protected Boolean showSequenceLogo;
1349         @XmlAttribute(name = "normaliseSequenceLogo")
1350         protected Boolean normaliseSequenceLogo;
1351         @XmlAttribute(name = "id")
1352         protected String id;
1353
1354         /**
1355          * Gets the value of the seq property.
1356          * 
1357          * <p>
1358          * This accessor method returns a reference to the live list,
1359          * not a snapshot. Therefore any modification you make to the
1360          * returned list will be present inside the JAXB object.
1361          * This is why there is not a <CODE>set</CODE> method for the seq property.
1362          * 
1363          * <p>
1364          * For example, to add a new item, do as follows:
1365          * <pre>
1366          *    getSeq().add(newItem);
1367          * </pre>
1368          * 
1369          * 
1370          * <p>
1371          * Objects of the following type(s) are allowed in the list
1372          * {@link String }
1373          * 
1374          * 
1375          */
1376         public List<String> getSeq() {
1377             if (seq == null) {
1378                 seq = new ArrayList<String>();
1379             }
1380             return this.seq;
1381         }
1382
1383         /**
1384          * Gets the value of the annotationColours property.
1385          * 
1386          * @return
1387          *     possible object is
1388          *     {@link AnnotationColourScheme }
1389          *     
1390          */
1391         public AnnotationColourScheme getAnnotationColours() {
1392             return annotationColours;
1393         }
1394
1395         /**
1396          * Sets the value of the annotationColours property.
1397          * 
1398          * @param value
1399          *     allowed object is
1400          *     {@link AnnotationColourScheme }
1401          *     
1402          */
1403         public void setAnnotationColours(AnnotationColourScheme value) {
1404             this.annotationColours = value;
1405         }
1406
1407         /**
1408          * Gets the value of the start property.
1409          * 
1410          * @return
1411          *     possible object is
1412          *     {@link Integer }
1413          *     
1414          */
1415         public Integer getStart() {
1416             return start;
1417         }
1418
1419         /**
1420          * Sets the value of the start property.
1421          * 
1422          * @param value
1423          *     allowed object is
1424          *     {@link Integer }
1425          *     
1426          */
1427         public void setStart(Integer value) {
1428             this.start = value;
1429         }
1430
1431         /**
1432          * Gets the value of the end property.
1433          * 
1434          * @return
1435          *     possible object is
1436          *     {@link Integer }
1437          *     
1438          */
1439         public Integer getEnd() {
1440             return end;
1441         }
1442
1443         /**
1444          * Sets the value of the end property.
1445          * 
1446          * @param value
1447          *     allowed object is
1448          *     {@link Integer }
1449          *     
1450          */
1451         public void setEnd(Integer value) {
1452             this.end = value;
1453         }
1454
1455         /**
1456          * Gets the value of the name property.
1457          * 
1458          * @return
1459          *     possible object is
1460          *     {@link String }
1461          *     
1462          */
1463         public String getName() {
1464             return name;
1465         }
1466
1467         /**
1468          * Sets the value of the name property.
1469          * 
1470          * @param value
1471          *     allowed object is
1472          *     {@link String }
1473          *     
1474          */
1475         public void setName(String value) {
1476             this.name = value;
1477         }
1478
1479         /**
1480          * Gets the value of the colour property.
1481          * 
1482          * @return
1483          *     possible object is
1484          *     {@link String }
1485          *     
1486          */
1487         public String getColour() {
1488             return colour;
1489         }
1490
1491         /**
1492          * Sets the value of the colour property.
1493          * 
1494          * @param value
1495          *     allowed object is
1496          *     {@link String }
1497          *     
1498          */
1499         public void setColour(String value) {
1500             this.colour = value;
1501         }
1502
1503         /**
1504          * Gets the value of the consThreshold property.
1505          * 
1506          * @return
1507          *     possible object is
1508          *     {@link Integer }
1509          *     
1510          */
1511         public Integer getConsThreshold() {
1512             return consThreshold;
1513         }
1514
1515         /**
1516          * Sets the value of the consThreshold property.
1517          * 
1518          * @param value
1519          *     allowed object is
1520          *     {@link Integer }
1521          *     
1522          */
1523         public void setConsThreshold(Integer value) {
1524             this.consThreshold = value;
1525         }
1526
1527         /**
1528          * Gets the value of the pidThreshold property.
1529          * 
1530          * @return
1531          *     possible object is
1532          *     {@link Integer }
1533          *     
1534          */
1535         public Integer getPidThreshold() {
1536             return pidThreshold;
1537         }
1538
1539         /**
1540          * Sets the value of the pidThreshold property.
1541          * 
1542          * @param value
1543          *     allowed object is
1544          *     {@link Integer }
1545          *     
1546          */
1547         public void setPidThreshold(Integer value) {
1548             this.pidThreshold = value;
1549         }
1550
1551         /**
1552          * Gets the value of the outlineColour property.
1553          * 
1554          * @return
1555          *     possible object is
1556          *     {@link Integer }
1557          *     
1558          */
1559         public Integer getOutlineColour() {
1560             return outlineColour;
1561         }
1562
1563         /**
1564          * Sets the value of the outlineColour property.
1565          * 
1566          * @param value
1567          *     allowed object is
1568          *     {@link Integer }
1569          *     
1570          */
1571         public void setOutlineColour(Integer value) {
1572             this.outlineColour = value;
1573         }
1574
1575         /**
1576          * Gets the value of the displayBoxes property.
1577          * 
1578          * @return
1579          *     possible object is
1580          *     {@link Boolean }
1581          *     
1582          */
1583         public Boolean isDisplayBoxes() {
1584             return displayBoxes;
1585         }
1586
1587         /**
1588          * Sets the value of the displayBoxes property.
1589          * 
1590          * @param value
1591          *     allowed object is
1592          *     {@link Boolean }
1593          *     
1594          */
1595         public void setDisplayBoxes(Boolean value) {
1596             this.displayBoxes = value;
1597         }
1598
1599         /**
1600          * Gets the value of the displayText property.
1601          * 
1602          * @return
1603          *     possible object is
1604          *     {@link Boolean }
1605          *     
1606          */
1607         public Boolean isDisplayText() {
1608             return displayText;
1609         }
1610
1611         /**
1612          * Sets the value of the displayText property.
1613          * 
1614          * @param value
1615          *     allowed object is
1616          *     {@link Boolean }
1617          *     
1618          */
1619         public void setDisplayText(Boolean value) {
1620             this.displayText = value;
1621         }
1622
1623         /**
1624          * Gets the value of the colourText property.
1625          * 
1626          * @return
1627          *     possible object is
1628          *     {@link Boolean }
1629          *     
1630          */
1631         public Boolean isColourText() {
1632             return colourText;
1633         }
1634
1635         /**
1636          * Sets the value of the colourText property.
1637          * 
1638          * @param value
1639          *     allowed object is
1640          *     {@link Boolean }
1641          *     
1642          */
1643         public void setColourText(Boolean value) {
1644             this.colourText = value;
1645         }
1646
1647         /**
1648          * Gets the value of the textCol1 property.
1649          * 
1650          * @return
1651          *     possible object is
1652          *     {@link Integer }
1653          *     
1654          */
1655         public Integer getTextCol1() {
1656             return textCol1;
1657         }
1658
1659         /**
1660          * Sets the value of the textCol1 property.
1661          * 
1662          * @param value
1663          *     allowed object is
1664          *     {@link Integer }
1665          *     
1666          */
1667         public void setTextCol1(Integer value) {
1668             this.textCol1 = value;
1669         }
1670
1671         /**
1672          * Gets the value of the textCol2 property.
1673          * 
1674          * @return
1675          *     possible object is
1676          *     {@link Integer }
1677          *     
1678          */
1679         public Integer getTextCol2() {
1680             return textCol2;
1681         }
1682
1683         /**
1684          * Sets the value of the textCol2 property.
1685          * 
1686          * @param value
1687          *     allowed object is
1688          *     {@link Integer }
1689          *     
1690          */
1691         public void setTextCol2(Integer value) {
1692             this.textCol2 = value;
1693         }
1694
1695         /**
1696          * Gets the value of the textColThreshold property.
1697          * 
1698          * @return
1699          *     possible object is
1700          *     {@link Integer }
1701          *     
1702          */
1703         public Integer getTextColThreshold() {
1704             return textColThreshold;
1705         }
1706
1707         /**
1708          * Sets the value of the textColThreshold property.
1709          * 
1710          * @param value
1711          *     allowed object is
1712          *     {@link Integer }
1713          *     
1714          */
1715         public void setTextColThreshold(Integer value) {
1716             this.textColThreshold = value;
1717         }
1718
1719         /**
1720          * Gets the value of the showUnconserved property.
1721          * 
1722          * @return
1723          *     possible object is
1724          *     {@link Boolean }
1725          *     
1726          */
1727         public Boolean isShowUnconserved() {
1728             return showUnconserved;
1729         }
1730
1731         /**
1732          * Sets the value of the showUnconserved property.
1733          * 
1734          * @param value
1735          *     allowed object is
1736          *     {@link Boolean }
1737          *     
1738          */
1739         public void setShowUnconserved(Boolean value) {
1740             this.showUnconserved = value;
1741         }
1742
1743         /**
1744          * Gets the value of the ignoreGapsinConsensus property.
1745          * 
1746          * @return
1747          *     possible object is
1748          *     {@link Boolean }
1749          *     
1750          */
1751         public boolean isIgnoreGapsinConsensus() {
1752             if (ignoreGapsinConsensus == null) {
1753                 return true;
1754             } else {
1755                 return ignoreGapsinConsensus;
1756             }
1757         }
1758
1759         /**
1760          * Sets the value of the ignoreGapsinConsensus property.
1761          * 
1762          * @param value
1763          *     allowed object is
1764          *     {@link Boolean }
1765          *     
1766          */
1767         public void setIgnoreGapsinConsensus(Boolean value) {
1768             this.ignoreGapsinConsensus = value;
1769         }
1770
1771         /**
1772          * Gets the value of the showConsensusHistogram property.
1773          * 
1774          * @return
1775          *     possible object is
1776          *     {@link Boolean }
1777          *     
1778          */
1779         public boolean isShowConsensusHistogram() {
1780             if (showConsensusHistogram == null) {
1781                 return true;
1782             } else {
1783                 return showConsensusHistogram;
1784             }
1785         }
1786
1787         /**
1788          * Sets the value of the showConsensusHistogram property.
1789          * 
1790          * @param value
1791          *     allowed object is
1792          *     {@link Boolean }
1793          *     
1794          */
1795         public void setShowConsensusHistogram(Boolean value) {
1796             this.showConsensusHistogram = value;
1797         }
1798
1799         /**
1800          * Gets the value of the showSequenceLogo property.
1801          * 
1802          * @return
1803          *     possible object is
1804          *     {@link Boolean }
1805          *     
1806          */
1807         public boolean isShowSequenceLogo() {
1808             if (showSequenceLogo == null) {
1809                 return false;
1810             } else {
1811                 return showSequenceLogo;
1812             }
1813         }
1814
1815         /**
1816          * Sets the value of the showSequenceLogo property.
1817          * 
1818          * @param value
1819          *     allowed object is
1820          *     {@link Boolean }
1821          *     
1822          */
1823         public void setShowSequenceLogo(Boolean value) {
1824             this.showSequenceLogo = value;
1825         }
1826
1827         /**
1828          * Gets the value of the normaliseSequenceLogo property.
1829          * 
1830          * @return
1831          *     possible object is
1832          *     {@link Boolean }
1833          *     
1834          */
1835         public boolean isNormaliseSequenceLogo() {
1836             if (normaliseSequenceLogo == null) {
1837                 return false;
1838             } else {
1839                 return normaliseSequenceLogo;
1840             }
1841         }
1842
1843         /**
1844          * Sets the value of the normaliseSequenceLogo property.
1845          * 
1846          * @param value
1847          *     allowed object is
1848          *     {@link Boolean }
1849          *     
1850          */
1851         public void setNormaliseSequenceLogo(Boolean value) {
1852             this.normaliseSequenceLogo = value;
1853         }
1854
1855         /**
1856          * Gets the value of the id property.
1857          * 
1858          * @return
1859          *     possible object is
1860          *     {@link String }
1861          *     
1862          */
1863         public String getId() {
1864             return id;
1865         }
1866
1867         /**
1868          * Sets the value of the id property.
1869          * 
1870          * @param value
1871          *     allowed object is
1872          *     {@link String }
1873          *     
1874          */
1875         public void setId(String value) {
1876             this.id = value;
1877         }
1878
1879     }
1880
1881
1882     /**
1883      * <p>Java class for anonymous complex type.
1884      * 
1885      * <p>The following schema fragment specifies the expected content contained within this class.
1886      * 
1887      * <pre>
1888      * &lt;complexType>
1889      *   &lt;complexContent>
1890      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1891      *       &lt;sequence>
1892      *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1893      *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1894      *           &lt;complexType>
1895      *             &lt;complexContent>
1896      *               &lt;extension base="{www.jalview.org}pdbentry">
1897      *                 &lt;sequence>
1898      *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
1899      *                     &lt;complexType>
1900      *                       &lt;simpleContent>
1901      *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
1902      *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1903      *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1904      *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1905      *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1906      *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1907      *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1908      *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1909      *                         &lt;/extension>
1910      *                       &lt;/simpleContent>
1911      *                     &lt;/complexType>
1912      *                   &lt;/element>
1913      *                 &lt;/sequence>
1914      *               &lt;/extension>
1915      *             &lt;/complexContent>
1916      *           &lt;/complexType>
1917      *         &lt;/element>
1918      *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1919      *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1920      *           &lt;complexType>
1921      *             &lt;complexContent>
1922      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1923      *                 &lt;sequence>
1924      *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
1925      *                     &lt;complexType>
1926      *                       &lt;complexContent>
1927      *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1928      *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1929      *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1930      *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1931      *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1932      *                         &lt;/restriction>
1933      *                       &lt;/complexContent>
1934      *                     &lt;/complexType>
1935      *                   &lt;/element>
1936      *                 &lt;/sequence>
1937      *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
1938      *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1939      *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1940      *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1941      *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1942      *               &lt;/restriction>
1943      *             &lt;/complexContent>
1944      *           &lt;/complexType>
1945      *         &lt;/element>
1946      *       &lt;/sequence>
1947      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1948      *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1949      *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1950      *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1951      *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1952      *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1953      *     &lt;/restriction>
1954      *   &lt;/complexContent>
1955      * &lt;/complexType>
1956      * </pre>
1957      * 
1958      * 
1959      */
1960     @XmlAccessorType(XmlAccessType.FIELD)
1961     @XmlType(name = "", propOrder = {
1962         "features",
1963         "pdbids",
1964         "hiddenSequences",
1965         "rnaViewer"
1966     })
1967     public static class JSeq {
1968
1969         @XmlElement(namespace = "www.jalview.org")
1970         protected List<Feature> features;
1971         @XmlElement(namespace = "www.jalview.org")
1972         protected List<JalviewModel.JSeq.Pdbids> pdbids;
1973         @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1974         protected List<Integer> hiddenSequences;
1975         @XmlElement(namespace = "www.jalview.org")
1976         protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1977         @XmlAttribute(name = "colour")
1978         protected Integer colour;
1979         @XmlAttribute(name = "start", required = true)
1980         protected int start;
1981         @XmlAttribute(name = "end", required = true)
1982         protected int end;
1983         @XmlAttribute(name = "id", required = true)
1984         protected String id;
1985         @XmlAttribute(name = "hidden")
1986         protected Boolean hidden;
1987         @XmlAttribute(name = "viewreference")
1988         protected Boolean viewreference;
1989
1990         /**
1991          * Gets the value of the features property.
