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Coverage Report

  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.xml.binding.jalview

File JalviewModel.java

 

Coverage histogram

../../../../img/srcFileCovDistChart9.png
13% of files have more coverage

Code metrics

88
486
398
21
6,911
2,400
442
0.91
1.22
18.95
1.11

Classes

Class Line # Actions
JalviewModel 396 26 20
0.8461538684.6%
JalviewModel.FeatureSettings 731 6 4
1.0100%
JalviewModel.FeatureSettings.Group 812 4 4
1.0100%
JalviewModel.FeatureSettings.Setting 906 31 29
0.967741996.8%
JalviewModel.JGroup 1328 51 46
0.941176594.1%
JalviewModel.JSeq 1992 24 20
0.979166797.9%
JalviewModel.JSeq.Pdbids 2291 3 2
1.0100%
JalviewModel.JSeq.Pdbids.StructureState 2352 28 25
0.821428682.1%
JalviewModel.JSeq.RnaViewer 2704 19 18
0.00%
JalviewModel.JSeq.RnaViewer.SecondaryStructure 2969 8 8
0.00%
JalviewModel.PcaViewer 3144 46 44
1.0100%
JalviewModel.PcaViewer.Axis 3741 6 6
1.0100%
JalviewModel.PcaViewer.SeqPointMax 3840 6 6
1.0100%
JalviewModel.PcaViewer.SeqPointMin 3939 6 6
1.0100%
JalviewModel.PcaViewer.SequencePoint 4040 8 8
1.0100%
JalviewModel.Tree 4194 42 40
0.904761990.5%
JalviewModel.UserColours 4730 4 4
0.00%
JalviewModel.Viewport 4930 138 123
0.913043591.3%
JalviewModel.Viewport.CalcIdParam 6485 8 7
0.00%
JalviewModel.Viewport.HiddenColumns 6589 4 4
1.0100%
JalviewModel.Viewport.Overview 6670 18 18
1.0100%
 

Contributing tests

This file is covered by 32 tests. .

Source view

1    //
2    // This file was generated by the Eclipse Implementation of JAXB, v2.3.3
3    // See https://eclipse-ee4j.github.io/jaxb-ri
4    // Any modifications to this file will be lost upon recompilation of the source schema.
5    // Generated on: 2023.11.01 at 07:03:09 PM GMT
6    //
7   
8    package jalview.xml.binding.jalview;
9   
10    import java.util.ArrayList;
11    import java.util.List;
12    import javax.xml.bind.annotation.XmlAccessType;
13    import javax.xml.bind.annotation.XmlAccessorType;
14    import javax.xml.bind.annotation.XmlAttribute;
15    import javax.xml.bind.annotation.XmlElement;
16    import javax.xml.bind.annotation.XmlID;
17    import javax.xml.bind.annotation.XmlSchemaType;
18    import javax.xml.bind.annotation.XmlType;
19    import javax.xml.bind.annotation.XmlValue;
20    import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
21    import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
22    import javax.xml.datatype.XMLGregorianCalendar;
23   
24    /**
25    * <p>Java class for JalviewModel complex type.
26    *
27    * <p>The following schema fragment specifies the expected content
28    * contained within this class.
29    *
30    * <pre> <complexType name="JalviewModel">
31    * <complexContent> <restriction
32    * base="{http://www.w3.org/2001/XMLSchema}anyType">
33    * <sequence> <element name="creationDate"
34    * type="{http://www.w3.org/2001/XMLSchema}dateTime"/> <element
35    * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
36    * <element name="vamsasModel"
37    * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
38    * <sequence> <element name="JSeq" maxOccurs="unbounded"
39    * minOccurs="0"> <complexType>
40    * <complexContent> <restriction
41    * base="{http://www.w3.org/2001/XMLSchema}anyType">
42    * <sequence> <element name="features"
43    * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
44    * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
45    * <complexType> <complexContent> <extension
46    * base="{www.jalview.org}pdbentry"> <sequence>
47    * <element name="structureState" maxOccurs="unbounded"
48    * minOccurs="0"> <complexType>
49    * <simpleContent> <extension
50    * base="<http://www.w3.org/2001/XMLSchema>string">
51    * <attGroup ref="{www.jalview.org}swingwindow"/>
52    * <attribute name="visible"
53    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
54    * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
55    * <attribute name="alignwithAlignPanel"
56    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
57    * <attribute name="colourwithAlignPanel"
58    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
59    * <attribute name="colourByJmol"
60    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61    * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
62    * /> </extension> </simpleContent>
63    * </complexType> </element>
64    * </sequence> </extension>
65    * </complexContent> </complexType>
66    * </element> <element name="hiddenSequences"
67    * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
68    * minOccurs="0"/> <element name="rnaViewer" maxOccurs="unbounded"
69    * minOccurs="0"> <complexType>
70    * <complexContent> <restriction
71    * base="{http://www.w3.org/2001/XMLSchema}anyType">
72    * <sequence> <element name="secondaryStructure"
73    * maxOccurs="unbounded"> <complexType>
74    * <complexContent> <restriction
75    * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attribute
76    * name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
77    * <attribute name="annotationId" use="required"
78    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
79    * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
80    * <attribute name="viewerState"
81    * type="{http://www.w3.org/2001/XMLSchema}string" />
82    * </restriction> </complexContent>
83    * </complexType> </element>
84    * </sequence> <attGroup
85    * ref="{www.jalview.org}swingwindow"/> <attribute name="title"
86    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
87    * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
88    * <attribute name="dividerLocation"
89    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
90    * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
91    * </restriction> </complexContent>
92    * </complexType> </element>
93    * </sequence> <attribute name="colour"
94    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
95    * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
96    * /> <attribute name="end" use="required"
97    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
98    * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
99    * /> <attribute name="hidden"
100    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
101    * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
102    * /> </restriction> </complexContent>
103    * </complexType> </element> <element
104    * name="JGroup" maxOccurs="unbounded" minOccurs="0">
105    * <complexType> <complexContent>
106    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
107    * <sequence> <element name="seq"
108    * type="{http://www.w3.org/2001/XMLSchema}string"
109    * maxOccurs="unbounded"/> <element name="annotationColours"
110    * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
111    * </sequence> <attribute name="start"
112    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
113    * name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
114    * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
115    * /> <attribute name="colour"
116    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
117    * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
118    * <attribute name="pidThreshold"
119    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
120    * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
121    * <attribute name="displayBoxes"
122    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
123    * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
124    * <attribute name="colourText"
125    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
126    * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
127    * <attribute name="textCol2"
128    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
129    * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
130    * /> <attribute name="showUnconserved"
131    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
132    * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
133    * default="true" /> <attribute name="showConsensusHistogram"
134    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
135    * <attribute name="showSequenceLogo"
136    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
137    * <attribute name="normaliseSequenceLogo"
138    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
139    * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
140    * /> </restriction> </complexContent>
141    * </complexType> </element> <element
142    * name="Viewport" maxOccurs="unbounded" minOccurs="0">
143    * <complexType> <complexContent>
144    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
145    * <sequence> <element name="AnnotationColours"
146    * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147    * <element name="hiddenColumns" maxOccurs="unbounded"
148    * minOccurs="0"> <complexType>
149    * <complexContent> <restriction
150    * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attribute
151    * name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152    * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
153    * /> </restriction> </complexContent>
154    * </complexType> </element> <element
155    * name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
156    * <complexType> <complexContent> <extension
157    * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
158    * <attribute name="calcId" use="required"
159    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
160    * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
161    * default="false" /> <attribute name="autoUpdate" use="required"
162    * type="{http://www.w3.org/2001/XMLSchema}boolean" />
163    * </extension> </complexContent>
164    * </complexType> </element> <element
165    * name="overview" minOccurs="0"> <complexType>
166    * <complexContent> <restriction
167    * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
168    * ref="{www.jalview.org}swingwindow"/> <attribute
169    * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
170    * <attribute name="residueColour"
171    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
172    * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
173    * <attribute name="hiddenColour"
174    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
175    * name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
176    * </restriction> </complexContent>
177    * </complexType> </element>
178    * </sequence> <attGroup
179    * ref="{www.jalview.org}swingwindow"/> <attribute
180    * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
181    * /> <attribute name="pidSelected"
182    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
183    * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
184    * <attribute name="consThreshold"
185    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
186    * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
187    * <attribute name="title"
188    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
189    * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
190    * <attribute name="rightAlignIds"
191    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
192    * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
193    * <attribute name="showColourText"
194    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
195    * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
196    * default="false" /> <attribute name="showBoxes"
197    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
198    * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
199    * /> <attribute name="renderGaps"
200    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
201    * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
202    * /> <attribute name="showNPfeatureTooltip"
203    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
204    * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
205    * /> <attribute name="followHighlight"
206    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
207    * <attribute name="followSelection"
208    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
209    * <attribute name="showAnnotation"
210    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
211    * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
212    * default="false" /> <attribute name="showGroupConservation"
213    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
214    * <attribute name="showGroupConsensus"
215    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
216    * <attribute name="showConsensusHistogram"
217    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
218    * <attribute name="showSequenceLogo"
219    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
220    * <attribute name="normaliseSequenceLogo"
221    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
222    * <attribute name="ignoreGapsinConsensus"
223    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
224    * <attribute name="startRes"
225    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
226    * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
227    * <attribute name="charWidth"
228    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
229    * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
230    * <attribute name="fontName"
231    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
232    * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
233    * <attribute name="fontStyle"
234    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
235    * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
236    * <attribute name="idWidthManuallyAdjusted"
237    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
238    * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
239    * default="true" /> <attribute name="viewName"
240    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
241    * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
242    * /> <attribute name="gatheredViews"
243    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
244    * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
245    * <attribute name="textCol2"
246    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
247    * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
248    * /> <attribute name="id"
249    * type="{http://www.w3.org/2001/XMLSchema}ID" /> <attribute
250    * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
251    * <attribute name="showComplementFeatures"
252    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
253    * <attribute name="showComplementFeaturesOnTop"
254    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
255    * </restriction> </complexContent>
256    * </complexType> </element> <element
257    * name="UserColours" maxOccurs="unbounded" minOccurs="0">
258    * <complexType> <complexContent>
259    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
260    * <sequence> <element name="UserColourScheme"
261    * type="{www.jalview.org/colours}JalviewUserColours"/>
262    * </sequence> <attribute name="id"
263    * type="{http://www.w3.org/2001/XMLSchema}string" />
264    * </restriction> </complexContent>
265    * </complexType> </element> <element
266    * name="tree" maxOccurs="unbounded" minOccurs="0">
267    * <complexType> <complexContent>
268    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
269    * <sequence minOccurs="0"> <element name="title"
270    * type="{http://www.w3.org/2001/XMLSchema}string"/> <element
271    * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
272    * </sequence> <attGroup
273    * ref="{www.jalview.org}swingwindow"/> <attribute name="fontName"
274    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
275    * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
276    * <attribute name="fontStyle"
277    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
278    * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
279    * <attribute name="showBootstrap"
280    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
281    * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
282    * /> <attribute name="markUnlinked"
283    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
284    * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
285    * <attribute name="currentTree"
286    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
287    * name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean"
288    * default="false" /> <attribute name="columnReference"
289    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
290    * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
291    * <attribute name="linkToAllViews"
292    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
293    * </restriction> </complexContent>
294    * </complexType> </element> <element
295    * name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
296    * <complexType> <complexContent>
297    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
298    * <sequence> <element name="sequencePoint"
299    * maxOccurs="unbounded"> <complexType>
300    * <complexContent> <restriction
301    * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
302    * ref="{www.jalview.org}position"/> <attribute name="sequenceRef"
303    * type="{http://www.w3.org/2001/XMLSchema}string" />
304    * </restriction> </complexContent>
305    * </complexType> </element> <element
306    * name="axis" maxOccurs="3" minOccurs="3"> <complexType>
307    * <complexContent> <restriction
308    * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
309    * ref="{www.jalview.org}position"/> </restriction>
310    * </complexContent> </complexType>
311    * </element> <element name="seqPointMin">
312    * <complexType> <complexContent>
313    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
314    * <attGroup ref="{www.jalview.org}position"/>
315    * </restriction> </complexContent>
316    * </complexType> </element> <element
317    * name="seqPointMax"> <complexType>
318    * <complexContent> <restriction
319    * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attGroup
320    * ref="{www.jalview.org}position"/> </restriction>
321    * </complexContent> </complexType>
322    * </element> <element name="pcaData"
323    * type="{www.jalview.org}PcaDataType"/> </sequence>
324    * <attGroup ref="{www.jalview.org}SimilarityParams"/>
325    * <attGroup ref="{www.jalview.org}swingwindow"/>
326    * <attribute name="title"
327    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
328    * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
329    * /> <attribute name="xDim"
330    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
331    * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
332    * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
333    * /> <attribute name="bgColour"
334    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
335    * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
336    * <attribute name="showLabels"
337    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
338    * name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean"
339    * /> </restriction> </complexContent>
340    * </complexType> </element> <element
341    * name="FeatureSettings" minOccurs="0"> <complexType>
342    * <complexContent> <restriction
343    * base="{http://www.w3.org/2001/XMLSchema}anyType">
344    * <sequence> <element name="setting" maxOccurs="unbounded"
345    * minOccurs="0"> <complexType>
346    * <complexContent> <restriction
347    * base="{http://www.w3.org/2001/XMLSchema}anyType">
348    * <sequence> <element name="attributeName"
349    * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
350    * minOccurs="0"/> <element name="matcherSet"
351    * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
352    * </sequence> <attribute name="type" use="required"
353    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
354    * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
355    * /> <attribute name="display" use="required"
356    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
357    * name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
358    * <attribute name="mincolour"
359    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
360    * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
361    * default="Min" /> <attribute name="threshold"
362    * type="{http://www.w3.org/2001/XMLSchema}float" /> <attribute
363    * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
364    * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
365    * /> <attribute name="min"
366    * type="{http://www.w3.org/2001/XMLSchema}float" /> <attribute
367    * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
368    * /> <attribute name="autoScale"
369    * type="{http://www.w3.org/2001/XMLSchema}boolean" />
370    * </restriction> </complexContent>
371    * </complexType> </element> <element
372    * name="group" maxOccurs="unbounded" minOccurs="0">
373    * <complexType> <complexContent>
374    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
375    * <attribute name="name" use="required"
376    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
377    * name="display" use="required"
378    * type="{http://www.w3.org/2001/XMLSchema}boolean" />
379    * </restriction> </complexContent>
380    * </complexType> </element>
381    * </sequence> </restriction>
382    * </complexContent> </complexType>
383    * </element> </sequence> </sequence>
384    * </restriction> </complexContent>
385    * </complexType> </pre>
386    *
387    *
388    */
389    @XmlAccessorType(XmlAccessType.FIELD)
390    @XmlType(
391    name = "JalviewModel",
392    namespace = "www.jalview.org",
393    propOrder =
394    { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
395    "userColours", "tree", "pcaViewer", "featureSettings" })
 
396    public class JalviewModel
397    {
398   
399    @XmlElement(required = true)
400    @XmlSchemaType(name = "dateTime")
401    protected XMLGregorianCalendar creationDate;
402   
403    @XmlElement(required = true)
404    protected String version;
405   
406    @XmlElement(required = true)
407    protected VAMSAS vamsasModel;
408   
409    @XmlElement(name = "JSeq")
410    protected List<JalviewModel.JSeq> jSeq;
411   
412    @XmlElement(name = "JGroup")
413    protected List<JalviewModel.JGroup> jGroup;
414   
415    @XmlElement(name = "Viewport")
416    protected List<JalviewModel.Viewport> viewport;
417   
418    @XmlElement(name = "UserColours")
419    protected List<JalviewModel.UserColours> userColours;
420   
421    protected List<JalviewModel.Tree> tree;
422   
423    @XmlElement(name = "PcaViewer")
424    protected List<JalviewModel.PcaViewer> pcaViewer;
425   
426    @XmlElement(name = "FeatureSettings")
427    protected JalviewModel.FeatureSettings featureSettings;
428   
429    /**
430    * Gets the value of the creationDate property.
431    *
432    * @return possible object is {@link XMLGregorianCalendar }
433    *
434    */
 
435  0 toggle public XMLGregorianCalendar getCreationDate()
436    {
437  0 return creationDate;
438    }
439   
440    /**
441    * Sets the value of the creationDate property.
442    *
443    * @param value
444    * allowed object is {@link XMLGregorianCalendar }
445    *
446    */
 
447  73 toggle public void setCreationDate(XMLGregorianCalendar value)
448    {
449  73 this.creationDate = value;
450    }
451   
452    /**
453    * Gets the value of the version property.
454    *
455    * @return possible object is {@link String }
456    *
457    */
 
458  203 toggle public String getVersion()
459    {
460  203 return version;
461    }
462   
463    /**
464    * Sets the value of the version property.
465    *
466    * @param value
467    * allowed object is {@link String }
468    *
469    */
 
470  73 toggle public void setVersion(String value)
471    {
472  73 this.version = value;
473    }
474   
475    /**
476    * Gets the value of the vamsasModel property.
477    *
478    * @return possible object is {@link VAMSAS }
479    *
480    */
 
481  193 toggle public VAMSAS getVamsasModel()
482    {
483  193 return vamsasModel;
484    }
485   
486    /**
487    * Sets the value of the vamsasModel property.
488    *
489    * @param value
490    * allowed object is {@link VAMSAS }
491    *
492    */
 
493  73 toggle public void setVamsasModel(VAMSAS value)
494    {
495  73 this.vamsasModel = value;
496    }
497   
498    /**
499    * Gets the value of the jSeq property.
500    *
501    * &lt;p&gt; This accessor method returns a reference to the live list, not a
502    * snapshot. Therefore any modification you make to the returned list will be
503    * present inside the JAXB object. This is why there is not a
504    * &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
505    *
506    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
507    * getJSeq().add(newItem); &lt;/pre&gt;
508    *
509    *
510    * &lt;p&gt; Objects of the following type(s) are allowed in the list
511    * {@link JalviewModel.JSeq }
512    *
513    *
514    */
 
515  1059 toggle public List<JalviewModel.JSeq> getJSeq()
516    {
517  1059 if (jSeq == null)
518    {
519  73 jSeq = new ArrayList<JalviewModel.JSeq>();
520    }
521  1059 return this.jSeq;
522    }
523   
524    /**
525    * Gets the value of the jGroup property.
526    *
527    * &lt;p&gt; This accessor method returns a reference to the live list, not a
528    * snapshot. Therefore any modification you make to the returned list will be
529    * present inside the JAXB object. This is why there is not a
530    * &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
531    *
532    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
533    * getJGroup().add(newItem); &lt;/pre&gt;
534    *
535    *
536    * &lt;p&gt; Objects of the following type(s) are allowed in the list
537    * {@link JalviewModel.JGroup }
538    *
539    *
540    */
 
541  156 toggle public List<JalviewModel.JGroup> getJGroup()
542    {
543  156 if (jGroup == null)
544    {
545  90 jGroup = new ArrayList<JalviewModel.JGroup>();
546    }
547  156 return this.jGroup;
548    }
549   
550    /**
551    * Gets the value of the viewport property.
552    *
553    * &lt;p&gt; This accessor method returns a reference to the live list, not a
554    * snapshot. Therefore any modification you make to the returned list will be
555    * present inside the JAXB object. This is why there is not a
556    * &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
557    *
558    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
559    * getViewport().add(newItem); &lt;/pre&gt;
560    *
561    *
562    * &lt;p&gt; Objects of the following type(s) are allowed in the list
563    * {@link JalviewModel.Viewport }
564    *
565    *
566    */
 
567  406 toggle public List<JalviewModel.Viewport> getViewport()
568    {
569  406 if (viewport == null)
570    {
571  71 viewport = new ArrayList<JalviewModel.Viewport>();
572    }
573  406 return this.viewport;
574    }
575   
576    /**
577    * Gets the value of the userColours property.
578    *
579    * &lt;p&gt; This accessor method returns a reference to the live list, not a
580    * snapshot. Therefore any modification you make to the returned list will be
581    * present inside the JAXB object. This is why there is not a
582    * &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
583    *
584    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
585    * getUserColours().add(newItem); &lt;/pre&gt;
586    *
587    *
588    * &lt;p&gt; Objects of the following type(s) are allowed in the list
589    * {@link JalviewModel.UserColours }
590    *
591    *
592    */
 
593  0 toggle public List<JalviewModel.UserColours> getUserColours()
594    {
595  0 if (userColours == null)
596    {
597  0 userColours = new ArrayList<JalviewModel.UserColours>();
598    }
599  0 return this.userColours;
600    }
601   
602    /**
603    * Gets the value of the tree property.
604    *
605    * &lt;p&gt; This accessor method returns a reference to the live list, not a
606    * snapshot. Therefore any modification you make to the returned list will be
607    * present inside the JAXB object. This is why there is not a
608    * &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
609    *
610    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
611    * getTree().add(newItem); &lt;/pre&gt;
612    *
613    *
614    * &lt;p&gt; Objects of the following type(s) are allowed in the list
615    * {@link JalviewModel.Tree }
616    *
617    *
618    */
 
619  103 toggle public List<JalviewModel.Tree> getTree()
620    {
621  103 if (tree == null)
622    {
623  67 tree = new ArrayList<JalviewModel.Tree>();
624    }
625  103 return this.tree;
626    }
627   
628    /**
629    * Gets the value of the pcaViewer property.
630    *
631    * &lt;p&gt; This accessor method returns a reference to the live list, not a
632    * snapshot. Therefore any modification you make to the returned list will be
633    * present inside the JAXB object. This is why there is not a
634    * &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
635    *
636    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
637    * getPcaViewer().add(newItem); &lt;/pre&gt;
638    *
639    *
640    * &lt;p&gt; Objects of the following type(s) are allowed in the list
641    * {@link JalviewModel.PcaViewer }
642    *
643    *
644    */
 
645  151 toggle public List<JalviewModel.PcaViewer> getPcaViewer()
646    {
647  151 if (pcaViewer == null)
648    {
649  75 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
650    }
651  151 return this.pcaViewer;
652    }
653   
654    /**
655    * Gets the value of the featureSettings property.
656    *
657    * @return possible object is {@link JalviewModel.FeatureSettings }
658    *
659    */
 
660  2071 toggle public JalviewModel.FeatureSettings getFeatureSettings()
661    {
662  2071 return featureSettings;
663    }
664   
665    /**
666    * Sets the value of the featureSettings property.
667    *
668    * @param value
669    * allowed object is {@link JalviewModel.FeatureSettings }
670    *
671    */
 
672  11 toggle public void setFeatureSettings(JalviewModel.FeatureSettings value)
673    {
674  11 this.featureSettings = value;
675    }
676   
677    /**
678    * &lt;p&gt;Java class for anonymous complex type.
679    *
680    * &lt;p&gt;The following schema fragment specifies the expected content
681    * contained within this class.
682    *
683    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
684    * &amp;lt;restriction
685    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
686    * &amp;lt;sequence&amp;gt; &amp;lt;element name="setting"
687    * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
688    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
689    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
690    * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
691    * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
692    * minOccurs="0"/&amp;gt; &amp;lt;element name="matcherSet"
693    * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
694    * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="type" use="required"
695    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
696    * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
697    * /&amp;gt; &amp;lt;attribute name="display" use="required"
698    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
699    * &amp;lt;attribute name="order"
700    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
701    * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
702    * &amp;lt;attribute name="noValueColour"
703    * type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
704    * &amp;lt;attribute name="threshold"
705    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
706    * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
707    * &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
708    * /&amp;gt; &amp;lt;attribute name="min"
709    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
710    * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
711    * /&amp;gt; &amp;lt;attribute name="autoScale"
712    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
713    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
714    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
715    * name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
716    * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
717    * &amp;lt;restriction
718    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
719    * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
720    * /&amp;gt; &amp;lt;attribute name="display" use="required"
721    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
722    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
723    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
724    * &amp;lt;/sequence&amp;gt; &amp;lt;/restriction&amp;gt;
725    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
726    *
727    *
728    */
729    @XmlAccessorType(XmlAccessType.FIELD)
730    @XmlType(name = "", propOrder = { "setting", "group" })
 