1992          * 
1993          * <p>
1994          * This accessor method returns a reference to the live list,
1995          * not a snapshot. Therefore any modification you make to the
1996          * returned list will be present inside the JAXB object.
1997          * This is why there is not a <CODE>set</CODE> method for the features property.
1998          * 
1999          * <p>
2000          * For example, to add a new item, do as follows:
2001          * <pre>
2002          *    getFeatures().add(newItem);
2003          * </pre>
2004          * 
2005          * 
2006          * <p>
2007          * Objects of the following type(s) are allowed in the list
2008          * {@link Feature }
2009          * 
2010          * 
2011          */
2012         public List<Feature> getFeatures() {
2013             if (features == null) {
2014                 features = new ArrayList<Feature>();
2015             }
2016             return this.features;
2017         }
2018
2019         /**
2020          * Gets the value of the pdbids property.
2021          * 
2022          * <p>
2023          * This accessor method returns a reference to the live list,
2024          * not a snapshot. Therefore any modification you make to the
2025          * returned list will be present inside the JAXB object.
2026          * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2027          * 
2028          * <p>
2029          * For example, to add a new item, do as follows:
2030          * <pre>
2031          *    getPdbids().add(newItem);
2032          * </pre>
2033          * 
2034          * 
2035          * <p>
2036          * Objects of the following type(s) are allowed in the list
2037          * {@link JalviewModel.JSeq.Pdbids }
2038          * 
2039          * 
2040          */
2041         public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2042             if (pdbids == null) {
2043                 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2044             }
2045             return this.pdbids;
2046         }
2047
2048         /**
2049          * Gets the value of the hiddenSequences property.
2050          * 
2051          * <p>
2052          * This accessor method returns a reference to the live list,
2053          * not a snapshot. Therefore any modification you make to the
2054          * returned list will be present inside the JAXB object.
2055          * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2056          * 
2057          * <p>
2058          * For example, to add a new item, do as follows:
2059          * <pre>
2060          *    getHiddenSequences().add(newItem);
2061          * </pre>
2062          * 
2063          * 
2064          * <p>
2065          * Objects of the following type(s) are allowed in the list
2066          * {@link Integer }
2067          * 
2068          * 
2069          */
2070         public List<Integer> getHiddenSequences() {
2071             if (hiddenSequences == null) {
2072                 hiddenSequences = new ArrayList<Integer>();
2073             }
2074             return this.hiddenSequences;
2075         }
2076
2077         /**
2078          * Gets the value of the rnaViewer property.
2079          * 
2080          * <p>
2081          * This accessor method returns a reference to the live list,
2082          * not a snapshot. Therefore any modification you make to the
2083          * returned list will be present inside the JAXB object.
2084          * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2085          * 
2086          * <p>
2087          * For example, to add a new item, do as follows:
2088          * <pre>
2089          *    getRnaViewer().add(newItem);
2090          * </pre>
2091          * 
2092          * 
2093          * <p>
2094          * Objects of the following type(s) are allowed in the list
2095          * {@link JalviewModel.JSeq.RnaViewer }
2096          * 
2097          * 
2098          */
2099         public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2100             if (rnaViewer == null) {
2101                 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2102             }
2103             return this.rnaViewer;
2104         }
2105
2106         /**
2107          * Gets the value of the colour property.
2108          * 
2109          * @return
2110          *     possible object is
2111          *     {@link Integer }
2112          *     
2113          */
2114         public Integer getColour() {
2115             return colour;
2116         }
2117
2118         /**
2119          * Sets the value of the colour property.
2120          * 
2121          * @param value
2122          *     allowed object is
2123          *     {@link Integer }
2124          *     
2125          */
2126         public void setColour(Integer value) {
2127             this.colour = value;
2128         }
2129
2130         /**
2131          * Gets the value of the start property.
2132          * 
2133          */
2134         public int getStart() {
2135             return start;
2136         }
2137
2138         /**
2139          * Sets the value of the start property.
2140          * 
2141          */
2142         public void setStart(int value) {
2143             this.start = value;
2144         }
2145
2146         /**
2147          * Gets the value of the end property.
2148          * 
2149          */
2150         public int getEnd() {
2151             return end;
2152         }
2153
2154         /**
2155          * Sets the value of the end property.
2156          * 
2157          */
2158         public void setEnd(int value) {
2159             this.end = value;
2160         }
2161
2162         /**
2163          * Gets the value of the id property.
2164          * 
2165          * @return
2166          *     possible object is
2167          *     {@link String }
2168          *     
2169          */
2170         public String getId() {
2171             return id;
2172         }
2173
2174         /**
2175          * Sets the value of the id property.
2176          * 
2177          * @param value
2178          *     allowed object is
2179          *     {@link String }
2180          *     
2181          */
2182         public void setId(String value) {
2183             this.id = value;
2184         }
2185
2186         /**
2187          * Gets the value of the hidden property.
2188          * 
2189          * @return
2190          *     possible object is
2191          *     {@link Boolean }
2192          *     
2193          */
2194         public Boolean isHidden() {
2195             return hidden;
2196         }
2197
2198         /**
2199          * Sets the value of the hidden property.
2200          * 
2201          * @param value
2202          *     allowed object is
2203          *     {@link Boolean }
2204          *     
2205          */
2206         public void setHidden(Boolean value) {
2207             this.hidden = value;
2208         }
2209
2210         /**
2211          * Gets the value of the viewreference property.
2212          * 
2213          * @return
2214          *     possible object is
2215          *     {@link Boolean }
2216          *     
2217          */
2218         public Boolean isViewreference() {
2219             return viewreference;
2220         }
2221
2222         /**
2223          * Sets the value of the viewreference property.
2224          * 
2225          * @param value
2226          *     allowed object is
2227          *     {@link Boolean }
2228          *     
2229          */
2230         public void setViewreference(Boolean value) {
2231             this.viewreference = value;
2232         }
2233
2234
2235         /**
2236          * <p>Java class for anonymous complex type.
2237          * 
2238          * <p>The following schema fragment specifies the expected content contained within this class.
2239          * 
2240          * <pre>
2241          * &lt;complexType>
2242          *   &lt;complexContent>
2243          *     &lt;extension base="{www.jalview.org}pdbentry">
2244          *       &lt;sequence>
2245          *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
2246          *           &lt;complexType>
2247          *             &lt;simpleContent>
2248          *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2249          *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2250          *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2251          *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2252          *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2253          *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2254          *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2255          *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2256          *               &lt;/extension>
2257          *             &lt;/simpleContent>
2258          *           &lt;/complexType>
2259          *         &lt;/element>
2260          *       &lt;/sequence>
2261          *     &lt;/extension>
2262          *   &lt;/complexContent>
2263          * &lt;/complexType>
2264          * </pre>
2265          * 
2266          * 
2267          */
2268         @XmlAccessorType(XmlAccessType.FIELD)
2269         @XmlType(name = "", propOrder = {
2270             "structureState"
2271         })
2272         public static class Pdbids
2273             extends Pdbentry
2274         {
2275
2276             @XmlElement(namespace = "www.jalview.org")
2277             protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2278
2279             /**
2280              * Gets the value of the structureState property.
2281              * 
2282              * <p>
2283              * This accessor method returns a reference to the live list,
2284              * not a snapshot. Therefore any modification you make to the
2285              * returned list will be present inside the JAXB object.
2286              * This is why there is not a <CODE>set</CODE> method for the structureState property.
2287              * 
2288              * <p>
2289              * For example, to add a new item, do as follows:
2290              * <pre>
2291              *    getStructureState().add(newItem);
2292              * </pre>
2293              * 
2294              * 
2295              * <p>
2296              * Objects of the following type(s) are allowed in the list
2297              * {@link JalviewModel.JSeq.Pdbids.StructureState }
2298              * 
2299              * 
2300              */
2301             public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2302                 if (structureState == null) {
2303                     structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2304                 }
2305                 return this.structureState;
2306             }
2307
2308
2309             /**
2310              * <p>Java class for anonymous complex type.
2311              * 
2312              * <p>The following schema fragment specifies the expected content contained within this class.
2313              * 
2314              * <pre>
2315              * &lt;complexType>
2316              *   &lt;simpleContent>
2317              *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
2318              *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2319              *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2320              *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2321              *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2322              *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2323              *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2324              *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2325              *     &lt;/extension>
2326              *   &lt;/simpleContent>
2327              * &lt;/complexType>
2328              * </pre>
2329              * 
2330              * 
2331              */
2332             @XmlAccessorType(XmlAccessType.FIELD)
2333             @XmlType(name = "", propOrder = {
2334                 "value"
2335             })
2336             public static class StructureState {
2337
2338                 @XmlValue
2339                 protected String value;
2340                 @XmlAttribute(name = "visible")
2341                 protected Boolean visible;
2342                 @XmlAttribute(name = "viewId")
2343                 protected String viewId;
2344                 @XmlAttribute(name = "alignwithAlignPanel")
2345                 protected Boolean alignwithAlignPanel;
2346                 @XmlAttribute(name = "colourwithAlignPanel")
2347                 protected Boolean colourwithAlignPanel;
2348                 @XmlAttribute(name = "colourByJmol")
2349                 protected Boolean colourByJmol;
2350                 @XmlAttribute(name = "type")
2351                 protected String type;
2352                 @XmlAttribute(name = "width")
2353                 protected Integer width;
2354                 @XmlAttribute(name = "height")
2355                 protected Integer height;
2356                 @XmlAttribute(name = "xpos")
2357                 protected Integer xpos;
2358                 @XmlAttribute(name = "ypos")
2359                 protected Integer ypos;
2360
2361                 /**
2362                  * Gets the value of the value property.
2363                  * 
2364                  * @return
2365                  *     possible object is
2366                  *     {@link String }
2367                  *     
2368                  */
2369                 public String getValue() {
2370                     return value;
2371                 }
2372
2373                 /**
2374                  * Sets the value of the value property.
2375                  * 
2376                  * @param value
2377                  *     allowed object is
2378                  *     {@link String }
2379                  *     
2380                  */
2381                 public void setValue(String value) {
2382                     this.value = value;
2383                 }
2384
2385                 /**
2386                  * Gets the value of the visible property.
2387                  * 
2388                  * @return
2389                  *     possible object is
2390                  *     {@link Boolean }
2391                  *     
2392                  */
2393                 public Boolean isVisible() {
2394                     return visible;
2395                 }
2396
2397                 /**
2398                  * Sets the value of the visible property.
2399                  * 
2400                  * @param value
2401                  *     allowed object is
2402                  *     {@link Boolean }
2403                  *     
2404                  */
2405                 public void setVisible(Boolean value) {
2406                     this.visible = value;
2407                 }
2408
2409                 /**
2410                  * Gets the value of the viewId property.
2411                  * 
2412                  * @return
2413                  *     possible object is
2414                  *     {@link String }
2415                  *     
2416                  */
2417                 public String getViewId() {
2418                     return viewId;
2419                 }
2420
2421                 /**
2422                  * Sets the value of the viewId property.
2423                  * 
2424                  * @param value
2425                  *     allowed object is
2426                  *     {@link String }
2427                  *     
2428                  */
2429                 public void setViewId(String value) {
2430                     this.viewId = value;
2431                 }
2432
2433                 /**
2434                  * Gets the value of the alignwithAlignPanel property.
2435                  * 
2436                  * @return
2437                  *     possible object is
2438                  *     {@link Boolean }
2439                  *     
2440                  */
2441                 public boolean isAlignwithAlignPanel() {
2442                     if (alignwithAlignPanel == null) {
2443                         return true;
2444                     } else {
2445                         return alignwithAlignPanel;
2446                     }
2447                 }
2448
2449                 /**
2450                  * Sets the value of the alignwithAlignPanel property.
2451                  * 
2452                  * @param value
2453                  *     allowed object is
2454                  *     {@link Boolean }
2455                  *     
2456                  */
2457                 public void setAlignwithAlignPanel(Boolean value) {
2458                     this.alignwithAlignPanel = value;
2459                 }
2460
2461                 /**
2462                  * Gets the value of the colourwithAlignPanel property.
2463                  * 
2464                  * @return
2465                  *     possible object is
2466                  *     {@link Boolean }
2467                  *     
2468                  */
2469                 public boolean isColourwithAlignPanel() {
2470                     if (colourwithAlignPanel == null) {
2471                         return false;
2472                     } else {
2473                         return colourwithAlignPanel;
2474                     }
2475                 }
2476
2477                 /**
2478                  * Sets the value of the colourwithAlignPanel property.
2479                  * 
2480                  * @param value
2481                  *     allowed object is
2482                  *     {@link Boolean }
2483                  *     
2484                  */
2485                 public void setColourwithAlignPanel(Boolean value) {
2486                     this.colourwithAlignPanel = value;
2487                 }
2488
2489                 /**
2490                  * Gets the value of the colourByJmol property.
2491                  * 
2492                  * @return
2493                  *     possible object is
2494                  *     {@link Boolean }
2495                  *     
2496                  */
2497                 public boolean isColourByJmol() {
2498                     if (colourByJmol == null) {
2499                         return true;
2500                     } else {
2501                         return colourByJmol;
2502                     }
2503                 }
2504
2505                 /**
2506                  * Sets the value of the colourByJmol property.
2507                  * 
2508                  * @param value
2509                  *     allowed object is
2510                  *     {@link Boolean }
2511                  *     
2512                  */
2513                 public void setColourByJmol(Boolean value) {
2514                     this.colourByJmol = value;
2515                 }
2516
2517                 /**
2518                  * Gets the value of the type property.
2519                  * 
2520                  * @return
2521                  *     possible object is
2522                  *     {@link String }
2523                  *     
2524                  */
2525                 public String getType() {
2526                     return type;
2527                 }
2528
2529                 /**
2530                  * Sets the value of the type property.
2531                  * 
2532                  * @param value
2533                  *     allowed object is
2534                  *     {@link String }
2535                  *     
2536                  */
2537                 public void setType(String value) {
2538                     this.type = value;
2539                 }
2540
2541                 /**
2542                  * Gets the value of the width property.
2543                  * 
2544                  * @return
2545                  *     possible object is
2546                  *     {@link Integer }
2547                  *     
2548                  */
2549                 public Integer getWidth() {
2550                     return width;
2551                 }
2552
2553                 /**
2554                  * Sets the value of the width property.
2555                  * 
2556                  * @param value
2557                  *     allowed object is
2558                  *     {@link Integer }
2559                  *     
2560                  */
2561                 public void setWidth(Integer value) {
2562                     this.width = value;
2563                 }
2564
2565                 /**
2566                  * Gets the value of the height property.