731    public static class FeatureSettings
732    {
733   
734    @XmlElement(namespace = "www.jalview.org")
735    protected List<JalviewModel.FeatureSettings.Setting> setting;
736   
737    @XmlElement(namespace = "www.jalview.org")
738    protected List<JalviewModel.FeatureSettings.Group> group;
739   
740    /**
741    * Gets the value of the setting property.
742    *
743    * &lt;p&gt; This accessor method returns a reference to the live list, not
744    * a snapshot. Therefore any modification you make to the returned list will
745    * be present inside the JAXB object. This is why there is not a
746    * &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
747    *
748    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
749    * getSetting().add(newItem); &lt;/pre&gt;
750    *
751    *
752    * &lt;p&gt; Objects of the following type(s) are allowed in the list
753    * {@link JalviewModel.FeatureSettings.Setting }
754    *
755    *
756    */
 
757  1887 toggle public List<JalviewModel.FeatureSettings.Setting> getSetting()
758    {
759  1887 if (setting == null)
760    {
761  11 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
762    }
763  1887 return this.setting;
764    }
765   
766    /**
767    * Gets the value of the group property.
768    *
769    * &lt;p&gt; This accessor method returns a reference to the live list, not
770    * a snapshot. Therefore any modification you make to the returned list will
771    * be present inside the JAXB object. This is why there is not a
772    * &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
773    *
774    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
775    * getGroup().add(newItem); &lt;/pre&gt;
776    *
777    *
778    * &lt;p&gt; Objects of the following type(s) are allowed in the list
779    * {@link JalviewModel.FeatureSettings.Group }
780    *
781    *
782    */
 
783  323 toggle public List<JalviewModel.FeatureSettings.Group> getGroup()
784    {
785  323 if (group == null)
786    {
787  11 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
788    }
789  323 return this.group;
790    }
791   
792    /**
793    * &lt;p&gt;Java class for anonymous complex type.
794    *
795    * &lt;p&gt;The following schema fragment specifies the expected content
796    * contained within this class.
797    *
798    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
799    * &amp;lt;restriction
800    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
801    * &amp;lt;attribute name="name" use="required"
802    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
803    * &amp;lt;attribute name="display" use="required"
804    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
805    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
806    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
807    *
808    *
809    */
810    @XmlAccessorType(XmlAccessType.FIELD)
811    @XmlType(name = "")
 
812    public static class Group
813    {
814   
815    @XmlAttribute(name = "name", required = true)
816    protected String name;
817   
818    @XmlAttribute(name = "display", required = true)
819    protected boolean display;
820   
821    /**
822    * Gets the value of the name property.
823    *
824    * @return possible object is {@link String }
825    *
826    */
 
827  127 toggle public String getName()
828    {
829  127 return name;
830    }
831   
832    /**
833    * Sets the value of the name property.
834    *
835    * @param value
836    * allowed object is {@link String }
837    *
838    */
 
839  33 toggle public void setName(String value)
840    {
841  33 this.name = value;
842    }
843   
844    /**
845    * Gets the value of the display property.
846    *
847    */
 
848  127 toggle public boolean isDisplay()
849    {
850  127 return display;
851    }
852   
853    /**
854    * Sets the value of the display property.
855    *
856    */
 
857  33 toggle public void setDisplay(boolean value)
858    {
859  33 this.display = value;
860    }
861   
862    }
863   
864    /**
865    * &lt;p&gt;Java class for anonymous complex type.
866    *
867    * &lt;p&gt;The following schema fragment specifies the expected content
868    * contained within this class.
869    *
870    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
871    * &amp;lt;restriction
872    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
873    * &amp;lt;sequence&amp;gt; &amp;lt;element name="attributeName"
874    * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
875    * minOccurs="0"/&amp;gt; &amp;lt;element name="matcherSet"
876    * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
877    * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="type" use="required"
878    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
879    * &amp;lt;attribute name="colour" use="required"
880    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
881    * name="display" use="required"
882    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
883    * &amp;lt;attribute name="order"
884    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
885    * &amp;lt;attribute name="mincolour"
886    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
887    * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
888    * default="Min" /&amp;gt; &amp;lt;attribute name="threshold"
889    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
890    * &amp;lt;attribute name="threshstate"
891    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
892    * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
893    * &amp;lt;attribute name="min"
894    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
895    * &amp;lt;attribute name="colourByLabel"
896    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
897    * &amp;lt;attribute name="autoScale"
898    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
899    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
900    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
901    *
902    *
903    */
904    @XmlAccessorType(XmlAccessType.FIELD)
905    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
 
906    public static class Setting
907    {
908   
909    @XmlElement(namespace = "www.jalview.org")
910    protected List<String> attributeName;
911   
912    @XmlElement(namespace = "www.jalview.org")
913    protected FeatureMatcherSet matcherSet;
914   
915    @XmlAttribute(name = "type", required = true)
916    protected String type;
917   
918    @XmlAttribute(name = "colour", required = true)
919    protected int colour;
920   
921    @XmlAttribute(name = "display", required = true)
922    protected boolean display;
923   
924    @XmlAttribute(name = "order")
925    protected Float order;
926   
927    @XmlAttribute(name = "mincolour")
928    protected Integer mincolour;
929   
930    @XmlAttribute(name = "noValueColour")
931    protected NoValueColour noValueColour;
932   
933    @XmlAttribute(name = "threshold")
934    protected Float threshold;
935   
936    @XmlAttribute(name = "threshstate")
937    protected Integer threshstate;
938   
939    @XmlAttribute(name = "max")
940    protected Float max;
941   
942    @XmlAttribute(name = "min")
943    protected Float min;
944   
945    @XmlAttribute(name = "colourByLabel")
946    protected Boolean colourByLabel;
947   
948    @XmlAttribute(name = "autoScale")
949    protected Boolean autoScale;
950   
951    /**
952    * Gets the value of the attributeName property.
953    *
954    * &lt;p&gt; This accessor method returns a reference to the live list,
955    * not a snapshot. Therefore any modification you make to the returned
956    * list will be present inside the JAXB object. This is why there is not a
957    * &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
958    *
959    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
960    * getAttributeName().add(newItem); &lt;/pre&gt;
961    *
962    *
963    * &lt;p&gt; Objects of the following type(s) are allowed in the list
964    * {@link String }
965    *
966    *
967    */
 
968  12 toggle public List<String> getAttributeName()
969    {
970  12 if (attributeName == null)
971    {
972  5 attributeName = new ArrayList<String>();
973    }
974  12 return this.attributeName;
975    }
976   
977    /**
978    * Gets the value of the matcherSet property.
979    *
980    * @return possible object is {@link FeatureMatcherSet }
981    *
982    */
 
983  812 toggle public FeatureMatcherSet getMatcherSet()
984    {
985  812 return matcherSet;
986    }
987   
988    /**
989    * Sets the value of the matcherSet property.
990    *
991    * @param value
992    * allowed object is {@link FeatureMatcherSet }
993    *
994    */
 
995  3 toggle public void setMatcherSet(FeatureMatcherSet value)
996    {
997  3 this.matcherSet = value;
998    }
999   
1000    /**
1001    * Gets the value of the type property.
1002    *
1003    * @return possible object is {@link String }
1004    *
1005    */
 
1006  812 toggle public String getType()
1007    {
1008  812 return type;
1009    }
1010   
1011    /**
1012    * Sets the value of the type property.
1013    *
1014    * @param value
1015    * allowed object is {@link String }
1016    *
1017    */
 
1018  191 toggle public void setType(String value)
1019    {
1020  191 this.type = value;
1021    }
1022   
1023    /**
1024    * Gets the value of the colour property.
1025    *
1026    */
 
1027  812 toggle public int getColour()
1028    {
1029  812 return colour;
1030    }
1031   
1032    /**
1033    * Sets the value of the colour property.
1034    *
1035    */
 
1036  191 toggle public void setColour(int value)
1037    {
1038  191 this.colour = value;
1039    }
1040   
1041    /**
1042    * Gets the value of the display property.
1043    *
1044    */
 
1045  812 toggle public boolean isDisplay()
1046    {
1047  812 return display;
1048    }
1049   
1050    /**
1051    * Sets the value of the display property.
1052    *
1053    */
 
1054  191 toggle public void setDisplay(boolean value)
1055    {
1056  191 this.display = value;
1057    }
1058   
1059    /**
1060    * Gets the value of the order property.
1061    *
1062    * @return possible object is {@link Float }
1063    *
1064    */
 
1065  1624 toggle public Float getOrder()
1066    {
1067  1624 return order;
1068    }
1069   
1070    /**
1071    * Sets the value of the order property.
1072    *
1073    * @param value
1074    * allowed object is {@link Float }
1075    *
1076    */
 
1077  191 toggle public void setOrder(Float value)
1078    {
1079  191 this.order = value;
1080    }
1081   
1082    /**
1083    * Gets the value of the mincolour property.
1084    *
1085    * @return possible object is {@link Integer }
1086    *
1087    */
 
1088  817 toggle public Integer getMincolour()
1089    {
1090  817 return mincolour;
1091    }
1092   
1093    /**
1094    * Sets the value of the mincolour property.
1095    *
1096    * @param value
1097    * allowed object is {@link Integer }
1098    *
1099    */
 
1100  4 toggle public void setMincolour(Integer value)
1101    {
1102  4 this.mincolour = value;
1103    }
1104   
1105    /**
1106    * Gets the value of the noValueColour property.
1107    *
1108    * @return possible object is {@link NoValueColour }
1109    *
1110    */
 
1111  5 toggle public NoValueColour getNoValueColour()
1112    {
1113  5 if (noValueColour == null)
1114    {
1115  0 return NoValueColour.MIN;
1116    }
1117    else
1118    {
1119  5 return noValueColour;
1120    }
1121    }
1122   
1123    /**
1124    * Sets the value of the noValueColour property.
1125    *
1126    * @param value
1127    * allowed object is {@link NoValueColour }
1128    *
1129    */
 
1130  4 toggle public void setNoValueColour(NoValueColour value)
1131    {
1132  4 this.noValueColour = value;
1133    }
1134   
1135    /**
1136    * Gets the value of the threshold property.
1137    *
1138    * @return possible object is {@link Float }
1139    *
1140    */
 
1141  10 toggle public Float getThreshold()
1142    {
1143  10 return threshold;
1144    }
1145   
1146    /**
1147    * Sets the value of the threshold property.
1148    *
1149    * @param value
1150    * allowed object is {@link Float }
1151    *
1152    */
 
1153  4 toggle public void setThreshold(Float value)
1154    {
1155  4 this.threshold = value;
1156    }
1157   
1158    /**
1159    * Gets the value of the threshstate property.
1160    *
1161    * @return possible object is {@link Integer }
1162    *
1163    */
 
1164  5 toggle public Integer getThreshstate()
1165    {
1166  5 return threshstate;
1167    }
1168   
1169    /**
1170    * Sets the value of the threshstate property.
1171    *
1172    * @param value
1173    * allowed object is {@link Integer }
1174    *
1175    */
 
1176  4 toggle public void setThreshstate(Integer value)
1177    {
1178  4 this.threshstate = value;
1179    }
1180   
1181    /**
1182    * Gets the value of the max property.
1183    *
1184    * @return possible object is {@link Float }
1185    *
1186    */
 
1187  10 toggle public Float getMax()
1188    {
1189  10 return max;
1190    }
1191   
1192    /**
1193    * Sets the value of the max property.
1194    *
1195    * @param value
1196    * allowed object is {@link Float }
1197    *
1198    */
 
1199  4 toggle public void setMax(Float value)
1200    {
1201  4 this.max = value;
1202    }
1203   
1204    /**
1205    * Gets the value of the min property.
1206    *
1207    * @return possible object is {@link Float }
1208    *
1209    */
 
1210  5 toggle public Float getMin()
1211    {
1212  5 return min;
1213    }
1214   
1215    /**
1216    * Sets the value of the min property.
1217    *
1218    * @param value
1219    * allowed object is {@link Float }
1220    *
1221    */
 
1222  4 toggle public void setMin(Float value)
1223    {
1224  4 this.min = value;
1225    }
1226   
1227    /**
1228    * Gets the value of the colourByLabel property.
1229    *
1230    * @return possible object is {@link Boolean }
1231    *
1232    */
 
1233  10 toggle public Boolean isColourByLabel()
1234    {
1235  10 return colourByLabel;
1236    }
1237   
1238    /**
1239    * Sets the value of the colourByLabel property.
1240    *
1241    * @param value
1242    * allowed object is {@link Boolean }
1243    *
1244    */
 
1245  4 toggle public void setColourByLabel(Boolean value)
1246    {
1247  4 this.colourByLabel = value;
1248    }
1249   
1250    /**
1251    * Gets the value of the autoScale property.
1252    *
1253    * @return possible object is {@link Boolean }
1254    *
1255    */
 
1256  10 toggle public Boolean isAutoScale()
1257    {
1258  10 return autoScale;
1259    }
1260   
1261    /**
1262    * Sets the value of the autoScale property.
1263    *
1264    * @param value
1265    * allowed object is {@link Boolean }
1266    *
1267    */
 
1268  4 toggle public void setAutoScale(Boolean value)
1269    {
1270  4 this.autoScale = value;
1271    }
1272   
1273    }
1274   
1275    }
1276   
1277    /**
1278    * &lt;p&gt;Java class for anonymous complex type.
1279    *
1280    * &lt;p&gt;The following schema fragment specifies the expected content
1281    * contained within this class.
1282    *
1283    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
1284    * &amp;lt;restriction
1285    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1286    * &amp;lt;sequence&amp;gt; &amp;lt;element name="seq"
1287    * type="{http://www.w3.org/2001/XMLSchema}string"
1288    * maxOccurs="unbounded"/&amp;gt; &amp;lt;element name="annotationColours"
1289    * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
1290    * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="start"
1291    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1292    * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1293    * &amp;lt;attribute name="name"
1294    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1295    * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1296    * &amp;lt;attribute name="consThreshold"
1297    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1298    * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1299    * &amp;lt;attribute name="outlineColour"
1300    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1301    * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
1302    * /&amp;gt; &amp;lt;attribute name="displayText"
1303    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1304    * &amp;lt;attribute name="colourText"
1305    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1306    * &amp;lt;attribute name="textCol1"
1307    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1308    * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1309    * &amp;lt;attribute name="textColThreshold"
1310    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1311    * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
1312    * /&amp;gt; &amp;lt;attribute name="ignoreGapsinConsensus"
1313    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1314    * &amp;lt;attribute name="showConsensusHistogram"
1315    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1316    * &amp;lt;attribute name="showSequenceLogo"
1317    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1318    * &amp;lt;attribute name="normaliseSequenceLogo"
1319    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1320    * &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
1321    * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1322    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
1323    *
1324    *
1325    */
1326    @XmlAccessorType(XmlAccessType.FIELD)
1327    @XmlType(name = "", propOrder = { "seq", "annotationColours" })
 
1328    public static class JGroup
1329    {
1330   
1331    @XmlElement(namespace = "www.jalview.org", required = true)
1332    protected List<String> seq;
1333   
1334    @XmlElement(namespace = "www.jalview.org")
1335    protected AnnotationColourScheme annotationColours;
1336   
1337    @XmlAttribute(name = "start")
1338    protected Integer start;
1339   
1340    @XmlAttribute(name = "end")
1341    protected Integer end;
1342   
1343    @XmlAttribute(name = "name")
1344    protected String name;
1345   
1346    @XmlAttribute(name = "colour")
1347    protected String colour;
1348   
1349    @XmlAttribute(name = "consThreshold")
1350    protected Integer consThreshold;
1351   
1352    @XmlAttribute(name = "pidThreshold")
1353    protected Integer pidThreshold;
1354   
1355    @XmlAttribute(name = "outlineColour")
1356    protected Integer outlineColour;
1357   
1358    @XmlAttribute(name = "displayBoxes")
1359    protected Boolean displayBoxes;
1360   
1361    @XmlAttribute(name = "displayText")
1362    protected Boolean displayText;
1363   
1364    @XmlAttribute(name = "colourText")
1365    protected Boolean colourText;
1366   
1367    @XmlAttribute(name = "textCol1")
1368    protected Integer textCol1;
1369   
1370    @XmlAttribute(name = "textCol2")
1371    protected Integer textCol2;
1372   
1373    @XmlAttribute(name = "textColThreshold")
1374    protected Integer textColThreshold;
1375   
1376    @XmlAttribute(name = "showUnconserved")
1377    protected Boolean showUnconserved;
1378   
1379    @XmlAttribute(name = "ignoreGapsinConsensus")
1380    protected Boolean ignoreGapsinConsensus;
1381   
1382    @XmlAttribute(name = "showConsensusHistogram")
1383    protected Boolean showConsensusHistogram;
1384   
1385    @XmlAttribute(name = "showSequenceLogo")
1386    protected Boolean showSequenceLogo;
1387   
1388    @XmlAttribute(name = "normaliseSequenceLogo")
1389    protected Boolean normaliseSequenceLogo;
1390   
1391    @XmlAttribute(name = "id")
1392    protected String id;
1393   
1394    /**
1395    * Gets the value of the seq property.
1396    *
1397    * &lt;p&gt; This accessor method returns a reference to the live list, not
1398    * a snapshot. Therefore any modification you make to the returned list will
1399    * be present inside the JAXB object. This is why there is not a
1400    * &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
1401    *
1402    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
1403    * getSeq().add(newItem); &lt;/pre&gt;
1404    *
1405    *
1406    * &lt;p&gt; Objects of the following type(s) are allowed in the list
1407    * {@link String }
1408    *
1409    *
1410    */
 
1411  929 toggle public List<String> getSeq()
1412    {
1413  929 if (seq == null)
1414    {
1415  15 seq = new ArrayList<String>();
1416    }
1417  929 return this.seq;
1418    }
1419   
1420    /**
1421    * Gets the value of the annotationColours property.
1422    *
1423    * @return possible object is {@link AnnotationColourScheme }
1424    *
1425    */
 
1426  2 toggle public AnnotationColourScheme getAnnotationColours()
1427    {
1428  2 return annotationColours;
1429    }
1430   
1431    /**
1432    * Sets the value of the annotationColours property.
1433    *
1434    * @param value
1435    * allowed object is {@link AnnotationColourScheme }
1436    *
1437    */
 
1438  1 toggle public void setAnnotationColours(AnnotationColourScheme value)
1439    {
1440  1 this.annotationColours = value;
1441    }
1442   
1443    /**
1444    * Gets the value of the start property.
1445    *
1446    * @return possible object is {@link Integer }
1447    *
1448    */
 
1449  47 toggle public Integer getStart()
1450    {
1451  47 return start;
1452    }
1453   
1454    /**
1455    * Sets the value of the start property.
1456    *
1457    * @param value
1458    * allowed object is {@link Integer }
1459    *
1460    */
 
1461  15 toggle public void setStart(Integer value)
1462    {
1463  15 this.start = value;
1464    }
1465   
1466    /**
1467    * Gets the value of the end property.
1468    *
1469    * @return possible object is {@link Integer }
1470    *
1471    */
 
1472  47 toggle public Integer getEnd()
1473    {
1474  47 return end;
1475    }
1476   
1477    /**
1478    * Sets the value of the end property.
1479    *
1480    * @param value
1481    * allowed object is {@link Integer }
1482    *
1483    */
 
1484  15 toggle public void setEnd(Integer value)
1485    {
1486  15 this.end = value;
1487    }
1488   
1489    /**
1490    * Gets the value of the name property.
1491    *
1492    * @return possible object is {@link String }
1493    *
1494    */
 
1495  47 toggle public String getName()
1496    {
1497  47 return name;
1498    }
1499   
1500    /**
1501    * Sets the value of the name property.
1502    *
1503    * @param value
1504    * allowed object is {@link String }
1505    *
1506    */
 
1507  15 toggle public void setName(String value)
1508    {
1509  15 this.name = value;
1510    }
1511   
1512    /**
1513    * Gets the value of the colour property.
1514    *
1515    * @return possible object is {@link String }
1516    *
1517    */
 
1518  115 toggle public String getColour()
1519    {
1520  115 return colour;
1521    }
1522   
1523    /**
1524    * Sets the value of the colour property.
1525    *
1526    * @param value
1527    * allowed object is {@link String }
1528    *
1529    */
 
1530  9 toggle public void setColour(String value)
1531    {
1532  9 this.colour = value;
1533    }
1534   
1535    /**
1536    * Gets the value of the consThreshold property.
1537    *
1538    * @return possible object is {@link Integer }
1539    *
1540    */
 
1541  96 toggle public Integer getConsThreshold()
1542    {
1543  96 return consThreshold;
1544    }
1545   
1546    /**
1547    * Sets the value of the consThreshold property.
1548    *
1549    * @param value
1550    * allowed object is {@link Integer }
1551    *
1552    */
 
1553  2 toggle public void setConsThreshold(Integer value)
1554    {
1555  2 this.consThreshold = value;
1556    }
1557   
1558    /**
1559    * Gets the value of the pidThreshold property.
1560    *
1561    * @return possible object is {@link Integer }
1562    *
1563    */
 
1564  47 toggle public Integer getPidThreshold()
1565    {
1566  47 return pidThreshold;
1567    }
1568   
1569    /**
1570    * Sets the value of the pidThreshold property.
1571    *
1572    * @param value
1573    * allowed object is {@link Integer }
1574    *
1575    */
 
1576  9 toggle public void setPidThreshold(Integer value)
1577    {
1578  9 this.pidThreshold = value;
1579    }
1580   
1581    /**
1582    * Gets the value of the outlineColour property.
1583    *
1584    * @return possible object is {@link Integer }
1585    *
1586    */
 
1587  47 toggle public Integer getOutlineColour()
1588    {
1589  47 return outlineColour;
1590    }
1591   
1592    /**
1593    * Sets the value of the outlineColour property.
1594    *
1595    * @param value
1596    * allowed object is {@link Integer }
1597    *
1598    */
 
1599  15 toggle public void setOutlineColour(Integer value)
1600    {
1601  15 this.outlineColour = value;
1602    }
1603   
1604    /**
1605    * Gets the value of the displayBoxes property.
1606    *
1607    * @return possible object is {@link Boolean }
1608    *
1609    */
 
1610  47 toggle public Boolean isDisplayBoxes()
1611    {
1612  47 return displayBoxes;
1613    }
1614   
1615    /**
1616    * Sets the value of the displayBoxes property.
1617    *
1618    * @param value
1619    * allowed object is {@link Boolean }
1620    *
1621    */
 
1622  15 toggle public void setDisplayBoxes(Boolean value)
1623    {
1624  15 this.displayBoxes = value;
1625    }
1626   
1627    /**
1628    * Gets the value of the displayText property.
1629    *
1630    * @return possible object is {@link Boolean }
1631    *
1632    */
 
1633  47 toggle public Boolean isDisplayText()
1634    {
1635  47 return displayText;
1636    }
1637   
1638    /**
1639    * Sets the value of the displayText property.
1640    *
1641    * @param value
1642    * allowed object is {@link Boolean }
1643    *
1644    */
 
1645  15 toggle public void setDisplayText(Boolean value)
1646    {
1647  15 this.displayText = value;
1648    }
1649   
1650    /**
1651    * Gets the value of the colourText property.
1652    *
1653    * @return possible object is {@link Boolean }
1654    *
1655    */
 