2567                  * 
2568                  * @return
2569                  *     possible object is
2570                  *     {@link Integer }
2571                  *     
2572                  */
2573                 public Integer getHeight() {
2574                     return height;
2575                 }
2576
2577                 /**
2578                  * Sets the value of the height property.
2579                  * 
2580                  * @param value
2581                  *     allowed object is
2582                  *     {@link Integer }
2583                  *     
2584                  */
2585                 public void setHeight(Integer value) {
2586                     this.height = value;
2587                 }
2588
2589                 /**
2590                  * Gets the value of the xpos property.
2591                  * 
2592                  * @return
2593                  *     possible object is
2594                  *     {@link Integer }
2595                  *     
2596                  */
2597                 public Integer getXpos() {
2598                     return xpos;
2599                 }
2600
2601                 /**
2602                  * Sets the value of the xpos property.
2603                  * 
2604                  * @param value
2605                  *     allowed object is
2606                  *     {@link Integer }
2607                  *     
2608                  */
2609                 public void setXpos(Integer value) {
2610                     this.xpos = value;
2611                 }
2612
2613                 /**
2614                  * Gets the value of the ypos property.
2615                  * 
2616                  * @return
2617                  *     possible object is
2618                  *     {@link Integer }
2619                  *     
2620                  */
2621                 public Integer getYpos() {
2622                     return ypos;
2623                 }
2624
2625                 /**
2626                  * Sets the value of the ypos property.
2627                  * 
2628                  * @param value
2629                  *     allowed object is
2630                  *     {@link Integer }
2631                  *     
2632                  */
2633                 public void setYpos(Integer value) {
2634                     this.ypos = value;
2635                 }
2636
2637             }
2638
2639         }
2640
2641
2642         /**
2643          * <p>Java class for anonymous complex type.
2644          * 
2645          * <p>The following schema fragment specifies the expected content contained within this class.
2646          * 
2647          * <pre>
2648          * &lt;complexType>
2649          *   &lt;complexContent>
2650          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2651          *       &lt;sequence>
2652          *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
2653          *           &lt;complexType>
2654          *             &lt;complexContent>
2655          *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2656          *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2657          *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2658          *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2659          *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2660          *               &lt;/restriction>
2661          *             &lt;/complexContent>
2662          *           &lt;/complexType>
2663          *         &lt;/element>
2664          *       &lt;/sequence>
2665          *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
2666          *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2667          *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2668          *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2669          *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2670          *     &lt;/restriction>
2671          *   &lt;/complexContent>
2672          * &lt;/complexType>
2673          * </pre>
2674          * 
2675          * 
2676          */
2677         @XmlAccessorType(XmlAccessType.FIELD)
2678         @XmlType(name = "", propOrder = {
2679             "secondaryStructure"
2680         })
2681         public static class RnaViewer {
2682
2683             @XmlElement(namespace = "www.jalview.org", required = true)
2684             protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2685             @XmlAttribute(name = "title")
2686             protected String title;
2687             @XmlAttribute(name = "viewId")
2688             protected String viewId;
2689             @XmlAttribute(name = "dividerLocation")
2690             protected Integer dividerLocation;
2691             @XmlAttribute(name = "selectedRna")
2692             protected Integer selectedRna;
2693             @XmlAttribute(name = "width")
2694             protected Integer width;
2695             @XmlAttribute(name = "height")
2696             protected Integer height;
2697             @XmlAttribute(name = "xpos")
2698             protected Integer xpos;
2699             @XmlAttribute(name = "ypos")
2700             protected Integer ypos;
2701
2702             /**
2703              * Gets the value of the secondaryStructure property.
2704              * 
2705              * <p>
2706              * This accessor method returns a reference to the live list,
2707              * not a snapshot. Therefore any modification you make to the
2708              * returned list will be present inside the JAXB object.
2709              * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2710              * 
2711              * <p>
2712              * For example, to add a new item, do as follows:
2713              * <pre>
2714              *    getSecondaryStructure().add(newItem);
2715              * </pre>
2716              * 
2717              * 
2718              * <p>
2719              * Objects of the following type(s) are allowed in the list
2720              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2721              * 
2722              * 
2723              */
2724             public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2725                 if (secondaryStructure == null) {
2726                     secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2727                 }
2728                 return this.secondaryStructure;
2729             }
2730
2731             /**
2732              * Gets the value of the title property.
2733              * 
2734              * @return
2735              *     possible object is
2736              *     {@link String }
2737              *     
2738              */
2739             public String getTitle() {
2740                 return title;
2741             }
2742
2743             /**
2744              * Sets the value of the title property.
2745              * 
2746              * @param value
2747              *     allowed object is
2748              *     {@link String }
2749              *     
2750              */
2751             public void setTitle(String value) {
2752                 this.title = value;
2753             }
2754
2755             /**
2756              * Gets the value of the viewId property.
2757              * 
2758              * @return
2759              *     possible object is
2760              *     {@link String }
2761              *     
2762              */
2763             public String getViewId() {
2764                 return viewId;
2765             }
2766
2767             /**
2768              * Sets the value of the viewId property.
2769              * 
2770              * @param value
2771              *     allowed object is
2772              *     {@link String }
2773              *     
2774              */
2775             public void setViewId(String value) {
2776                 this.viewId = value;
2777             }
2778
2779             /**
2780              * Gets the value of the dividerLocation property.
2781              * 
2782              * @return
2783              *     possible object is
2784              *     {@link Integer }
2785              *     
2786              */
2787             public Integer getDividerLocation() {
2788                 return dividerLocation;
2789             }
2790
2791             /**
2792              * Sets the value of the dividerLocation property.
2793              * 
2794              * @param value
2795              *     allowed object is
2796              *     {@link Integer }
2797              *     
2798              */
2799             public void setDividerLocation(Integer value) {
2800                 this.dividerLocation = value;
2801             }
2802
2803             /**
2804              * Gets the value of the selectedRna property.
2805              * 
2806              * @return
2807              *     possible object is
2808              *     {@link Integer }
2809              *     
2810              */
2811             public Integer getSelectedRna() {
2812                 return selectedRna;
2813             }
2814
2815             /**
2816              * Sets the value of the selectedRna property.
2817              * 
2818              * @param value
2819              *     allowed object is
2820              *     {@link Integer }
2821              *     
2822              */
2823             public void setSelectedRna(Integer value) {
2824                 this.selectedRna = value;
2825             }
2826
2827             /**
2828              * Gets the value of the width property.
2829              * 
2830              * @return
2831              *     possible object is
2832              *     {@link Integer }
2833              *     
2834              */
2835             public Integer getWidth() {
2836                 return width;
2837             }
2838
2839             /**
2840              * Sets the value of the width property.
2841              * 
2842              * @param value
2843              *     allowed object is
2844              *     {@link Integer }
2845              *     
2846              */
2847             public void setWidth(Integer value) {
2848                 this.width = value;
2849             }
2850
2851             /**
2852              * Gets the value of the height property.
2853              * 
2854              * @return
2855              *     possible object is
2856              *     {@link Integer }
2857              *     
2858              */
2859             public Integer getHeight() {
2860                 return height;
2861             }
2862
2863             /**
2864              * Sets the value of the height property.
2865              * 
2866              * @param value
2867              *     allowed object is
2868              *     {@link Integer }
2869              *     
2870              */
2871             public void setHeight(Integer value) {
2872                 this.height = value;
2873             }
2874
2875             /**
2876              * Gets the value of the xpos property.
2877              * 
2878              * @return
2879              *     possible object is
2880              *     {@link Integer }
2881              *     
2882              */
2883             public Integer getXpos() {
2884                 return xpos;
2885             }
2886
2887             /**
2888              * Sets the value of the xpos property.
2889              * 
2890              * @param value
2891              *     allowed object is
2892              *     {@link Integer }
2893              *     
2894              */
2895             public void setXpos(Integer value) {
2896                 this.xpos = value;
2897             }
2898
2899             /**
2900              * Gets the value of the ypos property.
2901              * 
2902              * @return
2903              *     possible object is
2904              *     {@link Integer }
2905              *     
2906              */
2907             public Integer getYpos() {
2908                 return ypos;
2909             }
2910
2911             /**
2912              * Sets the value of the ypos property.
2913              * 
2914              * @param value
2915              *     allowed object is
2916              *     {@link Integer }
2917              *     
2918              */
2919             public void setYpos(Integer value) {
2920                 this.ypos = value;
2921             }
2922
2923
2924             /**
2925              * <p>Java class for anonymous complex type.
2926              * 
2927              * <p>The following schema fragment specifies the expected content contained within this class.
2928              * 
2929              * <pre>
2930              * &lt;complexType>
2931              *   &lt;complexContent>
2932              *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2933              *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2934              *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2935              *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2936              *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2937              *     &lt;/restriction>
2938              *   &lt;/complexContent>
2939              * &lt;/complexType>
2940              * </pre>
2941              * 
2942              * 
2943              */
2944             @XmlAccessorType(XmlAccessType.FIELD)
2945             @XmlType(name = "")
2946             public static class SecondaryStructure {
2947
2948                 @XmlAttribute(name = "title")
2949                 protected String title;
2950                 @XmlAttribute(name = "annotationId", required = true)
2951                 protected String annotationId;
2952                 @XmlAttribute(name = "gapped")
2953                 protected Boolean gapped;
2954                 @XmlAttribute(name = "viewerState")
2955                 protected String viewerState;
2956
2957                 /**
2958                  * Gets the value of the title property.
2959                  * 
2960                  * @return
2961                  *     possible object is
2962                  *     {@link String }
2963                  *     
2964                  */
2965                 public String getTitle() {
2966                     return title;
2967                 }
2968
2969                 /**
2970                  * Sets the value of the title property.
2971                  * 
2972                  * @param value
2973                  *     allowed object is
2974                  *     {@link String }
2975                  *     
2976                  */
2977                 public void setTitle(String value) {
2978                     this.title = value;
2979                 }
2980
2981                 /**
2982                  * Gets the value of the annotationId property.
2983                  * 
2984                  * @return
2985                  *     possible object is
2986                  *     {@link String }
2987                  *     
2988                  */
2989                 public String getAnnotationId() {
2990                     return annotationId;
2991                 }
2992
2993                 /**
2994                  * Sets the value of the annotationId property.
2995                  * 
2996                  * @param value
2997                  *     allowed object is
2998                  *     {@link String }
2999                  *     
3000                  */
3001                 public void setAnnotationId(String value) {
3002                     this.annotationId = value;
3003                 }
3004
3005                 /**
3006                  * Gets the value of the gapped property.
3007                  * 
3008                  * @return
3009                  *     possible object is
3010                  *     {@link Boolean }
3011                  *     
3012                  */
3013                 public Boolean isGapped() {
3014                     return gapped;
3015                 }
3016
3017                 /**
3018                  * Sets the value of the gapped property.
3019                  * 
3020                  * @param value
3021                  *     allowed object is
3022                  *     {@link Boolean }
3023                  *     
3024                  */
3025                 public void setGapped(Boolean value) {
3026                     this.gapped = value;
3027                 }
3028
3029                 /**
3030                  * Gets the value of the viewerState property.
3031                  * 
3032                  * @return
3033                  *     possible object is
3034                  *     {@link String }
3035                  *     
3036                  */
3037                 public String getViewerState() {
3038                     return viewerState;
3039                 }
3040
3041                 /**
3042                  * Sets the value of the viewerState property.
3043                  * 
3044                  * @param value
3045                  *     allowed object is
3046                  *     {@link String }
3047                  *     
3048                  */
3049                 public void setViewerState(String value) {
3050                     this.viewerState = value;
3051                 }
3052
3053             }
3054
3055         }
3056
3057     }
3058
3059
3060     /**
3061      * <p>Java class for anonymous complex type.
3062      * 
3063      * <p>The following schema fragment specifies the expected content contained within this class.
3064      * 
3065      * <pre>
3066      * &lt;complexType>
3067      *   &lt;complexContent>
3068      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3069      *       &lt;sequence>
3070      *         &lt;element name="sequencePoint" maxOccurs="unbounded">
3071      *           &lt;complexType>
3072      *             &lt;complexContent>
3073      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3074      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3075      *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3076      *               &lt;/restriction>
3077      *             &lt;/complexContent>
3078      *           &lt;/complexType>
3079      *         &lt;/element>
3080      *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
3081      *           &lt;complexType>
3082      *             &lt;complexContent>
3083      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3084      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3085      *               &lt;/restriction>
3086      *             &lt;/complexContent>
3087      *           &lt;/complexType>
3088      *         &lt;/element>
3089      *         &lt;element name="seqPointMin">
3090      *           &lt;complexType>
3091      *             &lt;complexContent>
3092      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3093      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3094      *               &lt;/restriction>
3095      *             &lt;/complexContent>
3096      *           &lt;/complexType>
3097      *         &lt;/element>
3098      *         &lt;element name="seqPointMax">
3099      *           &lt;complexType>
3100      *             &lt;complexContent>
3101      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3102      *                 &lt;attGroup ref="{www.jalview.org}position"/>
3103      *               &lt;/restriction>
3104      *             &lt;/complexContent>
3105      *           &lt;/complexType>
3106      *         &lt;/element>
3107      *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3108      *       &lt;/sequence>
3109      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
3110      *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
3111      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3112      *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3113      *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3114      *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3115      *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3116      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3117      *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3118      *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3119      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3120      *     &lt;/restriction>
3121      *   &lt;/complexContent>
3122      * &lt;/complexType>
3123      * </pre>
3124      * 
3125      * 
3126      */
3127     @XmlAccessorType(XmlAccessType.FIELD)
3128     @XmlType(name = "", propOrder = {
3129         "sequencePoint",
3130         "axis",
3131         "seqPointMin",
3132         "seqPointMax",
3133         "pcaData"
3134     })
3135     public static class PcaViewer {
3136
3137         @XmlElement(namespace = "www.jalview.org", required = true)
3138         protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3139         @XmlElement(namespace = "www.jalview.org", required = true)
3140         protected List<JalviewModel.PcaViewer.Axis> axis;
3141         @XmlElement(namespace = "www.jalview.org", required = true)
3142         protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3143         @XmlElement(namespace = "www.jalview.org", required = true)
3144         protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3145         @XmlElement(namespace = "www.jalview.org", required = true)
3146         protected PcaDataType pcaData;
3147         @XmlAttribute(name = "title")
3148         protected String title;
3149         @XmlAttribute(name = "scoreModelName")
3150         protected String scoreModelName;
3151         @XmlAttribute(name = "xDim")
3152         protected Integer xDim;
3153         @XmlAttribute(name = "yDim")
3154         protected Integer yDim;
3155         @XmlAttribute(name = "zDim")
3156         protected Integer zDim;
3157         @XmlAttribute(name = "bgColour")
3158         protected Integer bgColour;
3159         @XmlAttribute(name = "scaleFactor")
3160         protected Float scaleFactor;
3161         @XmlAttribute(name = "showLabels")
3162         protected Boolean showLabels;
3163         @XmlAttribute(name = "linkToAllViews")
3164         protected Boolean linkToAllViews;
3165         @XmlAttribute(name = "width")
3166         protected Integer width;
3167         @XmlAttribute(name = "height")
3168         protected Integer height;
3169         @XmlAttribute(name = "xpos")
3170         protected Integer xpos;
3171         @XmlAttribute(name = "ypos")
3172         protected Integer ypos;
3173         @XmlAttribute(name = "includeGaps")
3174         protected Boolean includeGaps;
3175         @XmlAttribute(name = "matchGaps")
3176         protected Boolean matchGaps;
3177         @XmlAttribute(name = "includeGappedColumns")
3178         protected Boolean includeGappedColumns;
3179         @XmlAttribute(name = "denominateByShortestLength")
3180         protected Boolean denominateByShortestLength;
3181
3182         /**
3183          * Gets the value of the sequencePoint property.