1656  47 toggle public Boolean isColourText()
1657    {
1658  47 return colourText;
1659    }
1660   
1661    /**
1662    * Sets the value of the colourText property.
1663    *
1664    * @param value
1665    * allowed object is {@link Boolean }
1666    *
1667    */
 
1668  15 toggle public void setColourText(Boolean value)
1669    {
1670  15 this.colourText = value;
1671    }
1672   
1673    /**
1674    * Gets the value of the textCol1 property.
1675    *
1676    * @return possible object is {@link Integer }
1677    *
1678    */
 
1679  47 toggle public Integer getTextCol1()
1680    {
1681  47 return textCol1;
1682    }
1683   
1684    /**
1685    * Sets the value of the textCol1 property.
1686    *
1687    * @param value
1688    * allowed object is {@link Integer }
1689    *
1690    */
 
1691  15 toggle public void setTextCol1(Integer value)
1692    {
1693  15 this.textCol1 = value;
1694    }
1695   
1696    /**
1697    * Gets the value of the textCol2 property.
1698    *
1699    * @return possible object is {@link Integer }
1700    *
1701    */
 
1702  47 toggle public Integer getTextCol2()
1703    {
1704  47 return textCol2;
1705    }
1706   
1707    /**
1708    * Sets the value of the textCol2 property.
1709    *
1710    * @param value
1711    * allowed object is {@link Integer }
1712    *
1713    */
 
1714  15 toggle public void setTextCol2(Integer value)
1715    {
1716  15 this.textCol2 = value;
1717    }
1718   
1719    /**
1720    * Gets the value of the textColThreshold property.
1721    *
1722    * @return possible object is {@link Integer }
1723    *
1724    */
 
1725  47 toggle public Integer getTextColThreshold()
1726    {
1727  47 return textColThreshold;
1728    }
1729   
1730    /**
1731    * Sets the value of the textColThreshold property.
1732    *
1733    * @param value
1734    * allowed object is {@link Integer }
1735    *
1736    */
 
1737  15 toggle public void setTextColThreshold(Integer value)
1738    {
1739  15 this.textColThreshold = value;
1740    }
1741   
1742    /**
1743    * Gets the value of the showUnconserved property.
1744    *
1745    * @return possible object is {@link Boolean }
1746    *
1747    */
 
1748  47 toggle public Boolean isShowUnconserved()
1749    {
1750  47 return showUnconserved;
1751    }
1752   
1753    /**
1754    * Sets the value of the showUnconserved property.
1755    *
1756    * @param value
1757    * allowed object is {@link Boolean }
1758    *
1759    */
 
1760  15 toggle public void setShowUnconserved(Boolean value)
1761    {
1762  15 this.showUnconserved = value;
1763    }
1764   
1765    /**
1766    * Gets the value of the ignoreGapsinConsensus property.
1767    *
1768    * @return possible object is {@link Boolean }
1769    *
1770    */
 
1771  47 toggle public boolean isIgnoreGapsinConsensus()
1772    {
1773  47 if (ignoreGapsinConsensus == null)
1774    {
1775  0 return true;
1776    }
1777    else
1778    {
1779  47 return ignoreGapsinConsensus;
1780    }
1781    }
1782   
1783    /**
1784    * Sets the value of the ignoreGapsinConsensus property.
1785    *
1786    * @param value
1787    * allowed object is {@link Boolean }
1788    *
1789    */
 
1790  15 toggle public void setIgnoreGapsinConsensus(Boolean value)
1791    {
1792  15 this.ignoreGapsinConsensus = value;
1793    }
1794   
1795    /**
1796    * Gets the value of the showConsensusHistogram property.
1797    *
1798    * @return possible object is {@link Boolean }
1799    *
1800    */
 
1801  47 toggle public boolean isShowConsensusHistogram()
1802    {
1803  47 if (showConsensusHistogram == null)
1804    {
1805  0 return true;
1806    }
1807    else
1808    {
1809  47 return showConsensusHistogram;
1810    }
1811    }
1812   
1813    /**
1814    * Sets the value of the showConsensusHistogram property.
1815    *
1816    * @param value
1817    * allowed object is {@link Boolean }
1818    *
1819    */
 
1820  15 toggle public void setShowConsensusHistogram(Boolean value)
1821    {
1822  15 this.showConsensusHistogram = value;
1823    }
1824   
1825    /**
1826    * Gets the value of the showSequenceLogo property.
1827    *
1828    * @return possible object is {@link Boolean }
1829    *
1830    */
 
1831  47 toggle public boolean isShowSequenceLogo()
1832    {
1833  47 if (showSequenceLogo == null)
1834    {
1835  0 return false;
1836    }
1837    else
1838    {
1839  47 return showSequenceLogo;
1840    }
1841    }
1842   
1843    /**
1844    * Sets the value of the showSequenceLogo property.
1845    *
1846    * @param value
1847    * allowed object is {@link Boolean }
1848    *
1849    */
 
1850  15 toggle public void setShowSequenceLogo(Boolean value)
1851    {
1852  15 this.showSequenceLogo = value;
1853    }
1854   
1855    /**
1856    * Gets the value of the normaliseSequenceLogo property.
1857    *
1858    * @return possible object is {@link Boolean }
1859    *
1860    */
 
1861  47 toggle public boolean isNormaliseSequenceLogo()
1862    {
1863  47 if (normaliseSequenceLogo == null)
1864    {
1865  30 return false;
1866    }
1867    else
1868    {
1869  17 return normaliseSequenceLogo;
1870    }
1871    }
1872   
1873    /**
1874    * Sets the value of the normaliseSequenceLogo property.
1875    *
1876    * @param value
1877    * allowed object is {@link Boolean }
1878    *
1879    */
 
1880  15 toggle public void setNormaliseSequenceLogo(Boolean value)
1881    {
1882  15 this.normaliseSequenceLogo = value;
1883    }
1884   
1885    /**
1886    * Gets the value of the id property.
1887    *
1888    * @return possible object is {@link String }
1889    *
1890    */
 
1891  71 toggle public String getId()
1892    {
1893  71 return id;
1894    }
1895   
1896    /**
1897    * Sets the value of the id property.
1898    *
1899    * @param value
1900    * allowed object is {@link String }
1901    *
1902    */
 
1903  6 toggle public void setId(String value)
1904    {
1905  6 this.id = value;
1906    }
1907   
1908    }
1909   
1910    /**
1911    * &lt;p&gt;Java class for anonymous complex type.
1912    *
1913    * &lt;p&gt;The following schema fragment specifies the expected content
1914    * contained within this class.
1915    *
1916    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
1917    * &amp;lt;restriction
1918    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1919    * &amp;lt;sequence&amp;gt; &amp;lt;element name="features"
1920    * type="{www.jalview.org}feature" maxOccurs="unbounded"
1921    * minOccurs="0"/&amp;gt; &amp;lt;element name="pdbids" maxOccurs="unbounded"
1922    * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
1923    * &amp;lt;complexContent&amp;gt; &amp;lt;extension
1924    * base="{www.jalview.org}pdbentry"&amp;gt; &amp;lt;sequence&amp;gt;
1925    * &amp;lt;element name="structureState" maxOccurs="unbounded"
1926    * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
1927    * &amp;lt;simpleContent&amp;gt; &amp;lt;extension
1928    * base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
1929    * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
1930    * &amp;lt;attribute name="visible"
1931    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1932    * &amp;lt;attribute name="viewId"
1933    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1934    * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
1935    * default="true" /&amp;gt; &amp;lt;attribute name="colourwithAlignPanel"
1936    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
1937    * &amp;lt;attribute name="colourByJmol"
1938    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
1939    * &amp;lt;attribute name="type"
1940    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1941    * &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
1942    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
1943    * &amp;lt;/sequence&amp;gt; &amp;lt;/extension&amp;gt;
1944    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
1945    * &amp;lt;/element&amp;gt; &amp;lt;element name="hiddenSequences"
1946    * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
1947    * minOccurs="0"/&amp;gt; &amp;lt;element name="rnaViewer"
1948    * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
1949    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
1950    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
1951    * &amp;lt;sequence&amp;gt; &amp;lt;element name="secondaryStructure"
1952    * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
1953    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
1954    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
1955    * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1956    * &amp;lt;attribute name="annotationId" use="required"
1957    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1958    * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1959    * &amp;lt;attribute name="viewerState"
1960    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1961    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1962    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
1963    * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
1964    * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute name="title"
1965    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
1966    * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
1967    * &amp;lt;attribute name="dividerLocation"
1968    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1969    * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
1970    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1971    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
1972    * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="colour"
1973    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1974    * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
1975    * /&amp;gt; &amp;lt;attribute name="end" use="required"
1976    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
1977    * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
1978    * /&amp;gt; &amp;lt;attribute name="hidden"
1979    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1980    * &amp;lt;attribute name="viewreference"
1981    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
1982    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
1983    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
1984    *
1985    *
1986    */
1987    @XmlAccessorType(XmlAccessType.FIELD)
1988    @XmlType(
1989    name = "",
1990    propOrder =
1991    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
 
1992    public static class JSeq
1993    {
1994   
1995    @XmlElement(namespace = "www.jalview.org")
1996    protected List<Feature> features;
1997   
1998    @XmlElement(namespace = "www.jalview.org")
1999    protected List<JalviewModel.JSeq.Pdbids> pdbids;
2000   
2001    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
2002    protected List<Integer> hiddenSequences;
2003   
2004    @XmlElement(namespace = "www.jalview.org")
2005    protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
2006   
2007    @XmlAttribute(name = "colour")
2008    protected Integer colour;
2009   
2010    @XmlAttribute(name = "start", required = true)
2011    protected int start;
2012   
2013    @XmlAttribute(name = "end", required = true)
2014    protected int end;
2015   
2016    @XmlAttribute(name = "id", required = true)
2017    protected String id;
2018   
2019    @XmlAttribute(name = "hidden")
2020    protected Boolean hidden;
2021   
2022    @XmlAttribute(name = "viewreference")
2023    protected Boolean viewreference;
2024   
2025    /**
2026    * Gets the value of the features property.
2027    *
2028    * &lt;p&gt; This accessor method returns a reference to the live list, not
2029    * a snapshot. Therefore any modification you make to the returned list will
2030    * be present inside the JAXB object. This is why there is not a
2031    * &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
2032    *
2033    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2034    * getFeatures().add(newItem); &lt;/pre&gt;
2035    *
2036    *
2037    * &lt;p&gt; Objects of the following type(s) are allowed in the list
2038    * {@link Feature }
2039    *
2040    *
2041    */
 
2042  11962 toggle public List<Feature> getFeatures()
2043    {
2044  11962 if (features == null)
2045    {
2046  912 features = new ArrayList<Feature>();
2047    }
2048  11962 return this.features;
2049    }
2050   
2051    /**
2052    * Gets the value of the pdbids property.
2053    *
2054    * &lt;p&gt; This accessor method returns a reference to the live list, not
2055    * a snapshot. Therefore any modification you make to the returned list will
2056    * be present inside the JAXB object. This is why there is not a
2057    * &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
2058    *
2059    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2060    * getPdbids().add(newItem); &lt;/pre&gt;
2061    *
2062    *
2063    * &lt;p&gt; Objects of the following type(s) are allowed in the list
2064    * {@link JalviewModel.JSeq.Pdbids }
2065    *
2066    *
2067    */
 
2068  2178 toggle public List<JalviewModel.JSeq.Pdbids> getPdbids()
2069    {
2070  2178 if (pdbids == null)
2071    {
2072  1439 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2073    }
2074  2178 return this.pdbids;
2075    }
2076   
2077    /**
2078    * Gets the value of the hiddenSequences property.
2079    *
2080    * &lt;p&gt; This accessor method returns a reference to the live list, not
2081    * a snapshot. Therefore any modification you make to the returned list will
2082    * be present inside the JAXB object. This is why there is not a
2083    * &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
2084    *
2085    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2086    * getHiddenSequences().add(newItem); &lt;/pre&gt;
2087    *
2088    *
2089    * &lt;p&gt; Objects of the following type(s) are allowed in the list
2090    * {@link Integer }
2091    *
2092    *
2093    */
 
2094  676 toggle public List<Integer> getHiddenSequences()
2095    {
2096  676 if (hiddenSequences == null)
2097    {
2098  670 hiddenSequences = new ArrayList<Integer>();
2099    }
2100  676 return this.hiddenSequences;
2101    }
2102   
2103    /**
2104    * Gets the value of the rnaViewer property.
2105    *
2106    * &lt;p&gt; This accessor method returns a reference to the live list, not
2107    * a snapshot. Therefore any modification you make to the returned list will
2108    * be present inside the JAXB object. This is why there is not a
2109    * &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
2110    *
2111    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2112    * getRnaViewer().add(newItem); &lt;/pre&gt;
2113    *
2114    *
2115    * &lt;p&gt; Objects of the following type(s) are allowed in the list
2116    * {@link JalviewModel.JSeq.RnaViewer }
2117    *
2118    *
2119    */
 
2120  1070 toggle public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
2121    {
2122  1070 if (rnaViewer == null)
2123    {
2124  1070 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2125    }
2126  1070 return this.rnaViewer;
2127    }
2128   
2129    /**
2130    * Gets the value of the colour property.
2131    *
2132    * @return possible object is {@link Integer }
2133    *
2134    */
 
2135  1192 toggle public Integer getColour()
2136    {
2137  1192 return colour;
2138    }
2139   
2140    /**
2141    * Sets the value of the colour property.
2142    *
2143    * @param value
2144    * allowed object is {@link Integer }
2145    *
2146    */
 
2147  949 toggle public void setColour(Integer value)
2148    {
2149  949 this.colour = value;
2150    }
2151   
2152    /**
2153    * Gets the value of the start property.
2154    *
2155    */
 
2156  2608 toggle public int getStart()
2157    {
2158  2608 return start;
2159    }
2160   
2161    /**
2162    * Sets the value of the start property.
2163    *
2164    */
 
2165  949 toggle public void setStart(int value)
2166    {
2167  949 this.start = value;
2168    }
2169   
2170    /**
2171    * Gets the value of the end property.
2172    *
2173    */
 
2174  2608 toggle public int getEnd()
2175    {
2176  2608 return end;
2177    }
2178   
2179    /**
2180    * Sets the value of the end property.
2181    *
2182    */
 
2183  949 toggle public void setEnd(int value)
2184    {
2185  949 this.end = value;
2186    }
2187   
2188    /**
2189    * Gets the value of the id property.
2190    *
2191    * @return possible object is {@link String }
2192    *
2193    */
 
2194  1600 toggle public String getId()
2195    {
2196  1600 return id;
2197    }
2198   
2199    /**
2200    * Sets the value of the id property.
2201    *
2202    * @param value
2203    * allowed object is {@link String }
2204    *
2205    */
 
2206  949 toggle public void setId(String value)
2207    {
2208  949 this.id = value;
2209    }
2210   
2211    /**
2212    * Gets the value of the hidden property.
2213    *
2214    * @return possible object is {@link Boolean }
2215    *
2216    */
 
2217  2190 toggle public Boolean isHidden()
2218    {
2219  2190 return hidden;
2220    }
2221   
2222    /**
2223    * Sets the value of the hidden property.
2224    *
2225    * @param value
2226    * allowed object is {@link Boolean }
2227    *
2228    */
 
2229  190 toggle public void setHidden(Boolean value)
2230    {
2231  190 this.hidden = value;
2232    }
2233   
2234    /**
2235    * Gets the value of the viewreference property.
2236    *
2237    * @return possible object is {@link Boolean }
2238    *
2239    */
 
2240  1520 toggle public Boolean isViewreference()
2241    {
2242  1520 return viewreference;
2243    }
2244   
2245    /**
2246    * Sets the value of the viewreference property.
2247    *
2248    * @param value
2249    * allowed object is {@link Boolean }
2250    *
2251    */
 
2252  80 toggle public void setViewreference(Boolean value)
2253    {
2254  80 this.viewreference = value;
2255    }
2256   
2257    /**
2258    * &lt;p&gt;Java class for anonymous complex type.
2259    *
2260    * &lt;p&gt;The following schema fragment specifies the expected content
2261    * contained within this class.
2262    *
2263    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
2264    * &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
2265    * &amp;lt;sequence&amp;gt; &amp;lt;element name="structureState"
2266    * maxOccurs="unbounded" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
2267    * &amp;lt;simpleContent&amp;gt; &amp;lt;extension
2268    * base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2269    * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2270    * &amp;lt;attribute name="visible"
2271    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2272    * &amp;lt;attribute name="viewId"
2273    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2274    * &amp;lt;attribute name="alignwithAlignPanel"
2275    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2276    * &amp;lt;attribute name="colourwithAlignPanel"
2277    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
2278    * /&amp;gt; &amp;lt;attribute name="colourByJmol"
2279    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
2280    * &amp;lt;attribute name="type"
2281    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2282    * &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
2283    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
2284    * &amp;lt;/sequence&amp;gt; &amp;lt;/extension&amp;gt;
2285    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2286    *
2287    *
2288    */
2289    @XmlAccessorType(XmlAccessType.FIELD)
2290    @XmlType(name = "", propOrder = { "structureState" })
 
2291    public static class Pdbids extends Pdbentry
2292    {
2293   
2294    @XmlElement(namespace = "www.jalview.org")
2295    protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2296   
2297    /**
2298    * Gets the value of the structureState property.
2299    *
2300    * &lt;p&gt; This accessor method returns a reference to the live list,
2301    * not a snapshot. Therefore any modification you make to the returned
2302    * list will be present inside the JAXB object. This is why there is not a
2303    * &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
2304    *
2305    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2306    * getStructureState().add(newItem); &lt;/pre&gt;
2307    *
2308    *
2309    * &lt;p&gt; Objects of the following type(s) are allowed in the list
2310    * {@link JalviewModel.JSeq.Pdbids.StructureState }
2311    *
2312    *
2313    */
 
2314  297 toggle public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
2315    {
2316  297 if (structureState == null)
2317    {
2318  137 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2319    }
2320  297 return this.structureState;
2321    }
2322   
2323    /**
2324    * &lt;p&gt;Java class for anonymous complex type.
2325    *
2326    * &lt;p&gt;The following schema fragment specifies the expected content
2327    * contained within this class.
2328    *
2329    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;simpleContent&amp;gt;
2330    * &amp;lt;extension
2331    * base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
2332    * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
2333    * &amp;lt;attribute name="visible"
2334    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2335    * &amp;lt;attribute name="viewId"
2336    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2337    * &amp;lt;attribute name="alignwithAlignPanel"
2338    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
2339    * /&amp;gt; &amp;lt;attribute name="colourwithAlignPanel"
2340    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
2341    * /&amp;gt; &amp;lt;attribute name="colourByJmol"
2342    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
2343    * /&amp;gt; &amp;lt;attribute name="type"
2344    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2345    * &amp;lt;/extension&amp;gt; &amp;lt;/simpleContent&amp;gt;
2346    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2347    *
2348    *
2349    */
2350    @XmlAccessorType(XmlAccessType.FIELD)
2351    @XmlType(name = "", propOrder = { "value" })
 
2352    public static class StructureState
2353    {
2354   
2355    @XmlValue
2356    protected String value;
2357   
2358    @XmlAttribute(name = "visible")
2359    protected Boolean visible;
2360   
2361    @XmlAttribute(name = "viewId")
2362    protected String viewId;
2363   
2364    @XmlAttribute(name = "alignwithAlignPanel")
2365    protected Boolean alignwithAlignPanel;
2366   
2367    @XmlAttribute(name = "colourwithAlignPanel")
2368    protected Boolean colourwithAlignPanel;
2369   
2370    @XmlAttribute(name = "colourByJmol")
2371    protected Boolean colourByJmol;
2372   
2373    @XmlAttribute(name = "type")
2374    protected String type;
2375   
2376    @XmlAttribute(name = "width")
2377    protected Integer width;
2378   
2379    @XmlAttribute(name = "height")
2380    protected Integer height;
2381   
2382    @XmlAttribute(name = "xpos")
2383    protected Integer xpos;
2384   
2385    @XmlAttribute(name = "ypos")
2386    protected Integer ypos;
2387   
2388    /**
2389    * Gets the value of the value property.
2390    *
2391    * @return possible object is {@link String }
2392    *
2393    */
 
2394  110 toggle public String getValue()
2395    {
2396  110 return value;
2397    }
2398   
2399    /**
2400    * Sets the value of the value property.
2401    *
2402    * @param value
2403    * allowed object is {@link String }
2404    *
2405    */
 
2406  0 toggle public void setValue(String value)
2407    {
2408  0 this.value = value;
2409    }
2410   
2411    /**
2412    * Gets the value of the visible property.
2413    *
2414    * @return possible object is {@link Boolean }
2415    *
2416    */
 
2417  0 toggle public Boolean isVisible()
2418    {
2419  0 return visible;
2420    }
2421   
2422    /**
2423    * Sets the value of the visible property.
2424    *
2425    * @param value
2426    * allowed object is {@link Boolean }
2427    *
2428    */
 
2429  20 toggle public void setVisible(Boolean value)
2430    {
2431  20 this.visible = value;
2432    }
2433   
2434    /**
2435    * Gets the value of the viewId property.
2436    *
2437    * @return possible object is {@link String }
2438    *
2439    */
 
2440  200 toggle public String getViewId()
2441    {
2442  200 return viewId;
2443    }
2444   
2445    /**
2446    * Sets the value of the viewId property.
2447    *
2448    * @param value
2449    * allowed object is {@link String }
2450    *
2451    */
 
2452  20 toggle public void setViewId(String value)
2453    {
2454  20 this.viewId = value;
2455    }
2456   
2457    /**
2458    * Gets the value of the alignwithAlignPanel property.
2459    *
2460    * @return possible object is {@link Boolean }
2461    *
2462    */
 
2463  80 toggle public boolean isAlignwithAlignPanel()
2464    {
2465  80 if (alignwithAlignPanel == null)
2466    {
2467  0 return true;
2468    }
2469    else
2470    {
2471  80 return alignwithAlignPanel;
2472    }
2473    }
2474   
2475    /**
2476    * Sets the value of the alignwithAlignPanel property.
2477    *
2478    * @param value
2479    * allowed object is {@link Boolean }
2480    *
2481    */
 
2482  20 toggle public void setAlignwithAlignPanel(Boolean value)
2483    {
2484  20 this.alignwithAlignPanel = value;
2485    }
2486   
2487    /**
2488    * Gets the value of the colourwithAlignPanel property.
2489    *
2490    * @return possible object is {@link Boolean }
2491    *
2492    */
 
2493  80 toggle public boolean isColourwithAlignPanel()
2494    {
2495  80 if (colourwithAlignPanel == null)
2496    {
2497  0 return false;
2498    }
2499    else
2500    {
2501  80 return colourwithAlignPanel;
2502    }
2503    }
2504   
2505    /**
2506    * Sets the value of the colourwithAlignPanel property.
2507    *
2508    * @param value
2509    * allowed object is {@link Boolean }
2510    *
2511    */
 
2512  20 toggle public void setColourwithAlignPanel(Boolean value)
2513    {
2514  20 this.colourwithAlignPanel = value;
2515    }
2516   
2517    /**
2518    * Gets the value of the colourByJmol property.
2519    *
2520    * @return possible object is {@link Boolean }
2521    *
2522    */
 
2523  80 toggle public boolean isColourByJmol()
2524    {
2525  80 if (colourByJmol == null)
2526    {
2527  0 return true;
2528    }
2529    else
2530    {
2531  80 return colourByJmol;
2532    }
2533    }
2534   
2535    /**
2536    * Sets the value of the colourByJmol property.
2537    *
2538    * @param value
2539    * allowed object is {@link Boolean }
2540    *
2541    */
 