3184          * 
3185          * <p>
3186          * This accessor method returns a reference to the live list,
3187          * not a snapshot. Therefore any modification you make to the
3188          * returned list will be present inside the JAXB object.
3189          * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3190          * 
3191          * <p>
3192          * For example, to add a new item, do as follows:
3193          * <pre>
3194          *    getSequencePoint().add(newItem);
3195          * </pre>
3196          * 
3197          * 
3198          * <p>
3199          * Objects of the following type(s) are allowed in the list
3200          * {@link JalviewModel.PcaViewer.SequencePoint }
3201          * 
3202          * 
3203          */
3204         public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3205             if (sequencePoint == null) {
3206                 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3207             }
3208             return this.sequencePoint;
3209         }
3210
3211         /**
3212          * Gets the value of the axis property.
3213          * 
3214          * <p>
3215          * This accessor method returns a reference to the live list,
3216          * not a snapshot. Therefore any modification you make to the
3217          * returned list will be present inside the JAXB object.
3218          * This is why there is not a <CODE>set</CODE> method for the axis property.
3219          * 
3220          * <p>
3221          * For example, to add a new item, do as follows:
3222          * <pre>
3223          *    getAxis().add(newItem);
3224          * </pre>
3225          * 
3226          * 
3227          * <p>
3228          * Objects of the following type(s) are allowed in the list
3229          * {@link JalviewModel.PcaViewer.Axis }
3230          * 
3231          * 
3232          */
3233         public List<JalviewModel.PcaViewer.Axis> getAxis() {
3234             if (axis == null) {
3235                 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3236             }
3237             return this.axis;
3238         }
3239
3240         /**
3241          * Gets the value of the seqPointMin property.
3242          * 
3243          * @return
3244          *     possible object is
3245          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3246          *     
3247          */
3248         public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3249             return seqPointMin;
3250         }
3251
3252         /**
3253          * Sets the value of the seqPointMin property.
3254          * 
3255          * @param value
3256          *     allowed object is
3257          *     {@link JalviewModel.PcaViewer.SeqPointMin }
3258          *     
3259          */
3260         public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3261             this.seqPointMin = value;
3262         }
3263
3264         /**
3265          * Gets the value of the seqPointMax property.
3266          * 
3267          * @return
3268          *     possible object is
3269          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3270          *     
3271          */
3272         public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3273             return seqPointMax;
3274         }
3275
3276         /**
3277          * Sets the value of the seqPointMax property.
3278          * 
3279          * @param value
3280          *     allowed object is
3281          *     {@link JalviewModel.PcaViewer.SeqPointMax }
3282          *     
3283          */
3284         public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3285             this.seqPointMax = value;
3286         }
3287
3288         /**
3289          * Gets the value of the pcaData property.
3290          * 
3291          * @return
3292          *     possible object is
3293          *     {@link PcaDataType }
3294          *     
3295          */
3296         public PcaDataType getPcaData() {
3297             return pcaData;
3298         }
3299
3300         /**
3301          * Sets the value of the pcaData property.
3302          * 
3303          * @param value
3304          *     allowed object is
3305          *     {@link PcaDataType }
3306          *     
3307          */
3308         public void setPcaData(PcaDataType value) {
3309             this.pcaData = value;
3310         }
3311
3312         /**
3313          * Gets the value of the title property.
3314          * 
3315          * @return
3316          *     possible object is
3317          *     {@link String }
3318          *     
3319          */
3320         public String getTitle() {
3321             return title;
3322         }
3323
3324         /**
3325          * Sets the value of the title property.
3326          * 
3327          * @param value
3328          *     allowed object is
3329          *     {@link String }
3330          *     
3331          */
3332         public void setTitle(String value) {
3333             this.title = value;
3334         }
3335
3336         /**
3337          * Gets the value of the scoreModelName property.
3338          * 
3339          * @return
3340          *     possible object is
3341          *     {@link String }
3342          *     
3343          */
3344         public String getScoreModelName() {
3345             return scoreModelName;
3346         }
3347
3348         /**
3349          * Sets the value of the scoreModelName property.
3350          * 
3351          * @param value
3352          *     allowed object is
3353          *     {@link String }
3354          *     
3355          */
3356         public void setScoreModelName(String value) {
3357             this.scoreModelName = value;
3358         }
3359
3360         /**
3361          * Gets the value of the xDim property.
3362          * 
3363          * @return
3364          *     possible object is
3365          *     {@link Integer }
3366          *     
3367          */
3368         public Integer getXDim() {
3369             return xDim;
3370         }
3371
3372         /**
3373          * Sets the value of the xDim property.
3374          * 
3375          * @param value
3376          *     allowed object is
3377          *     {@link Integer }
3378          *     
3379          */
3380         public void setXDim(Integer value) {
3381             this.xDim = value;
3382         }
3383
3384         /**
3385          * Gets the value of the yDim property.
3386          * 
3387          * @return
3388          *     possible object is
3389          *     {@link Integer }
3390          *     
3391          */
3392         public Integer getYDim() {
3393             return yDim;
3394         }
3395
3396         /**
3397          * Sets the value of the yDim property.
3398          * 
3399          * @param value
3400          *     allowed object is
3401          *     {@link Integer }
3402          *     
3403          */
3404         public void setYDim(Integer value) {
3405             this.yDim = value;
3406         }
3407
3408         /**
3409          * Gets the value of the zDim property.
3410          * 
3411          * @return
3412          *     possible object is
3413          *     {@link Integer }
3414          *     
3415          */
3416         public Integer getZDim() {
3417             return zDim;
3418         }
3419
3420         /**
3421          * Sets the value of the zDim property.
3422          * 
3423          * @param value
3424          *     allowed object is
3425          *     {@link Integer }
3426          *     
3427          */
3428         public void setZDim(Integer value) {
3429             this.zDim = value;
3430         }
3431
3432         /**
3433          * Gets the value of the bgColour property.
3434          * 
3435          * @return
3436          *     possible object is
3437          *     {@link Integer }
3438          *     
3439          */
3440         public Integer getBgColour() {
3441             return bgColour;
3442         }
3443
3444         /**
3445          * Sets the value of the bgColour property.
3446          * 
3447          * @param value
3448          *     allowed object is
3449          *     {@link Integer }
3450          *     
3451          */
3452         public void setBgColour(Integer value) {
3453             this.bgColour = value;
3454         }
3455
3456         /**
3457          * Gets the value of the scaleFactor property.
3458          * 
3459          * @return
3460          *     possible object is
3461          *     {@link Float }
3462          *     
3463          */
3464         public Float getScaleFactor() {
3465             return scaleFactor;
3466         }
3467
3468         /**
3469          * Sets the value of the scaleFactor property.
3470          * 
3471          * @param value
3472          *     allowed object is
3473          *     {@link Float }
3474          *     
3475          */
3476         public void setScaleFactor(Float value) {
3477             this.scaleFactor = value;
3478         }
3479
3480         /**
3481          * Gets the value of the showLabels property.
3482          * 
3483          * @return
3484          *     possible object is
3485          *     {@link Boolean }
3486          *     
3487          */
3488         public Boolean isShowLabels() {
3489             return showLabels;
3490         }
3491
3492         /**
3493          * Sets the value of the showLabels property.
3494          * 
3495          * @param value
3496          *     allowed object is
3497          *     {@link Boolean }
3498          *     
3499          */
3500         public void setShowLabels(Boolean value) {
3501             this.showLabels = value;
3502         }
3503
3504         /**
3505          * Gets the value of the linkToAllViews property.
3506          * 
3507          * @return
3508          *     possible object is
3509          *     {@link Boolean }
3510          *     
3511          */
3512         public Boolean isLinkToAllViews() {
3513             return linkToAllViews;
3514         }
3515
3516         /**
3517          * Sets the value of the linkToAllViews property.
3518          * 
3519          * @param value
3520          *     allowed object is
3521          *     {@link Boolean }
3522          *     
3523          */
3524         public void setLinkToAllViews(Boolean value) {
3525             this.linkToAllViews = value;
3526         }
3527
3528         /**
3529          * Gets the value of the width property.
3530          * 
3531          * @return
3532          *     possible object is
3533          *     {@link Integer }
3534          *     
3535          */
3536         public Integer getWidth() {
3537             return width;
3538         }
3539
3540         /**
3541          * Sets the value of the width property.
3542          * 
3543          * @param value
3544          *     allowed object is
3545          *     {@link Integer }
3546          *     
3547          */
3548         public void setWidth(Integer value) {
3549             this.width = value;
3550         }
3551
3552         /**
3553          * Gets the value of the height property.
3554          * 
3555          * @return
3556          *     possible object is
3557          *     {@link Integer }
3558          *     
3559          */
3560         public Integer getHeight() {
3561             return height;
3562         }
3563
3564         /**
3565          * Sets the value of the height property.
3566          * 
3567          * @param value
3568          *     allowed object is
3569          *     {@link Integer }
3570          *     
3571          */
3572         public void setHeight(Integer value) {
3573             this.height = value;
3574         }
3575
3576         /**
3577          * Gets the value of the xpos property.
3578          * 
3579          * @return
3580          *     possible object is
3581          *     {@link Integer }
3582          *     
3583          */
3584         public Integer getXpos() {
3585             return xpos;
3586         }
3587
3588         /**
3589          * Sets the value of the xpos property.
3590          * 
3591          * @param value
3592          *     allowed object is
3593          *     {@link Integer }
3594          *     
3595          */
3596         public void setXpos(Integer value) {
3597             this.xpos = value;
3598         }
3599
3600         /**
3601          * Gets the value of the ypos property.
3602          * 
3603          * @return
3604          *     possible object is
3605          *     {@link Integer }
3606          *     
3607          */
3608         public Integer getYpos() {
3609             return ypos;
3610         }
3611
3612         /**
3613          * Sets the value of the ypos property.
3614          * 
3615          * @param value
3616          *     allowed object is
3617          *     {@link Integer }
3618          *     
3619          */
3620         public void setYpos(Integer value) {
3621             this.ypos = value;
3622         }
3623
3624         /**
3625          * Gets the value of the includeGaps property.
3626          * 
3627          * @return
3628          *     possible object is
3629          *     {@link Boolean }
3630          *     
3631          */
3632         public Boolean isIncludeGaps() {
3633             return includeGaps;
3634         }
3635
3636         /**
3637          * Sets the value of the includeGaps property.
3638          * 
3639          * @param value
3640          *     allowed object is
3641          *     {@link Boolean }
3642          *     
3643          */
3644         public void setIncludeGaps(Boolean value) {
3645             this.includeGaps = value;
3646         }
3647
3648         /**
3649          * Gets the value of the matchGaps property.
3650          * 
3651          * @return
3652          *     possible object is
3653          *     {@link Boolean }
3654          *     
3655          */
3656         public Boolean isMatchGaps() {
3657             return matchGaps;
3658         }
3659
3660         /**
3661          * Sets the value of the matchGaps property.
3662          * 
3663          * @param value
3664          *     allowed object is
3665          *     {@link Boolean }
3666          *     
3667          */
3668         public void setMatchGaps(Boolean value) {
3669             this.matchGaps = value;
3670         }
3671
3672         /**
3673          * Gets the value of the includeGappedColumns property.
3674          * 
3675          * @return
3676          *     possible object is
3677          *     {@link Boolean }
3678          *     
3679          */
3680         public Boolean isIncludeGappedColumns() {
3681             return includeGappedColumns;
3682         }
3683
3684         /**
3685          * Sets the value of the includeGappedColumns property.
3686          * 
3687          * @param value
3688          *     allowed object is
3689          *     {@link Boolean }
3690          *     
3691          */
3692         public void setIncludeGappedColumns(Boolean value) {
3693             this.includeGappedColumns = value;
3694         }
3695
3696         /**
3697          * Gets the value of the denominateByShortestLength property.
3698          * 
3699          * @return
3700          *     possible object is
3701          *     {@link Boolean }
3702          *     
3703          */
3704         public Boolean isDenominateByShortestLength() {
3705             return denominateByShortestLength;
3706         }
3707
3708         /**
3709          * Sets the value of the denominateByShortestLength property.
3710          * 
3711          * @param value
3712          *     allowed object is
3713          *     {@link Boolean }
3714          *     
3715          */
3716         public void setDenominateByShortestLength(Boolean value) {
3717             this.denominateByShortestLength = value;
3718         }
3719
3720
3721         /**
3722          * <p>Java class for anonymous complex type.
3723          * 
3724          * <p>The following schema fragment specifies the expected content contained within this class.
3725          * 
3726          * <pre>
3727          * &lt;complexType>
3728          *   &lt;complexContent>
3729          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3730          *       &lt;attGroup ref="{www.jalview.org}position"/>
3731          *     &lt;/restriction>
3732          *   &lt;/complexContent>
3733          * &lt;/complexType>
3734          * </pre>
3735          * 
3736          * 
3737          */
3738         @XmlAccessorType(XmlAccessType.FIELD)
3739         @XmlType(name = "")
3740         public static class Axis {
3741
3742             @XmlAttribute(name = "xPos")
3743             protected Float xPos;
3744             @XmlAttribute(name = "yPos")
3745             protected Float yPos;
3746             @XmlAttribute(name = "zPos")
3747             protected Float zPos;
3748
3749             /**
3750              * Gets the value of the xPos property.
3751              * 
3752              * @return
3753              *     possible object is
3754              *     {@link Float }
3755              *     
3756              */
3757             public Float getXPos() {
3758                 return xPos;
3759             }
3760
3761             /**
3762              * Sets the value of the xPos property.
3763              * 
3764              * @param value
3765              *     allowed object is
3766              *     {@link Float }
3767              *     
3768              */
3769             public void setXPos(Float value) {
3770                 this.xPos = value;
3771             }
3772
3773             /**
3774              * Gets the value of the yPos property.
3775              * 
3776              * @return
3777              *     possible object is
3778              *     {@link Float }
3779              *     
3780              */
3781             public Float getYPos() {
3782                 return yPos;
3783             }
3784
3785             /**
3786              * Sets the value of the yPos property.
3787              * 
3788              * @param value
3789              *     allowed object is
3790              *     {@link Float }
3791              *     
3792              */
3793             public void setYPos(Float value) {
3794                 this.yPos = value;
3795             }
3796
3797             /**
3798              * Gets the value of the zPos property.
3799              * 
3800              * @return
3801              *     possible object is
3802              *     {@link Float }
3803              *     
3804              */
3805             public Float getZPos() {
3806                 return zPos;
3807             }
3808
3809             /**
3810              * Sets the value of the zPos property.