2542  20 toggle public void setColourByJmol(Boolean value)
2543    {
2544  20 this.colourByJmol = value;
2545    }
2546   
2547    /**
2548    * Gets the value of the type property.
2549    *
2550    * @return possible object is {@link String }
2551    *
2552    */
 
2553  40 toggle public String getType()
2554    {
2555  40 return type;
2556    }
2557   
2558    /**
2559    * Sets the value of the type property.
2560    *
2561    * @param value
2562    * allowed object is {@link String }
2563    *
2564    */
 
2565  20 toggle public void setType(String value)
2566    {
2567  20 this.type = value;
2568    }
2569   
2570    /**
2571    * Gets the value of the width property.
2572    *
2573    * @return possible object is {@link Integer }
2574    *
2575    */
 
2576  80 toggle public Integer getWidth()
2577    {
2578  80 return width;
2579    }
2580   
2581    /**
2582    * Sets the value of the width property.
2583    *
2584    * @param value
2585    * allowed object is {@link Integer }
2586    *
2587    */
 
2588  20 toggle public void setWidth(Integer value)
2589    {
2590  20 this.width = value;
2591    }
2592   
2593    /**
2594    * Gets the value of the height property.
2595    *
2596    * @return possible object is {@link Integer }
2597    *
2598    */
 
2599  80 toggle public Integer getHeight()
2600    {
2601  80 return height;
2602    }
2603   
2604    /**
2605    * Sets the value of the height property.
2606    *
2607    * @param value
2608    * allowed object is {@link Integer }
2609    *
2610    */
 
2611  20 toggle public void setHeight(Integer value)
2612    {
2613  20 this.height = value;
2614    }
2615   
2616    /**
2617    * Gets the value of the xpos property.
2618    *
2619    * @return possible object is {@link Integer }
2620    *
2621    */
 
2622  80 toggle public Integer getXpos()
2623    {
2624  80 return xpos;
2625    }
2626   
2627    /**
2628    * Sets the value of the xpos property.
2629    *
2630    * @param value
2631    * allowed object is {@link Integer }
2632    *
2633    */
 
2634  20 toggle public void setXpos(Integer value)
2635    {
2636  20 this.xpos = value;
2637    }
2638   
2639    /**
2640    * Gets the value of the ypos property.
2641    *
2642    * @return possible object is {@link Integer }
2643    *
2644    */
 
2645  80 toggle public Integer getYpos()
2646    {
2647  80 return ypos;
2648    }
2649   
2650    /**
2651    * Sets the value of the ypos property.
2652    *
2653    * @param value
2654    * allowed object is {@link Integer }
2655    *
2656    */
 
2657  20 toggle public void setYpos(Integer value)
2658    {
2659  20 this.ypos = value;
2660    }
2661   
2662    }
2663   
2664    }
2665   
2666    /**
2667    * &lt;p&gt;Java class for anonymous complex type.
2668    *
2669    * &lt;p&gt;The following schema fragment specifies the expected content
2670    * contained within this class.
2671    *
2672    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
2673    * &amp;lt;restriction
2674    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2675    * &amp;lt;sequence&amp;gt; &amp;lt;element name="secondaryStructure"
2676    * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
2677    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
2678    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2679    * &amp;lt;attribute name="title"
2680    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2681    * &amp;lt;attribute name="annotationId" use="required"
2682    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2683    * &amp;lt;attribute name="gapped"
2684    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2685    * &amp;lt;attribute name="viewerState"
2686    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2687    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
2688    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
2689    * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
2690    * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
2691    * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2692    * &amp;lt;attribute name="viewId"
2693    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2694    * &amp;lt;attribute name="dividerLocation"
2695    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
2696    * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
2697    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
2698    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2699    *
2700    *
2701    */
2702    @XmlAccessorType(XmlAccessType.FIELD)
2703    @XmlType(name = "", propOrder = { "secondaryStructure" })
 
2704    public static class RnaViewer
2705    {
2706   
2707    @XmlElement(namespace = "www.jalview.org", required = true)
2708    protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2709   
2710    @XmlAttribute(name = "title")
2711    protected String title;
2712   
2713    @XmlAttribute(name = "viewId")
2714    protected String viewId;
2715   
2716    @XmlAttribute(name = "dividerLocation")
2717    protected Integer dividerLocation;
2718   
2719    @XmlAttribute(name = "selectedRna")
2720    protected Integer selectedRna;
2721   
2722    @XmlAttribute(name = "width")
2723    protected Integer width;
2724   
2725    @XmlAttribute(name = "height")
2726    protected Integer height;
2727   
2728    @XmlAttribute(name = "xpos")
2729    protected Integer xpos;
2730   
2731    @XmlAttribute(name = "ypos")
2732    protected Integer ypos;
2733   
2734    /**
2735    * Gets the value of the secondaryStructure property.
2736    *
2737    * &lt;p&gt; This accessor method returns a reference to the live list,
2738    * not a snapshot. Therefore any modification you make to the returned
2739    * list will be present inside the JAXB object. This is why there is not a
2740    * &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure
2741    * property.
2742    *
2743    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
2744    * getSecondaryStructure().add(newItem); &lt;/pre&gt;
2745    *
2746    *
2747    * &lt;p&gt; Objects of the following type(s) are allowed in the list
2748    * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2749    *
2750    *
2751    */
 
2752  0 toggle public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
2753    {
2754  0 if (secondaryStructure == null)
2755    {
2756  0 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2757    }
2758  0 return this.secondaryStructure;
2759    }
2760   
2761    /**
2762    * Gets the value of the title property.
2763    *
2764    * @return possible object is {@link String }
2765    *
2766    */
 
2767  0 toggle public String getTitle()
2768    {
2769  0 return title;
2770    }
2771   
2772    /**
2773    * Sets the value of the title property.
2774    *
2775    * @param value
2776    * allowed object is {@link String }
2777    *
2778    */
 
2779  0 toggle public void setTitle(String value)
2780    {
2781  0 this.title = value;
2782    }
2783   
2784    /**
2785    * Gets the value of the viewId property.
2786    *
2787    * @return possible object is {@link String }
2788    *
2789    */
 
2790  0 toggle public String getViewId()
2791    {
2792  0 return viewId;
2793    }
2794   
2795    /**
2796    * Sets the value of the viewId property.
2797    *
2798    * @param value
2799    * allowed object is {@link String }
2800    *
2801    */
 
2802  0 toggle public void setViewId(String value)
2803    {
2804  0 this.viewId = value;
2805    }
2806   
2807    /**
2808    * Gets the value of the dividerLocation property.
2809    *
2810    * @return possible object is {@link Integer }
2811    *
2812    */
 
2813  0 toggle public Integer getDividerLocation()
2814    {
2815  0 return dividerLocation;
2816    }
2817   
2818    /**
2819    * Sets the value of the dividerLocation property.
2820    *
2821    * @param value
2822    * allowed object is {@link Integer }
2823    *
2824    */
 
2825  0 toggle public void setDividerLocation(Integer value)
2826    {
2827  0 this.dividerLocation = value;
2828    }
2829   
2830    /**
2831    * Gets the value of the selectedRna property.
2832    *
2833    * @return possible object is {@link Integer }
2834    *
2835    */
 
2836  0 toggle public Integer getSelectedRna()
2837    {
2838  0 return selectedRna;
2839    }
2840   
2841    /**
2842    * Sets the value of the selectedRna property.
2843    *
2844    * @param value
2845    * allowed object is {@link Integer }
2846    *
2847    */
 
2848  0 toggle public void setSelectedRna(Integer value)
2849    {
2850  0 this.selectedRna = value;
2851    }
2852   
2853    /**
2854    * Gets the value of the width property.
2855    *
2856    * @return possible object is {@link Integer }
2857    *
2858    */
 
2859  0 toggle public Integer getWidth()
2860    {
2861  0 return width;
2862    }
2863   
2864    /**
2865    * Sets the value of the width property.
2866    *
2867    * @param value
2868    * allowed object is {@link Integer }
2869    *
2870    */
 
2871  0 toggle public void setWidth(Integer value)
2872    {
2873  0 this.width = value;
2874    }
2875   
2876    /**
2877    * Gets the value of the height property.
2878    *
2879    * @return possible object is {@link Integer }
2880    *
2881    */
 
2882  0 toggle public Integer getHeight()
2883    {
2884  0 return height;
2885    }
2886   
2887    /**
2888    * Sets the value of the height property.
2889    *
2890    * @param value
2891    * allowed object is {@link Integer }
2892    *
2893    */
 
2894  0 toggle public void setHeight(Integer value)
2895    {
2896  0 this.height = value;
2897    }
2898   
2899    /**
2900    * Gets the value of the xpos property.
2901    *
2902    * @return possible object is {@link Integer }
2903    *
2904    */
 
2905  0 toggle public Integer getXpos()
2906    {
2907  0 return xpos;
2908    }
2909   
2910    /**
2911    * Sets the value of the xpos property.
2912    *
2913    * @param value
2914    * allowed object is {@link Integer }
2915    *
2916    */
 
2917  0 toggle public void setXpos(Integer value)
2918    {
2919  0 this.xpos = value;
2920    }
2921   
2922    /**
2923    * Gets the value of the ypos property.
2924    *
2925    * @return possible object is {@link Integer }
2926    *
2927    */
 
2928  0 toggle public Integer getYpos()
2929    {
2930  0 return ypos;
2931    }
2932   
2933    /**
2934    * Sets the value of the ypos property.
2935    *
2936    * @param value
2937    * allowed object is {@link Integer }
2938    *
2939    */
 
2940  0 toggle public void setYpos(Integer value)
2941    {
2942  0 this.ypos = value;
2943    }
2944   
2945    /**
2946    * &lt;p&gt;Java class for anonymous complex type.
2947    *
2948    * &lt;p&gt;The following schema fragment specifies the expected content
2949    * contained within this class.
2950    *
2951    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
2952    * &amp;lt;restriction
2953    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
2954    * &amp;lt;attribute name="title"
2955    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2956    * &amp;lt;attribute name="annotationId" use="required"
2957    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2958    * &amp;lt;attribute name="gapped"
2959    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
2960    * &amp;lt;attribute name="viewerState"
2961    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
2962    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
2963    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
2964    *
2965    *
2966    */
2967    @XmlAccessorType(XmlAccessType.FIELD)
2968    @XmlType(name = "")
 
2969    public static class SecondaryStructure
2970    {
2971   
2972    @XmlAttribute(name = "title")
2973    protected String title;
2974   
2975    @XmlAttribute(name = "annotationId", required = true)
2976    protected String annotationId;
2977   
2978    @XmlAttribute(name = "gapped")
2979    protected Boolean gapped;
2980   
2981    @XmlAttribute(name = "viewerState")
2982    protected String viewerState;
2983   
2984    /**
2985    * Gets the value of the title property.
2986    *
2987    * @return possible object is {@link String }
2988    *
2989    */
 
2990  0 toggle public String getTitle()
2991    {
2992  0 return title;
2993    }
2994   
2995    /**
2996    * Sets the value of the title property.
2997    *
2998    * @param value
2999    * allowed object is {@link String }
3000    *
3001    */
 
3002  0 toggle public void setTitle(String value)
3003    {
3004  0 this.title = value;
3005    }
3006   
3007    /**
3008    * Gets the value of the annotationId property.
3009    *
3010    * @return possible object is {@link String }
3011    *
3012    */
 
3013  0 toggle public String getAnnotationId()
3014    {
3015  0 return annotationId;
3016    }
3017   
3018    /**
3019    * Sets the value of the annotationId property.
3020    *
3021    * @param value
3022    * allowed object is {@link String }
3023    *
3024    */
 
3025  0 toggle public void setAnnotationId(String value)
3026    {
3027  0 this.annotationId = value;
3028    }
3029   
3030    /**
3031    * Gets the value of the gapped property.
3032    *
3033    * @return possible object is {@link Boolean }
3034    *
3035    */
 
3036  0 toggle public Boolean isGapped()
3037    {
3038  0 return gapped;
3039    }
3040   
3041    /**
3042    * Sets the value of the gapped property.
3043    *
3044    * @param value
3045    * allowed object is {@link Boolean }
3046    *
3047    */
 