3811              * 
3812              * @param value
3813              *     allowed object is
3814              *     {@link Float }
3815              *     
3816              */
3817             public void setZPos(Float value) {
3818                 this.zPos = value;
3819             }
3820
3821         }
3822
3823
3824         /**
3825          * <p>Java class for anonymous complex type.
3826          * 
3827          * <p>The following schema fragment specifies the expected content contained within this class.
3828          * 
3829          * <pre>
3830          * &lt;complexType>
3831          *   &lt;complexContent>
3832          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3833          *       &lt;attGroup ref="{www.jalview.org}position"/>
3834          *     &lt;/restriction>
3835          *   &lt;/complexContent>
3836          * &lt;/complexType>
3837          * </pre>
3838          * 
3839          * 
3840          */
3841         @XmlAccessorType(XmlAccessType.FIELD)
3842         @XmlType(name = "")
3843         public static class SeqPointMax {
3844
3845             @XmlAttribute(name = "xPos")
3846             protected Float xPos;
3847             @XmlAttribute(name = "yPos")
3848             protected Float yPos;
3849             @XmlAttribute(name = "zPos")
3850             protected Float zPos;
3851
3852             /**
3853              * Gets the value of the xPos property.
3854              * 
3855              * @return
3856              *     possible object is
3857              *     {@link Float }
3858              *     
3859              */
3860             public Float getXPos() {
3861                 return xPos;
3862             }
3863
3864             /**
3865              * Sets the value of the xPos property.
3866              * 
3867              * @param value
3868              *     allowed object is
3869              *     {@link Float }
3870              *     
3871              */
3872             public void setXPos(Float value) {
3873                 this.xPos = value;
3874             }
3875
3876             /**
3877              * Gets the value of the yPos property.
3878              * 
3879              * @return
3880              *     possible object is
3881              *     {@link Float }
3882              *     
3883              */
3884             public Float getYPos() {
3885                 return yPos;
3886             }
3887
3888             /**
3889              * Sets the value of the yPos property.
3890              * 
3891              * @param value
3892              *     allowed object is
3893              *     {@link Float }
3894              *     
3895              */
3896             public void setYPos(Float value) {
3897                 this.yPos = value;
3898             }
3899
3900             /**
3901              * Gets the value of the zPos property.
3902              * 
3903              * @return
3904              *     possible object is
3905              *     {@link Float }
3906              *     
3907              */
3908             public Float getZPos() {
3909                 return zPos;
3910             }
3911
3912             /**
3913              * Sets the value of the zPos property.
3914              * 
3915              * @param value
3916              *     allowed object is
3917              *     {@link Float }
3918              *     
3919              */
3920             public void setZPos(Float value) {
3921                 this.zPos = value;
3922             }
3923
3924         }
3925
3926
3927         /**
3928          * <p>Java class for anonymous complex type.
3929          * 
3930          * <p>The following schema fragment specifies the expected content contained within this class.
3931          * 
3932          * <pre>
3933          * &lt;complexType>
3934          *   &lt;complexContent>
3935          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3936          *       &lt;attGroup ref="{www.jalview.org}position"/>
3937          *     &lt;/restriction>
3938          *   &lt;/complexContent>
3939          * &lt;/complexType>
3940          * </pre>
3941          * 
3942          * 
3943          */
3944         @XmlAccessorType(XmlAccessType.FIELD)
3945         @XmlType(name = "")
3946         public static class SeqPointMin {
3947
3948             @XmlAttribute(name = "xPos")
3949             protected Float xPos;
3950             @XmlAttribute(name = "yPos")
3951             protected Float yPos;
3952             @XmlAttribute(name = "zPos")
3953             protected Float zPos;
3954
3955             /**
3956              * Gets the value of the xPos property.
3957              * 
3958              * @return
3959              *     possible object is
3960              *     {@link Float }
3961              *     
3962              */
3963             public Float getXPos() {
3964                 return xPos;
3965             }
3966
3967             /**
3968              * Sets the value of the xPos property.
3969              * 
3970              * @param value
3971              *     allowed object is
3972              *     {@link Float }
3973              *     
3974              */
3975             public void setXPos(Float value) {
3976                 this.xPos = value;
3977             }
3978
3979             /**
3980              * Gets the value of the yPos property.
3981              * 
3982              * @return
3983              *     possible object is
3984              *     {@link Float }
3985              *     
3986              */
3987             public Float getYPos() {
3988                 return yPos;
3989             }
3990
3991             /**
3992              * Sets the value of the yPos property.
3993              * 
3994              * @param value
3995              *     allowed object is
3996              *     {@link Float }
3997              *     
3998              */
3999             public void setYPos(Float value) {
4000                 this.yPos = value;
4001             }
4002
4003             /**
4004              * Gets the value of the zPos property.
4005              * 
4006              * @return
4007              *     possible object is
4008              *     {@link Float }
4009              *     
4010              */
4011             public Float getZPos() {
4012                 return zPos;
4013             }
4014
4015             /**
4016              * Sets the value of the zPos property.
4017              * 
4018              * @param value
4019              *     allowed object is
4020              *     {@link Float }
4021              *     
4022              */
4023             public void setZPos(Float value) {
4024                 this.zPos = value;
4025             }
4026
4027         }
4028
4029
4030         /**
4031          * <p>Java class for anonymous complex type.
4032          * 
4033          * <p>The following schema fragment specifies the expected content contained within this class.
4034          * 
4035          * <pre>
4036          * &lt;complexType>
4037          *   &lt;complexContent>
4038          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4039          *       &lt;attGroup ref="{www.jalview.org}position"/>
4040          *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4041          *     &lt;/restriction>
4042          *   &lt;/complexContent>
4043          * &lt;/complexType>
4044          * </pre>
4045          * 
4046          * 
4047          */
4048         @XmlAccessorType(XmlAccessType.FIELD)
4049         @XmlType(name = "")
4050         public static class SequencePoint {
4051
4052             @XmlAttribute(name = "sequenceRef")
4053             protected String sequenceRef;
4054             @XmlAttribute(name = "xPos")
4055             protected Float xPos;
4056             @XmlAttribute(name = "yPos")
4057             protected Float yPos;
4058             @XmlAttribute(name = "zPos")
4059             protected Float zPos;
4060
4061             /**
4062              * Gets the value of the sequenceRef property.
4063              * 
4064              * @return
4065              *     possible object is
4066              *     {@link String }
4067              *     
4068              */
4069             public String getSequenceRef() {
4070                 return sequenceRef;
4071             }
4072
4073             /**
4074              * Sets the value of the sequenceRef property.
4075              * 
4076              * @param value
4077              *     allowed object is
4078              *     {@link String }
4079              *     
4080              */
4081             public void setSequenceRef(String value) {
4082                 this.sequenceRef = value;
4083             }
4084
4085             /**
4086              * Gets the value of the xPos property.
4087              * 
4088              * @return
4089              *     possible object is
4090              *     {@link Float }
4091              *     
4092              */
4093             public Float getXPos() {
4094                 return xPos;
4095             }
4096
4097             /**
4098              * Sets the value of the xPos property.
4099              * 
4100              * @param value
4101              *     allowed object is
4102              *     {@link Float }
4103              *     
4104              */
4105             public void setXPos(Float value) {
4106                 this.xPos = value;
4107             }
4108
4109             /**
4110              * Gets the value of the yPos property.
4111              * 
4112              * @return
4113              *     possible object is
4114              *     {@link Float }
4115              *     
4116              */
4117             public Float getYPos() {
4118                 return yPos;
4119             }
4120
4121             /**
4122              * Sets the value of the yPos property.
4123              * 
4124              * @param value
4125              *     allowed object is
4126              *     {@link Float }
4127              *     
4128              */
4129             public void setYPos(Float value) {
4130                 this.yPos = value;
4131             }
4132
4133             /**
4134              * Gets the value of the zPos property.
4135              * 
4136              * @return
4137              *     possible object is
4138              *     {@link Float }
4139              *     
4140              */
4141             public Float getZPos() {
4142                 return zPos;
4143             }
4144
4145             /**
4146              * Sets the value of the zPos property.
4147              * 
4148              * @param value
4149              *     allowed object is
4150              *     {@link Float }
4151              *     
4152              */
4153             public void setZPos(Float value) {
4154                 this.zPos = value;
4155             }
4156
4157         }
4158
4159     }
4160
4161
4162     /**
4163      * <p>Java class for anonymous complex type.
4164      * 
4165      * <p>The following schema fragment specifies the expected content contained within this class.
4166      * 
4167      * <pre>
4168      * &lt;complexType>
4169      *   &lt;complexContent>
4170      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4171      *       &lt;sequence minOccurs="0">
4172      *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4173      *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4174      *       &lt;/sequence>
4175      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4176      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4177      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4178      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4179      *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4180      *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4181      *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4182      *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4183      *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4184      *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4185      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4186      *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4187      *     &lt;/restriction>
4188      *   &lt;/complexContent>
4189      * &lt;/complexType>
4190      * </pre>
4191      * 
4192      * 
4193      */
4194     @XmlAccessorType(XmlAccessType.FIELD)
4195     @XmlType(name = "", propOrder = {
4196         "title",
4197         "newick"
4198     })
4199     public static class Tree {
4200
4201         @XmlElement(namespace = "www.jalview.org")
4202         protected String title;
4203         @XmlElement(namespace = "www.jalview.org")
4204         protected String newick;
4205         @XmlAttribute(name = "fontName")
4206         protected String fontName;
4207         @XmlAttribute(name = "fontSize")
4208         protected Integer fontSize;
4209         @XmlAttribute(name = "fontStyle")
4210         protected Integer fontStyle;
4211         @XmlAttribute(name = "threshold")
4212         protected Float threshold;
4213         @XmlAttribute(name = "showBootstrap")
4214         protected Boolean showBootstrap;
4215         @XmlAttribute(name = "showDistances")
4216         protected Boolean showDistances;
4217         @XmlAttribute(name = "markUnlinked")
4218         protected Boolean markUnlinked;
4219         @XmlAttribute(name = "fitToWindow")
4220         protected Boolean fitToWindow;
4221         @XmlAttribute(name = "currentTree")
4222         protected Boolean currentTree;
4223         @XmlAttribute(name = "id")
4224         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4225         @XmlID
4226         @XmlSchemaType(name = "ID")
4227         protected String id;
4228         @XmlAttribute(name = "linkToAllViews")
4229         protected Boolean linkToAllViews;
4230         @XmlAttribute(name = "width")
4231         protected Integer width;
4232         @XmlAttribute(name = "height")
4233         protected Integer height;
4234         @XmlAttribute(name = "xpos")
4235         protected Integer xpos;
4236         @XmlAttribute(name = "ypos")
4237         protected Integer ypos;
4238
4239         /**
4240          * Gets the value of the title property.
4241          * 
4242          * @return
4243          *     possible object is
4244          *     {@link String }
4245          *     
4246          */
4247         public String getTitle() {
4248             return title;
4249         }
4250
4251         /**
4252          * Sets the value of the title property.
4253          * 
4254          * @param value
4255          *     allowed object is
4256          *     {@link String }
4257          *     
4258          */
4259         public void setTitle(String value) {
4260             this.title = value;
4261         }
4262
4263         /**
4264          * Gets the value of the newick property.
4265          * 
4266          * @return
4267          *     possible object is
4268          *     {@link String }
4269          *     
4270          */
4271         public String getNewick() {
4272             return newick;
4273         }
4274
4275         /**
4276          * Sets the value of the newick property.
4277          * 
4278          * @param value
4279          *     allowed object is
4280          *     {@link String }
4281          *     
4282          */
4283         public void setNewick(String value) {
4284             this.newick = value;
4285         }
4286
4287         /**
4288          * Gets the value of the fontName property.
4289          * 
4290          * @return
4291          *     possible object is
4292          *     {@link String }
4293          *     
4294          */
4295         public String getFontName() {
4296             return fontName;
4297         }
4298
4299         /**
4300          * Sets the value of the fontName property.
4301          * 
4302          * @param value
4303          *     allowed object is
4304          *     {@link String }
4305          *     
4306          */
4307         public void setFontName(String value) {
4308             this.fontName = value;
4309         }
4310
4311         /**
4312          * Gets the value of the fontSize property.
4313          * 
4314          * @return
4315          *     possible object is
4316          *     {@link Integer }
4317          *     
4318          */
4319         public Integer getFontSize() {
4320             return fontSize;
4321         }
4322
4323         /**
4324          * Sets the value of the fontSize property.
4325          * 
4326          * @param value
4327          *     allowed object is
4328          *     {@link Integer }
4329          *     
4330          */
4331         public void setFontSize(Integer value) {
4332             this.fontSize = value;
4333         }
4334
4335         /**
4336          * Gets the value of the fontStyle property.
4337          * 
4338          * @return
4339          *     possible object is
4340          *     {@link Integer }
4341          *     
4342          */
4343         public Integer getFontStyle() {
4344             return fontStyle;
4345         }
4346
4347         /**
4348          * Sets the value of the fontStyle property.
4349          * 
4350          * @param value
4351          *     allowed object is
4352          *     {@link Integer }
4353          *     
4354          */
4355         public void setFontStyle(Integer value) {
4356             this.fontStyle = value;
4357         }
4358
4359         /**
4360          * Gets the value of the threshold property.
4361          * 
4362          * @return
4363          *     possible object is
4364          *     {@link Float }
4365          *     
4366          */
4367         public Float getThreshold() {
4368             return threshold;
4369         }
4370
4371         /**
4372          * Sets the value of the threshold property.
4373          * 
4374          * @param value
4375          *     allowed object is
4376          *     {@link Float }
4377          *     
4378          */
4379         public void setThreshold(Float value) {
4380             this.threshold = value;
4381         }
4382
4383         /**
4384          * Gets the value of the showBootstrap property.
4385          * 
4386          * @return
4387          *     possible object is
4388          *     {@link Boolean }
4389          *     
4390          */
4391         public Boolean isShowBootstrap() {
4392             return showBootstrap;
4393         }
4394
4395         /**
4396          * Sets the value of the showBootstrap property.
4397          * 
4398          * @param value
4399          *     allowed object is
4400          *     {@link Boolean }
4401          *     
4402          */
4403         public void setShowBootstrap(Boolean value) {
4404             this.showBootstrap = value;
4405         }
4406
4407         /**
4408          * Gets the value of the showDistances property.
4409          * 
4410          * @return
4411          *     possible object is
4412          *     {@link Boolean }
4413          *     
4414          */
4415         public Boolean isShowDistances() {
4416             return showDistances;
4417         }
4418
4419         /**
4420          * Sets the value of the showDistances property.
4421          * 
4422          * @param value
4423          *     allowed object is
4424          *     {@link Boolean }
4425          *     
4426          */
4427         public void setShowDistances(Boolean value) {
4428             this.showDistances = value;
4429         }
4430
4431         /**
4432          * Gets the value of the markUnlinked property.
4433          * 
4434          * @return
4435          *     possible object is
4436          *     {@link Boolean }
4437          *     
4438          */
4439         public Boolean isMarkUnlinked() {
4440             return markUnlinked;
4441         }
4442
4443         /**
4444          * Sets the value of the markUnlinked property.
4445          * 
4446          * @param value
4447          *     allowed object is
4448          *     {@link Boolean }
4449          *     
4450          */
4451         public void setMarkUnlinked(Boolean value) {
4452             this.markUnlinked = value;
4453         }
4454
4455         /**
4456          * Gets the value of the fitToWindow property.
4457          * 
4458          * @return
4459          *     possible object is
4460          *     {@link Boolean }
4461          *     
4462          */
4463         public Boolean isFitToWindow() {
4464             return fitToWindow;
4465         }
4466
4467         /**
4468          * Sets the value of the fitToWindow property.
4469          * 
4470          * @param value
4471          *     allowed object is
4472          *     {@link Boolean }
4473          *     
4474          */
4475         public void setFitToWindow(Boolean value) {
4476             this.fitToWindow = value;
4477         }
4478
4479         /**
4480          * Gets the value of the currentTree property.
4481          * 
4482          * @return
4483          *     possible object is
4484          *     {@link Boolean }
4485          *     
4486          */
4487         public Boolean isCurrentTree() {
4488             return currentTree;
4489         }
4490
4491         /**
4492          * Sets the value of the currentTree property.
4493          * 
4494          * @param value
4495          *     allowed object is
4496          *     {@link Boolean }
4497          *     
4498          */
4499         public void setCurrentTree(Boolean value) {
4500             this.currentTree = value;
4501         }
4502
4503         /**
4504          * Gets the value of the id property.
4505          * 
4506          * @return
4507          *     possible object is
4508          *     {@link String }
4509          *     
4510          */
4511         public String getId() {
4512             return id;
4513         }
4514
4515         /**
4516          * Sets the value of the id property.
4517          * 
4518          * @param value
4519          *     allowed object is
4520          *     {@link String }
4521          *     
4522          */
4523         public void setId(String value) {
4524             this.id = value;
4525         }
4526
4527         /**
4528          * Gets the value of the linkToAllViews property.
4529          * 
4530          * @return
4531          *     possible object is
4532          *     {@link Boolean }
4533          *     
4534          */
4535         public boolean isLinkToAllViews() {
4536             if (linkToAllViews == null) {
4537                 return false;
4538             } else {
4539                 return linkToAllViews;
4540             }
4541         }
4542
4543         /**
4544          * Sets the value of the linkToAllViews property.
4545          * 
4546          * @param value
4547          *     allowed object is
4548          *     {@link Boolean }
4549          *     
4550          */
4551         public void setLinkToAllViews(Boolean value) {
4552             this.linkToAllViews = value;
4553         }
4554
4555         /**
4556          * Gets the value of the width property.
4557          * 
4558          * @return
4559          *     possible object is
4560          *     {@link Integer }
4561          *     
4562          */
4563         public Integer getWidth() {
4564             return width;
4565         }
4566
4567         /**
4568          * Sets the value of the width property.
4569          * 
4570          * @param value
4571          *     allowed object is
4572          *     {@link Integer }
4573          *     
4574          */
4575         public void setWidth(Integer value) {
4576             this.width = value;
4577         }
4578
4579         /**
4580          * Gets the value of the height property.
4581          * 
4582          * @return
4583          *     possible object is
4584          *     {@link Integer }
4585          *     
4586          */
4587         public Integer getHeight() {
4588             return height;
4589         }
4590
4591         /**
4592          * Sets the value of the height property.
4593          * 
4594          * @param value
4595          *     allowed object is
4596          *     {@link Integer }
4597          *     
4598          */
4599         public void setHeight(Integer value) {
4600             this.height = value;
4601         }
4602
4603         /**
4604          * Gets the value of the xpos property.
4605          * 
4606          * @return
4607          *     possible object is
4608          *     {@link Integer }
4609          *     
4610          */
4611         public Integer getXpos() {
4612             return xpos;
4613         }
4614
4615         /**
4616          * Sets the value of the xpos property.
4617          * 
4618          * @param value
4619          *     allowed object is
4620          *     {@link Integer }
4621          *     
4622          */
4623         public void setXpos(Integer value) {
4624             this.xpos = value;
4625         }
4626
4627         /**
4628          * Gets the value of the ypos property.
4629          * 
4630          * @return
4631          *     possible object is
4632          *     {@link Integer }
4633          *     
4634          */
4635         public Integer getYpos() {
4636             return ypos;
4637         }
4638
4639         /**
4640          * Sets the value of the ypos property.
4641          * 
4642          * @param value
4643          *     allowed object is
4644          *     {@link Integer }
4645          *     
4646          */
4647         public void setYpos(Integer value) {
4648             this.ypos = value;
4649         }
4650
4651     }
4652
4653
4654     /**
4655      * <p>Java class for anonymous complex type.
4656      * 
4657      * <p>The following schema fragment specifies the expected content contained within this class.
4658      * 
4659      * <pre>
4660      * &lt;complexType>
4661      *   &lt;complexContent>
4662      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4663      *       &lt;sequence>
4664      *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4665      *       &lt;/sequence>
4666      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4667      *     &lt;/restriction>
4668      *   &lt;/complexContent>
4669      * &lt;/complexType>
4670      * </pre>
4671      * 
4672      * 
4673      */
4674     @XmlAccessorType(XmlAccessType.FIELD)
4675     @XmlType(name = "", propOrder = {
4676         "userColourScheme"
4677     })
4678     public static class UserColours {
4679
4680         @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4681         protected JalviewUserColours userColourScheme;
4682         @XmlAttribute(name = "id")
4683         protected String id;
4684
4685         /**
4686          * Gets the value of the userColourScheme property.
4687          * 
4688          * @return
4689          *     possible object is
4690          *     {@link JalviewUserColours }
4691          *     
4692          */
4693         public JalviewUserColours getUserColourScheme() {
4694             return userColourScheme;
4695         }
4696
4697         /**
4698          * Sets the value of the userColourScheme property.
4699          * 
4700          * @param value
4701          *     allowed object is
4702          *     {@link JalviewUserColours }
4703          *     
4704          */
4705         public void setUserColourScheme(JalviewUserColours value) {
4706             this.userColourScheme = value;
4707         }
4708
4709         /**
4710          * Gets the value of the id property.
4711          * 
4712          * @return
4713          *     possible object is
4714          *     {@link String }
4715          *     
4716          */
4717         public String getId() {
4718             return id;
4719         }
4720
4721         /**
4722          * Sets the value of the id property.
4723          * 
4724          * @param value
4725          *     allowed object is
4726          *     {@link String }
4727          *     
4728          */
4729         public void setId(String value) {
4730             this.id = value;
4731         }
4732
4733     }
4734
4735
4736     /**
4737      * <p>Java class for anonymous complex type.
4738      * 
4739      * <p>The following schema fragment specifies the expected content contained within this class.
4740      * 
4741      * <pre>
4742      * &lt;complexType>
4743      *   &lt;complexContent>
4744      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4745      *       &lt;sequence>
4746      *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4747      *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4748      *           &lt;complexType>
4749      *             &lt;complexContent>
4750      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4751      *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4752      *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4753      *               &lt;/restriction>
4754      *             &lt;/complexContent>
4755      *           &lt;/complexType>
4756      *         &lt;/element>
4757      *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4758      *           &lt;complexType>
4759      *             &lt;complexContent>
4760      *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4761      *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4762      *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4763      *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4764      *               &lt;/extension>
4765      *             &lt;/complexContent>
4766      *           &lt;/complexType>
4767      *         &lt;/element>
4768      *       &lt;/sequence>
4769      *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
4770      *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4771      *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4772      *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4773      *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4774      *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4775      *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4776      *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4777      *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4778      *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4779      *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4780      *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4781      *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4782      *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4783      *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4784      *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4785      *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4786      *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4787      *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4788      *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4789      *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4790      *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4791      *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4792      *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4793      *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4794      *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4795      *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4796      *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4797      *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4798      *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4799      *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4800      *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4801      *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4802      *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4803      *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4804      *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4805      *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4806      *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4807      *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4808      *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4809      *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4810      *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4811      *     &lt;/restriction>
4812      *   &lt;/complexContent>
4813      * &lt;/complexType>
4814      * </pre>
4815      * 
4816      * 
4817      */
4818     @XmlAccessorType(XmlAccessType.FIELD)
4819     @XmlType(name = "", propOrder = {
4820         "annotationColours",
4821         "hiddenColumns",
4822         "calcIdParam"
4823     })
4824     public static class Viewport {
4825
4826         @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4827         protected AnnotationColourScheme annotationColours;
4828         @XmlElement(namespace = "www.jalview.org")
4829         protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4830         @XmlElement(namespace = "www.jalview.org")
4831         protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4832         @XmlAttribute(name = "conservationSelected")
4833         protected Boolean conservationSelected;
4834         @XmlAttribute(name = "pidSelected")
4835         protected Boolean pidSelected;
4836         @XmlAttribute(name = "bgColour")
4837         protected String bgColour;
4838         @XmlAttribute(name = "consThreshold")
4839         protected Integer consThreshold;
4840         @XmlAttribute(name = "pidThreshold")
4841         protected Integer pidThreshold;
4842         @XmlAttribute(name = "title")
4843         protected String title;
4844         @XmlAttribute(name = "showFullId")
4845         protected Boolean showFullId;
4846         @XmlAttribute(name = "rightAlignIds")
4847         protected Boolean rightAlignIds;
4848         @XmlAttribute(name = "showText")
4849         protected Boolean showText;
4850         @XmlAttribute(name = "showColourText")
4851         protected Boolean showColourText;
4852         @XmlAttribute(name = "showUnconserved")
4853         protected Boolean showUnconserved;
4854         @XmlAttribute(name = "showBoxes")
4855         protected Boolean showBoxes;
4856         @XmlAttribute(name = "wrapAlignment")
4857         protected Boolean wrapAlignment;
4858         @XmlAttribute(name = "renderGaps")
4859         protected Boolean renderGaps;
4860         @XmlAttribute(name = "showSequenceFeatures")
4861         protected Boolean showSequenceFeatures;
4862         @XmlAttribute(name = "showNPfeatureTooltip")
4863         protected Boolean showNPfeatureTooltip;
4864         @XmlAttribute(name = "showDbRefTooltip")
4865         protected Boolean showDbRefTooltip;
4866         @XmlAttribute(name = "followHighlight")
4867         protected Boolean followHighlight;
4868         @XmlAttribute(name = "followSelection")
4869         protected Boolean followSelection;
4870         @XmlAttribute(name = "showAnnotation")
4871         protected Boolean showAnnotation;
4872         @XmlAttribute(name = "centreColumnLabels")
4873         protected Boolean centreColumnLabels;
4874         @XmlAttribute(name = "showGroupConservation")
4875         protected Boolean showGroupConservation;
4876         @XmlAttribute(name = "showGroupConsensus")
4877         protected Boolean showGroupConsensus;
4878         @XmlAttribute(name = "showConsensusHistogram")
4879         protected Boolean showConsensusHistogram;
4880         @XmlAttribute(name = "showSequenceLogo")
4881         protected Boolean showSequenceLogo;
4882         @XmlAttribute(name = "normaliseSequenceLogo")
4883         protected Boolean normaliseSequenceLogo;
4884         @XmlAttribute(name = "ignoreGapsinConsensus")
4885         protected Boolean ignoreGapsinConsensus;
4886         @XmlAttribute(name = "startRes")
4887         protected Integer startRes;
4888         @XmlAttribute(name = "startSeq")
4889         protected Integer startSeq;
4890         @XmlAttribute(name = "fontName")
4891         protected String fontName;
4892         @XmlAttribute(name = "fontSize")
4893         protected Integer fontSize;
4894         @XmlAttribute(name = "fontStyle")
4895         protected Integer fontStyle;
4896         @XmlAttribute(name = "scaleProteinAsCdna")
4897         protected Boolean scaleProteinAsCdna;
4898         @XmlAttribute(name = "viewName")
4899         protected String viewName;
4900         @XmlAttribute(name = "sequenceSetId")
4901         protected String sequenceSetId;
4902         @XmlAttribute(name = "gatheredViews")
4903         protected Boolean gatheredViews;
4904         @XmlAttribute(name = "textCol1")
4905         protected Integer textCol1;
4906         @XmlAttribute(name = "textCol2")
4907         protected Integer textCol2;
4908         @XmlAttribute(name = "textColThreshold")
4909         protected Integer textColThreshold;
4910         @XmlAttribute(name = "id")
4911         @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4912         @XmlID
4913         @XmlSchemaType(name = "ID")
4914         protected String id;
4915         @XmlAttribute(name = "complementId")
4916         protected String complementId;
4917         @XmlAttribute(name = "width")
4918         protected Integer width;
4919         @XmlAttribute(name = "height")
4920         protected Integer height;
4921         @XmlAttribute(name = "xpos")
4922         protected Integer xpos;
4923         @XmlAttribute(name = "ypos")
4924         protected Integer ypos;
4925
4926         /**
4927          * Gets the value of the annotationColours property.
4928          * 
4929          * @return
4930          *     possible object is
4931          *     {@link AnnotationColourScheme }
4932          *     
4933          */
4934         public AnnotationColourScheme getAnnotationColours() {
4935             return annotationColours;
4936         }
4937
4938         /**
4939          * Sets the value of the annotationColours property.
4940          * 
4941          * @param value
4942          *     allowed object is
4943          *     {@link AnnotationColourScheme }
4944          *     
4945          */
4946         public void setAnnotationColours(AnnotationColourScheme value) {
4947             this.annotationColours = value;
4948         }
4949
4950         /**
4951          * Gets the value of the hiddenColumns property.
4952          * 
4953          * <p>
4954          * This accessor method returns a reference to the live list,
4955          * not a snapshot. Therefore any modification you make to the
4956          * returned list will be present inside the JAXB object.
4957          * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4958          * 
4959          * <p>
4960          * For example, to add a new item, do as follows:
4961          * <pre>
4962          *    getHiddenColumns().add(newItem);
4963          * </pre>
4964          * 
4965          * 
4966          * <p>
4967          * Objects of the following type(s) are allowed in the list
4968          * {@link JalviewModel.Viewport.HiddenColumns }
4969          * 
4970          * 
4971          */
4972         public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
4973             if (hiddenColumns == null) {
4974                 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
4975             }
4976             return this.hiddenColumns;
4977         }
4978
4979         /**
4980          * Gets the value of the calcIdParam property.
4981          * 
4982          * <p>
4983          * This accessor method returns a reference to the live list,
4984          * not a snapshot. Therefore any modification you make to the
4985          * returned list will be present inside the JAXB object.
4986          * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
4987          * 
4988          * <p>
4989          * For example, to add a new item, do as follows:
4990          * <pre>
4991          *    getCalcIdParam().add(newItem);
4992          * </pre>
4993          * 
4994          * 
4995          * <p>
4996          * Objects of the following type(s) are allowed in the list
4997          * {@link JalviewModel.Viewport.CalcIdParam }
4998          * 
4999          * 
5000          */
5001         public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5002             if (calcIdParam == null) {
5003                 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5004             }
5005             return this.calcIdParam;
5006         }
5007
5008         /**
5009          * Gets the value of the conservationSelected property.
5010          * 
5011          * @return
5012          *     possible object is
5013          *     {@link Boolean }
5014          *     
5015          */
5016         public Boolean isConservationSelected() {
5017             return conservationSelected;
5018         }
5019
5020         /**
5021          * Sets the value of the conservationSelected property.
5022          * 
5023          * @param value
5024          *     allowed object is
5025          *     {@link Boolean }
5026          *     
5027          */
5028         public void setConservationSelected(Boolean value) {
5029             this.conservationSelected = value;
5030         }
5031
5032         /**
5033          * Gets the value of the pidSelected property.
5034          * 
5035          * @return
5036          *     possible object is
5037          *     {@link Boolean }
5038          *     
5039          */
5040         public Boolean isPidSelected() {
5041             return pidSelected;
5042         }
5043
5044         /**
5045          * Sets the value of the pidSelected property.
5046          * 
5047          * @param value
5048          *     allowed object is
5049          *     {@link Boolean }
5050          *     
5051          */
5052         public void setPidSelected(Boolean value) {
5053             this.pidSelected = value;
5054         }
5055
5056         /**
5057          * Gets the value of the bgColour property.
5058          * 
5059          * @return
5060          *     possible object is
5061          *     {@link String }
5062          *     
5063          */
5064         public String getBgColour() {
5065             return bgColour;
5066         }
5067
5068         /**
5069          * Sets the value of the bgColour property.
5070          * 
5071          * @param value
5072          *     allowed object is
5073          *     {@link String }
5074          *     
5075          */
5076         public void setBgColour(String value) {
5077             this.bgColour = value;
5078         }
5079
5080         /**
5081          * Gets the value of the consThreshold property.
5082          * 
5083          * @return
5084          *     possible object is
5085          *     {@link Integer }
5086          *     
5087          */
5088         public Integer getConsThreshold() {
5089             return consThreshold;
5090         }
5091
5092         /**
5093          * Sets the value of the consThreshold property.
5094          * 
5095          * @param value
5096          *     allowed object is
5097          *     {@link Integer }
5098          *     
5099          */
5100         public void setConsThreshold(Integer value) {
5101             this.consThreshold = value;
5102         }
5103
5104         /**
5105          * Gets the value of the pidThreshold property.
5106          * 
5107          * @return
5108          *     possible object is
5109          *     {@link Integer }
5110          *     
5111          */
5112         public Integer getPidThreshold() {
5113             return pidThreshold;
5114         }
5115
5116         /**
5117          * Sets the value of the pidThreshold property.
5118          * 
5119          * @param value
5120          *     allowed object is
5121          *     {@link Integer }
5122          *     
5123          */
5124         public void setPidThreshold(Integer value) {
5125             this.pidThreshold = value;
5126         }
5127
5128         /**
5129          * Gets the value of the title property.
5130          * 
5131          * @return
5132          *     possible object is
5133          *     {@link String }
5134          *     
5135          */
5136         public String getTitle() {
5137             return title;
5138         }
5139
5140         /**
5141          * Sets the value of the title property.
5142          * 
5143          * @param value
5144          *     allowed object is
5145          *     {@link String }
5146          *     
5147          */
5148         public void setTitle(String value) {
5149             this.title = value;
5150         }
5151
5152         /**
5153          * Gets the value of the showFullId property.
5154          * 
5155          * @return
5156          *     possible object is
5157          *     {@link Boolean }
5158          *     
5159          */
5160         public Boolean isShowFullId() {
5161             return showFullId;
5162         }
5163
5164         /**
5165          * Sets the value of the showFullId property.
5166          * 
5167          * @param value
5168          *     allowed object is
5169          *     {@link Boolean }
5170          *     
5171          */
5172         public void setShowFullId(Boolean value) {
5173             this.showFullId = value;
5174         }
5175
5176         /**
5177          * Gets the value of the rightAlignIds property.
5178          * 
5179          * @return
5180          *     possible object is
5181          *     {@link Boolean }
5182          *     
5183          */
5184         public Boolean isRightAlignIds() {
5185             return rightAlignIds;
5186         }
5187
5188         /**
5189          * Sets the value of the rightAlignIds property.
5190          * 
5191          * @param value
5192          *     allowed object is
5193          *     {@link Boolean }
5194          *     
5195          */
5196         public void setRightAlignIds(Boolean value) {
5197             this.rightAlignIds = value;
5198         }
5199
5200         /**
5201          * Gets the value of the showText property.
5202          * 
5203          * @return
5204          *     possible object is
5205          *     {@link Boolean }
5206          *     
5207          */
5208         public Boolean isShowText() {
5209             return showText;
5210         }
5211
5212         /**
5213          * Sets the value of the showText property.
5214          * 
5215          * @param value
5216          *     allowed object is
5217          *     {@link Boolean }
5218          *     
5219          */
5220         public void setShowText(Boolean value) {
5221             this.showText = value;
5222         }
5223
5224         /**
5225          * Gets the value of the showColourText property.
5226          * 
5227          * @return
5228          *     possible object is
5229          *     {@link Boolean }
5230          *     
5231          */
5232         public Boolean isShowColourText() {
5233             return showColourText;
5234         }
5235
5236         /**
5237          * Sets the value of the showColourText property.
5238          * 
5239          * @param value
5240          *     allowed object is
5241          *     {@link Boolean }
5242          *     
5243          */
5244         public void setShowColourText(Boolean value) {
5245             this.showColourText = value;
5246         }
5247
5248         /**
5249          * Gets the value of the showUnconserved property.
5250          * 
5251          * @return
5252          *     possible object is
5253          *     {@link Boolean }
5254          *     
5255          */
5256         public boolean isShowUnconserved() {
5257             if (showUnconserved == null) {
5258                 return false;
5259             } else {
5260                 return showUnconserved;
5261             }
5262         }
5263
5264         /**
5265          * Sets the value of the showUnconserved property.
5266          * 
5267          * @param value
5268          *     allowed object is
5269          *     {@link Boolean }
5270          *     
5271          */
5272         public void setShowUnconserved(Boolean value) {
5273             this.showUnconserved = value;
5274         }
5275
5276         /**
5277          * Gets the value of the showBoxes property.
5278          * 
5279          * @return
5280          *     possible object is
5281          *     {@link Boolean }
5282          *     
5283          */
5284         public Boolean isShowBoxes() {
5285             return showBoxes;
5286         }
5287
5288         /**
5289          * Sets the value of the showBoxes property.
5290          * 
5291          * @param value
5292          *     allowed object is
5293          *     {@link Boolean }
5294          *     
5295          */
5296         public void setShowBoxes(Boolean value) {
5297             this.showBoxes = value;
5298         }
5299
5300         /**
5301          * Gets the value of the wrapAlignment property.
5302          * 
5303          * @return
5304          *     possible object is
5305          *     {@link Boolean }
5306          *     
5307          */
5308         public Boolean isWrapAlignment() {
5309             return wrapAlignment;
5310         }
5311
5312         /**
5313          * Sets the value of the wrapAlignment property.
5314          * 
5315          * @param value
5316          *     allowed object is
5317          *     {@link Boolean }
5318          *     
5319          */
5320         public void setWrapAlignment(Boolean value) {
5321             this.wrapAlignment = value;
5322         }
5323
5324         /**
5325          * Gets the value of the renderGaps property.
5326          * 
5327          * @return
5328          *     possible object is
5329          *     {@link Boolean }
5330          *     
5331          */
5332         public Boolean isRenderGaps() {
5333             return renderGaps;
5334         }
5335
5336         /**
5337          * Sets the value of the renderGaps property.
5338          * 
5339          * @param value
5340          *     allowed object is
5341          *     {@link Boolean }
5342          *     
5343          */
5344         public void setRenderGaps(Boolean value) {
5345             this.renderGaps = value;
5346         }
5347
5348         /**
5349          * Gets the value of the showSequenceFeatures property.
5350          * 
5351          * @return
5352          *     possible object is
5353          *     {@link Boolean }
5354          *     
5355          */
5356         public Boolean isShowSequenceFeatures() {
5357             return showSequenceFeatures;
5358         }
5359
5360         /**
5361          * Sets the value of the showSequenceFeatures property.
5362          * 
5363          * @param value
5364          *     allowed object is
5365          *     {@link Boolean }
5366          *     
5367          */
5368         public void setShowSequenceFeatures(Boolean value) {
5369             this.showSequenceFeatures = value;
5370         }
5371
5372         /**
5373          * Gets the value of the showNPfeatureTooltip property.
5374          * 
5375          * @return
5376          *     possible object is
5377          *     {@link Boolean }
5378          *     
5379          */
5380         public Boolean isShowNPfeatureTooltip() {
5381             return showNPfeatureTooltip;
5382         }
5383
5384         /**
5385          * Sets the value of the showNPfeatureTooltip property.
5386          * 
5387          * @param value
5388          *     allowed object is
5389          *     {@link Boolean }
5390          *     
5391          */
5392         public void setShowNPfeatureTooltip(Boolean value) {
5393             this.showNPfeatureTooltip = value;
5394         }
5395
5396         /**
5397          * Gets the value of the showDbRefTooltip property.
5398          * 
5399          * @return
5400          *     possible object is
5401          *     {@link Boolean }
5402          *     
5403          */
5404         public Boolean isShowDbRefTooltip() {
5405             return showDbRefTooltip;
5406         }
5407
5408         /**
5409          * Sets the value of the showDbRefTooltip property.
5410          * 
5411          * @param value
5412          *     allowed object is
5413          *     {@link Boolean }
5414          *     
5415          */
5416         public void setShowDbRefTooltip(Boolean value) {
5417             this.showDbRefTooltip = value;
5418         }
5419
5420         /**
5421          * Gets the value of the followHighlight property.
5422          * 
5423          * @return
5424          *     possible object is
5425          *     {@link Boolean }
5426          *     
5427          */
5428         public boolean isFollowHighlight() {
5429             if (followHighlight == null) {
5430                 return true;
5431             } else {
5432                 return followHighlight;
5433             }
5434         }
5435
5436         /**
5437          * Sets the value of the followHighlight property.
5438          * 
5439          * @param value
5440          *     allowed object is
5441          *     {@link Boolean }
5442          *     
5443          */
5444         public void setFollowHighlight(Boolean value) {
5445             this.followHighlight = value;
5446         }
5447
5448         /**
5449          * Gets the value of the followSelection property.
5450          * 
5451          * @return
5452          *     possible object is
5453          *     {@link Boolean }
5454          *     
5455          */
5456         public boolean isFollowSelection() {
5457             if (followSelection == null) {
5458                 return true;
5459             } else {
5460                 return followSelection;
5461             }
5462         }
5463
5464         /**
5465          * Sets the value of the followSelection property.
5466          * 
5467          * @param value
5468          *     allowed object is
5469          *     {@link Boolean }
5470          *     
5471          */
5472         public void setFollowSelection(Boolean value) {
5473             this.followSelection = value;
5474         }
5475
5476         /**
5477          * Gets the value of the showAnnotation property.
5478          * 
5479          * @return
5480          *     possible object is
5481          *     {@link Boolean }
5482          *     
5483          */
5484         public Boolean isShowAnnotation() {
5485             return showAnnotation;
5486         }
5487
5488         /**
5489          * Sets the value of the showAnnotation property.
5490          * 
5491          * @param value
5492          *     allowed object is
5493          *     {@link Boolean }
5494          *     
5495          */
5496         public void setShowAnnotation(Boolean value) {
5497             this.showAnnotation = value;
5498         }
5499
5500         /**
5501          * Gets the value of the centreColumnLabels property.
5502          * 
5503          * @return
5504          *     possible object is
5505          *     {@link Boolean }
5506          *     
5507          */
5508         public boolean isCentreColumnLabels() {
5509             if (centreColumnLabels == null) {
5510                 return false;
5511             } else {
5512                 return centreColumnLabels;
5513             }
5514         }
5515
5516         /**
5517          * Sets the value of the centreColumnLabels property.
5518          * 
5519          * @param value
5520          *     allowed object is
5521          *     {@link Boolean }
5522          *     
5523          */
5524         public void setCentreColumnLabels(Boolean value) {
5525             this.centreColumnLabels = value;
5526         }
5527
5528         /**
5529          * Gets the value of the showGroupConservation property.
5530          * 
5531          * @return
5532          *     possible object is
5533          *     {@link Boolean }
5534          *     
5535          */
5536         public boolean isShowGroupConservation() {
5537             if (showGroupConservation == null) {
5538                 return false;
5539             } else {
5540                 return showGroupConservation;
5541             }
5542         }
5543
5544         /**
5545          * Sets the value of the showGroupConservation property.
5546          * 
5547          * @param value
5548          *     allowed object is
5549          *     {@link Boolean }
5550          *     
5551          */
5552         public void setShowGroupConservation(Boolean value) {
5553             this.showGroupConservation = value;
5554         }
5555
5556         /**
5557          * Gets the value of the showGroupConsensus property.
5558          * 
5559          * @return
5560          *     possible object is
5561          *     {@link Boolean }
5562          *     
5563          */
5564         public boolean isShowGroupConsensus() {
5565             if (showGroupConsensus == null) {
5566                 return false;
5567             } else {
5568                 return showGroupConsensus;
5569             }
5570         }
5571
5572         /**
5573          * Sets the value of the showGroupConsensus property.
5574          * 
5575          * @param value
5576          *     allowed object is
5577          *     {@link Boolean }
5578          *     
5579          */
5580         public void setShowGroupConsensus(Boolean value) {
5581             this.showGroupConsensus = value;
5582         }
5583
5584         /**
5585          * Gets the value of the showConsensusHistogram property.
5586          * 
5587          * @return
5588          *     possible object is
5589          *     {@link Boolean }
5590          *     
5591          */
5592         public boolean isShowConsensusHistogram() {
5593             if (showConsensusHistogram == null) {
5594                 return true;
5595             } else {
5596                 return showConsensusHistogram;
5597             }
5598         }
5599
5600         /**
5601          * Sets the value of the showConsensusHistogram property.
5602          * 
5603          * @param value
5604          *     allowed object is
5605          *     {@link Boolean }
5606          *     
5607          */
5608         public void setShowConsensusHistogram(Boolean value) {
5609             this.showConsensusHistogram = value;
5610         }
5611
5612         /**
5613          * Gets the value of the showSequenceLogo property.
5614          * 
5615          * @return
5616          *     possible object is
5617          *     {@link Boolean }
5618          *     
5619          */
5620         public boolean isShowSequenceLogo() {
5621             if (showSequenceLogo == null) {
5622                 return false;
5623             } else {
5624                 return showSequenceLogo;
5625             }
5626         }
5627
5628         /**
5629          * Sets the value of the showSequenceLogo property.
5630          * 
5631          * @param value
5632          *     allowed object is
5633          *     {@link Boolean }
5634          *     
5635          */
5636         public void setShowSequenceLogo(Boolean value) {
5637             this.showSequenceLogo = value;
5638         }
5639
5640         /**
5641          * Gets the value of the normaliseSequenceLogo property.
5642          * 
5643          * @return
5644          *     possible object is
5645          *     {@link Boolean }
5646          *     
5647          */
5648         public boolean isNormaliseSequenceLogo() {
5649             if (normaliseSequenceLogo == null) {
5650                 return false;
5651             } else {
5652                 return normaliseSequenceLogo;
5653             }
5654         }
5655
5656         /**
5657          * Sets the value of the normaliseSequenceLogo property.
5658          * 
5659          * @param value
5660          *     allowed object is
5661          *     {@link Boolean }
5662          *     
5663          */
5664         public void setNormaliseSequenceLogo(Boolean value) {
5665             this.normaliseSequenceLogo = value;
5666         }
5667
5668         /**
5669          * Gets the value of the ignoreGapsinConsensus property.
5670          * 
5671          * @return
5672          *     possible object is
5673          *     {@link Boolean }
5674          *     
5675          */
5676         public boolean isIgnoreGapsinConsensus() {
5677             if (ignoreGapsinConsensus == null) {
5678                 return true;
5679             } else {
5680                 return ignoreGapsinConsensus;
5681             }
5682         }
5683
5684         /**
5685          * Sets the value of the ignoreGapsinConsensus property.
5686          * 
5687          * @param value
5688          *     allowed object is
5689          *     {@link Boolean }
5690          *     
5691          */
5692         public void setIgnoreGapsinConsensus(Boolean value) {
5693             this.ignoreGapsinConsensus = value;
5694         }
5695
5696         /**
5697          * Gets the value of the startRes property.
5698          * 
5699          * @return
5700          *     possible object is
5701          *     {@link Integer }
5702          *     
5703          */
5704         public Integer getStartRes() {
5705             return startRes;
5706         }
5707
5708         /**
5709          * Sets the value of the startRes property.
5710          * 
5711          * @param value
5712          *     allowed object is
5713          *     {@link Integer }
5714          *     
5715          */
5716         public void setStartRes(Integer value) {
5717             this.startRes = value;
5718         }
5719
5720         /**
5721          * Gets the value of the startSeq property.
5722          * 
5723          * @return
5724          *     possible object is
5725          *     {@link Integer }
5726          *     
5727          */
5728         public Integer getStartSeq() {
5729             return startSeq;
5730         }
5731
5732         /**
5733          * Sets the value of the startSeq property.
5734          * 
5735          * @param value
5736          *     allowed object is
5737          *     {@link Integer }
5738          *     
5739          */
5740         public void setStartSeq(Integer value) {
5741             this.startSeq = value;
5742         }
5743
5744         /**
5745          * Gets the value of the fontName property.
5746          * 
5747          * @return
5748          *     possible object is
5749          *     {@link String }
5750          *     
5751          */
5752         public String getFontName() {
5753             return fontName;
5754         }
5755
5756         /**
5757          * Sets the value of the fontName property.
5758          * 
5759          * @param value
5760          *     allowed object is
5761          *     {@link String }
5762          *     
5763          */
5764         public void setFontName(String value) {
5765             this.fontName = value;
5766         }
5767
5768         /**
5769          * Gets the value of the fontSize property.
5770          * 
5771          * @return
5772          *     possible object is
5773          *     {@link Integer }
5774          *     
5775          */
5776         public Integer getFontSize() {
5777             return fontSize;
5778         }
5779
5780         /**
5781          * Sets the value of the fontSize property.
5782          * 
5783          * @param value
5784          *     allowed object is
5785          *     {@link Integer }
5786          *     
5787          */
5788         public void setFontSize(Integer value) {
5789             this.fontSize = value;
5790         }
5791
5792         /**
5793          * Gets the value of the fontStyle property.
5794          * 
5795          * @return
5796          *     possible object is
5797          *     {@link Integer }
5798          *     
5799          */
5800         public Integer getFontStyle() {
5801             return fontStyle;
5802         }
5803
5804         /**
5805          * Sets the value of the fontStyle property.
5806          * 
5807          * @param value
5808          *     allowed object is
5809          *     {@link Integer }
5810          *     
5811          */
5812         public void setFontStyle(Integer value) {
5813             this.fontStyle = value;
5814         }
5815
5816         /**
5817          * Gets the value of the scaleProteinAsCdna property.
5818          * 
5819          * @return
5820          *     possible object is
5821          *     {@link Boolean }
5822          *     
5823          */
5824         public boolean isScaleProteinAsCdna() {
5825             if (scaleProteinAsCdna == null) {
5826                 return true;
5827             } else {
5828                 return scaleProteinAsCdna;
5829             }
5830         }
5831
5832         /**
5833          * Sets the value of the scaleProteinAsCdna property.
5834          * 
5835          * @param value
5836          *     allowed object is
5837          *     {@link Boolean }
5838          *     
5839          */
5840         public void setScaleProteinAsCdna(Boolean value) {
5841             this.scaleProteinAsCdna = value;
5842         }
5843
5844         /**
5845          * Gets the value of the viewName property.
5846          * 
5847          * @return
5848          *     possible object is
5849          *     {@link String }
5850          *     
5851          */
5852         public String getViewName() {
5853             return viewName;
5854         }
5855
5856         /**
5857          * Sets the value of the viewName property.
5858          * 
5859          * @param value
5860          *     allowed object is
5861          *     {@link String }
5862          *     
5863          */
5864         public void setViewName(String value) {
5865             this.viewName = value;
5866         }
5867
5868         /**
5869          * Gets the value of the sequenceSetId property.
5870          * 
5871          * @return
5872          *     possible object is
5873          *     {@link String }
5874          *     
5875          */
5876         public String getSequenceSetId() {
5877             return sequenceSetId;
5878         }
5879
5880         /**
5881          * Sets the value of the sequenceSetId property.
5882          * 
5883          * @param value
5884          *     allowed object is
5885          *     {@link String }
5886          *     
5887          */
5888         public void setSequenceSetId(String value) {
5889             this.sequenceSetId = value;
5890         }
5891
5892         /**
5893          * Gets the value of the gatheredViews property.
5894          * 
5895          * @return
5896          *     possible object is
5897          *     {@link Boolean }
5898          *     
5899          */
5900         public Boolean isGatheredViews() {
5901             return gatheredViews;
5902         }
5903
5904         /**
5905          * Sets the value of the gatheredViews property.
5906          * 
5907          * @param value
5908          *     allowed object is
5909          *     {@link Boolean }
5910          *     
5911          */
5912         public void setGatheredViews(Boolean value) {
5913             this.gatheredViews = value;
5914         }
5915
5916         /**
5917          * Gets the value of the textCol1 property.
5918          * 
5919          * @return
5920          *     possible object is
5921          *     {@link Integer }
5922          *     
5923          */
5924         public Integer getTextCol1() {
5925             return textCol1;
5926         }
5927
5928         /**
5929          * Sets the value of the textCol1 property.
5930          * 
5931          * @param value
5932          *     allowed object is
5933          *     {@link Integer }
5934          *     
5935          */
5936         public void setTextCol1(Integer value) {
5937             this.textCol1 = value;
5938         }
5939
5940         /**
5941          * Gets the value of the textCol2 property.
5942          * 
5943          * @return
5944          *     possible object is
5945          *     {@link Integer }
5946          *     
5947          */
5948         public Integer getTextCol2() {
5949             return textCol2;
5950         }
5951
5952         /**
5953          * Sets the value of the textCol2 property.
5954          * 
5955          * @param value
5956          *     allowed object is
5957          *     {@link Integer }
5958          *     
5959          */
5960         public void setTextCol2(Integer value) {
5961             this.textCol2 = value;
5962         }
5963
5964         /**
5965          * Gets the value of the textColThreshold property.
5966          * 
5967          * @return
5968          *     possible object is
5969          *     {@link Integer }
5970          *     
5971          */
5972         public Integer getTextColThreshold() {
5973             return textColThreshold;
5974         }
5975
5976         /**
5977          * Sets the value of the textColThreshold property.
5978          * 
5979          * @param value
5980          *     allowed object is
5981          *     {@link Integer }
5982          *     
5983          */
5984         public void setTextColThreshold(Integer value) {
5985             this.textColThreshold = value;
5986         }
5987
5988         /**
5989          * Gets the value of the id property.
5990          * 
5991          * @return
5992          *     possible object is
5993          *     {@link String }
5994          *     
5995          */
5996         public String getId() {
5997             return id;
5998         }
5999
6000         /**
6001          * Sets the value of the id property.
6002          * 
6003          * @param value
6004          *     allowed object is
6005          *     {@link String }
6006          *     
6007          */
6008         public void setId(String value) {
6009             this.id = value;
6010         }
6011
6012         /**
6013          * Gets the value of the complementId property.
6014          * 
6015          * @return
6016          *     possible object is
6017          *     {@link String }
6018          *     
6019          */
6020         public String getComplementId() {
6021             return complementId;
6022         }
6023
6024         /**
6025          * Sets the value of the complementId property.
6026          * 
6027          * @param value
6028          *     allowed object is
6029          *     {@link String }
6030          *     
6031          */
6032         public void setComplementId(String value) {
6033             this.complementId = value;
6034         }
6035
6036         /**
6037          * Gets the value of the width property.
6038          * 
6039          * @return
6040          *     possible object is
6041          *     {@link Integer }
6042          *     
6043          */
6044         public Integer getWidth() {
6045             return width;
6046         }
6047
6048         /**
6049          * Sets the value of the width property.
6050          * 
6051          * @param value
6052          *     allowed object is
6053          *     {@link Integer }
6054          *     
6055          */
6056         public void setWidth(Integer value) {
6057             this.width = value;
6058         }
6059
6060         /**
6061          * Gets the value of the height property.
6062          * 
6063          * @return
6064          *     possible object is
6065          *     {@link Integer }
6066          *     
6067          */
6068         public Integer getHeight() {
6069             return height;
6070         }
6071
6072         /**
6073          * Sets the value of the height property.
6074          * 
6075          * @param value
6076          *     allowed object is
6077          *     {@link Integer }
6078          *     
6079          */
6080         public void setHeight(Integer value) {
6081             this.height = value;
6082         }
6083
6084         /**
6085          * Gets the value of the xpos property.
6086          * 
6087          * @return
6088          *     possible object is
6089          *     {@link Integer }
6090          *     
6091          */
6092         public Integer getXpos() {
6093             return xpos;
6094         }
6095
6096         /**
6097          * Sets the value of the xpos property.
6098          * 
6099          * @param value
6100          *     allowed object is
6101          *     {@link Integer }
6102          *     
6103          */
6104         public void setXpos(Integer value) {
6105             this.xpos = value;
6106         }
6107
6108         /**
6109          * Gets the value of the ypos property.
6110          * 
6111          * @return
6112          *     possible object is
6113          *     {@link Integer }
6114          *     
6115          */
6116         public Integer getYpos() {
6117             return ypos;
6118         }
6119
6120         /**
6121          * Sets the value of the ypos property.
6122          * 
6123          * @param value
6124          *     allowed object is
6125          *     {@link Integer }
6126          *     
6127          */
6128         public void setYpos(Integer value) {
6129             this.ypos = value;
6130         }
6131
6132
6133         /**
6134          * <p>Java class for anonymous complex type.
6135          * 
6136          * <p>The following schema fragment specifies the expected content contained within this class.
6137          * 
6138          * <pre>
6139          * &lt;complexType>
6140          *   &lt;complexContent>
6141          *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6142          *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6143          *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6144          *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6145          *     &lt;/extension>
6146          *   &lt;/complexContent>
6147          * &lt;/complexType>
6148          * </pre>
6149          * 
6150          * 
6151          */
6152         @XmlAccessorType(XmlAccessType.FIELD)
6153         @XmlType(name = "")
6154         public static class CalcIdParam
6155             extends WebServiceParameterSet
6156         {
6157
6158             @XmlAttribute(name = "calcId", required = true)
6159             protected String calcId;
6160             @XmlAttribute(name = "needsUpdate")
6161             protected Boolean needsUpdate;
6162             @XmlAttribute(name = "autoUpdate", required = true)
6163             protected boolean autoUpdate;
6164
6165             /**
6166              * Gets the value of the calcId property.
6167              * 
6168              * @return
6169              *     possible object is
6170              *     {@link String }
6171              *     
6172              */
6173             public String getCalcId() {
6174                 return calcId;
6175             }
6176
6177             /**
6178              * Sets the value of the calcId property.
6179              * 
6180              * @param value
6181              *     allowed object is
6182              *     {@link String }
6183              *     
6184              */
6185             public void setCalcId(String value) {
6186                 this.calcId = value;
6187             }
6188
6189             /**
6190              * Gets the value of the needsUpdate property.
6191              * 
6192              * @return
6193              *     possible object is
6194              *     {@link Boolean }
6195              *     
6196              */
6197             public boolean isNeedsUpdate() {
6198                 if (needsUpdate == null) {
6199                     return false;
6200                 } else {
6201                     return needsUpdate;
6202                 }
6203             }
6204
6205             /**
6206              * Sets the value of the needsUpdate property.
6207              * 
6208              * @param value
6209              *     allowed object is
6210              *     {@link Boolean }
6211              *     
6212              */
6213             public void setNeedsUpdate(Boolean value) {
6214                 this.needsUpdate = value;
6215             }
6216
6217             /**
6218              * Gets the value of the autoUpdate property.
6219              * 
6220              */
6221             public boolean isAutoUpdate() {
6222                 return autoUpdate;
6223             }
6224
6225             /**
6226              * Sets the value of the autoUpdate property.
6227              * 
6228              */
6229             public void setAutoUpdate(boolean value) {
6230                 this.autoUpdate = value;
6231             }
6232
6233         }
6234
6235
6236         /**
6237          * <p>Java class for anonymous complex type.
6238          * 
6239          * <p>The following schema fragment specifies the expected content contained within this class.
6240          * 
6241          * <pre>
6242          * &lt;complexType>
6243          *   &lt;complexContent>
6244          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6245          *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6246          *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6247          *     &lt;/restriction>
6248          *   &lt;/complexContent>
6249          * &lt;/complexType>
6250          * </pre>
6251          * 
6252          * 
6253          */
6254         @XmlAccessorType(XmlAccessType.FIELD)
6255         @XmlType(name = "")
6256         public static class HiddenColumns {
6257
6258             @XmlAttribute(name = "start")
6259             protected Integer start;
6260             @XmlAttribute(name = "end")
6261             protected Integer end;
6262
6263             /**
6264              * Gets the value of the start property.
6265              * 
6266              * @return
6267              *     possible object is
6268              *     {@link Integer }
6269              *     
6270              */
6271             public Integer getStart() {
6272                 return start;
6273             }
6274
6275             /**
6276              * Sets the value of the start property.
6277              * 
6278              * @param value
6279              *     allowed object is
6280              *     {@link Integer }
6281              *     
6282              */
6283             public void setStart(Integer value) {
6284                 this.start = value;
6285             }
6286
6287             /**
6288              * Gets the value of the end property.
6289              * 
6290              * @return
6291              *     possible object is
6292              *     {@link Integer }
6293              *     
6294              */
6295             public Integer getEnd() {
6296                 return end;
6297             }
6298
6299             /**
6300              * Sets the value of the end property.
6301              * 
6302              * @param value
6303              *     allowed object is
6304              *     {@link Integer }
6305              *     
6306              */
6307             public void setEnd(Integer value) {
6308                 this.end = value;
6309             }
6310
6311         }
6312
6313     }
6314
6315 }