3048  0 toggle public void setGapped(Boolean value)
3049    {
3050  0 this.gapped = value;
3051    }
3052   
3053    /**
3054    * Gets the value of the viewerState property.
3055    *
3056    * @return possible object is {@link String }
3057    *
3058    */
 
3059  0 toggle public String getViewerState()
3060    {
3061  0 return viewerState;
3062    }
3063   
3064    /**
3065    * Sets the value of the viewerState property.
3066    *
3067    * @param value
3068    * allowed object is {@link String }
3069    *
3070    */
 
3071  0 toggle public void setViewerState(String value)
3072    {
3073  0 this.viewerState = value;
3074    }
3075   
3076    }
3077   
3078    }
3079   
3080    }
3081   
3082    /**
3083    * &lt;p&gt;Java class for anonymous complex type.
3084    *
3085    * &lt;p&gt;The following schema fragment specifies the expected content
3086    * contained within this class.
3087    *
3088    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3089    * &amp;lt;restriction
3090    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
3091    * &amp;lt;sequence&amp;gt; &amp;lt;element name="sequencePoint"
3092    * maxOccurs="unbounded"&amp;gt; &amp;lt;complexType&amp;gt;
3093    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
3094    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3095    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;attribute
3096    * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
3097    * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
3098    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
3099    * name="axis" maxOccurs="3" minOccurs="3"&amp;gt; &amp;lt;complexType&amp;gt;
3100    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
3101    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3102    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3103    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
3104    * &amp;lt;/element&amp;gt; &amp;lt;element name="seqPointMin"&amp;gt;
3105    * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3106    * &amp;lt;restriction
3107    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3108    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3109    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
3110    * &amp;lt;/element&amp;gt; &amp;lt;element name="seqPointMax"&amp;gt;
3111    * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3112    * &amp;lt;restriction
3113    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3114    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3115    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt;
3116    * &amp;lt;/element&amp;gt; &amp;lt;element name="pcaData"
3117    * type="{www.jalview.org}PcaDataType"/&amp;gt; &amp;lt;/sequence&amp;gt;
3118    * &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
3119    * &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
3120    * &amp;lt;attribute name="title"
3121    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
3122    * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
3123    * /&amp;gt; &amp;lt;attribute name="xDim"
3124    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
3125    * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
3126    * &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
3127    * /&amp;gt; &amp;lt;attribute name="bgColour"
3128    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
3129    * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
3130    * &amp;lt;attribute name="showLabels"
3131    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3132    * &amp;lt;attribute name="linkToAllViews"
3133    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
3134    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
3135    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3136    *
3137    *
3138    */
3139    @XmlAccessorType(XmlAccessType.FIELD)
3140    @XmlType(
3141    name = "",
3142    propOrder =
3143    { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
 
3144    public static class PcaViewer
3145    {
3146   
3147    @XmlElement(namespace = "www.jalview.org", required = true)
3148    protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3149   
3150    @XmlElement(namespace = "www.jalview.org", required = true)
3151    protected List<JalviewModel.PcaViewer.Axis> axis;
3152   
3153    @XmlElement(namespace = "www.jalview.org", required = true)
3154    protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3155   
3156    @XmlElement(namespace = "www.jalview.org", required = true)
3157    protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3158   
3159    @XmlElement(namespace = "www.jalview.org", required = true)
3160    protected PcaDataType pcaData;
3161   
3162    @XmlAttribute(name = "title")
3163    protected String title;
3164   
3165    @XmlAttribute(name = "scoreModelName")
3166    protected String scoreModelName;
3167   
3168    @XmlAttribute(name = "xDim")
3169    protected Integer xDim;
3170   
3171    @XmlAttribute(name = "yDim")
3172    protected Integer yDim;
3173   
3174    @XmlAttribute(name = "zDim")
3175    protected Integer zDim;
3176   
3177    @XmlAttribute(name = "bgColour")
3178    protected Integer bgColour;
3179   
3180    @XmlAttribute(name = "scaleFactor")
3181    protected Float scaleFactor;
3182   
3183    @XmlAttribute(name = "showLabels")
3184    protected Boolean showLabels;
3185   
3186    @XmlAttribute(name = "linkToAllViews")
3187    protected Boolean linkToAllViews;
3188   
3189    @XmlAttribute(name = "includeGaps")
3190    protected Boolean includeGaps;
3191   
3192    @XmlAttribute(name = "matchGaps")
3193    protected Boolean matchGaps;
3194   
3195    @XmlAttribute(name = "includeGappedColumns")
3196    protected Boolean includeGappedColumns;
3197   
3198    @XmlAttribute(name = "denominateByShortestLength")
3199    protected Boolean denominateByShortestLength;
3200   
3201    @XmlAttribute(name = "width")
3202    protected Integer width;
3203   
3204    @XmlAttribute(name = "height")
3205    protected Integer height;
3206   
3207    @XmlAttribute(name = "xpos")
3208    protected Integer xpos;
3209   
3210    @XmlAttribute(name = "ypos")
3211    protected Integer ypos;
3212   
3213    /**
3214    * Gets the value of the sequencePoint property.
3215    *
3216    * &lt;p&gt; This accessor method returns a reference to the live list, not
3217    * a snapshot. Therefore any modification you make to the returned list will
3218    * be present inside the JAXB object. This is why there is not a
3219    * &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
3220    *
3221    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
3222    * getSequencePoint().add(newItem); &lt;/pre&gt;
3223    *
3224    *
3225    * &lt;p&gt; Objects of the following type(s) are allowed in the list
3226    * {@link JalviewModel.PcaViewer.SequencePoint }
3227    *
3228    *
3229    */
 
3230  16 toggle public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
3231    {
3232  16 if (sequencePoint == null)
3233    {
3234  1 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3235    }
3236  16 return this.sequencePoint;
3237    }
3238   
3239    /**
3240    * Gets the value of the axis property.
3241    *
3242    * &lt;p&gt; This accessor method returns a reference to the live list, not
3243    * a snapshot. Therefore any modification you make to the returned list will
3244    * be present inside the JAXB object. This is why there is not a
3245    * &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
3246    *
3247    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
3248    * getAxis().add(newItem); &lt;/pre&gt;
3249    *
3250    *
3251    * &lt;p&gt; Objects of the following type(s) are allowed in the list
3252    * {@link JalviewModel.PcaViewer.Axis }
3253    *
3254    *
3255    */
 
3256  6 toggle public List<JalviewModel.PcaViewer.Axis> getAxis()
3257    {
3258  6 if (axis == null)
3259    {
3260  1 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3261    }
3262  6 return this.axis;
3263    }
3264   
3265    /**
3266    * Gets the value of the seqPointMin property.
3267    *
3268    * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
3269    *
3270    */
 
3271  1 toggle public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
3272    {
3273  1 return seqPointMin;
3274    }
3275   
3276    /**
3277    * Sets the value of the seqPointMin property.
3278    *
3279    * @param value
3280    * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
3281    *
3282    */
 
3283  1 toggle public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
3284    {
3285  1 this.seqPointMin = value;
3286    }
3287   
3288    /**
3289    * Gets the value of the seqPointMax property.
3290    *
3291    * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
3292    *
3293    */
 
3294  1 toggle public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
3295    {
3296  1 return seqPointMax;
3297    }
3298   
3299    /**
3300    * Sets the value of the seqPointMax property.
3301    *
3302    * @param value
3303    * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
3304    *
3305    */
 
3306  1 toggle public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
3307    {
3308  1 this.seqPointMax = value;
3309    }
3310   
3311    /**
3312    * Gets the value of the pcaData property.
3313    *
3314    * @return possible object is {@link PcaDataType }
3315    *
3316    */
 
3317  1 toggle public PcaDataType getPcaData()
3318    {
3319  1 return pcaData;
3320    }
3321   
3322    /**
3323    * Sets the value of the pcaData property.
3324    *
3325    * @param value
3326    * allowed object is {@link PcaDataType }
3327    *
3328    */
 
3329  1 toggle public void setPcaData(PcaDataType value)
3330    {
3331  1 this.pcaData = value;
3332    }
3333   
3334    /**
3335    * Gets the value of the title property.
3336    *
3337    * @return possible object is {@link String }
3338    *
3339    */
 
3340  3 toggle public String getTitle()
3341    {
3342  3 return title;
3343    }
3344   
3345    /**
3346    * Sets the value of the title property.
3347    *
3348    * @param value
3349    * allowed object is {@link String }
3350    *
3351    */
 
3352  1 toggle public void setTitle(String value)
3353    {
3354  1 this.title = value;
3355    }
3356   
3357    /**
3358    * Gets the value of the scoreModelName property.
3359    *
3360    * @return possible object is {@link String }
3361    *
3362    */
 
3363  1 toggle public String getScoreModelName()
3364    {
3365  1 return scoreModelName;
3366    }
3367   
3368    /**
3369    * Sets the value of the scoreModelName property.
3370    *
3371    * @param value
3372    * allowed object is {@link String }
3373    *
3374    */
 
3375  1 toggle public void setScoreModelName(String value)
3376    {
3377  1 this.scoreModelName = value;
3378    }
3379   
3380    /**
3381    * Gets the value of the xDim property.
3382    *
3383    * @return possible object is {@link Integer }
3384    *
3385    */
 
3386  1 toggle public Integer getXDim()
3387    {
3388  1 return xDim;
3389    }
3390   
3391    /**
3392    * Sets the value of the xDim property.
3393    *
3394    * @param value
3395    * allowed object is {@link Integer }
3396    *
3397    */
 
3398  1 toggle public void setXDim(Integer value)
3399    {
3400  1 this.xDim = value;
3401    }
3402   
3403    /**
3404    * Gets the value of the yDim property.
3405    *
3406    * @return possible object is {@link Integer }
3407    *
3408    */
 
3409  1 toggle public Integer getYDim()
3410    {
3411  1 return yDim;
3412    }
3413   
3414    /**
3415    * Sets the value of the yDim property.
3416    *
3417    * @param value
3418    * allowed object is {@link Integer }
3419    *
3420    */
 
3421  1 toggle public void setYDim(Integer value)
3422    {
3423  1 this.yDim = value;
3424    }
3425   
3426    /**
3427    * Gets the value of the zDim property.
3428    *
3429    * @return possible object is {@link Integer }
3430    *
3431    */
 
3432  1 toggle public Integer getZDim()
3433    {
3434  1 return zDim;
3435    }
3436   
3437    /**
3438    * Sets the value of the zDim property.
3439    *
3440    * @param value
3441    * allowed object is {@link Integer }
3442    *
3443    */
 
3444  1 toggle public void setZDim(Integer value)
3445    {
3446  1 this.zDim = value;
3447    }
3448   
3449    /**
3450    * Gets the value of the bgColour property.
3451    *
3452    * @return possible object is {@link Integer }
3453    *
3454    */
 
3455  1 toggle public Integer getBgColour()
3456    {
3457  1 return bgColour;
3458    }
3459   
3460    /**
3461    * Sets the value of the bgColour property.
3462    *
3463    * @param value
3464    * allowed object is {@link Integer }
3465    *
3466    */
 
3467  1 toggle public void setBgColour(Integer value)
3468    {
3469  1 this.bgColour = value;
3470    }
3471   
3472    /**
3473    * Gets the value of the scaleFactor property.
3474    *
3475    * @return possible object is {@link Float }
3476    *
3477    */
 
3478  1 toggle public Float getScaleFactor()
3479    {
3480  1 return scaleFactor;
3481    }
3482   
3483    /**
3484    * Sets the value of the scaleFactor property.
3485    *
3486    * @param value
3487    * allowed object is {@link Float }
3488    *
3489    */
 
3490  1 toggle public void setScaleFactor(Float value)
3491    {
3492  1 this.scaleFactor = value;
3493    }
3494   
3495    /**
3496    * Gets the value of the showLabels property.
3497    *
3498    * @return possible object is {@link Boolean }
3499    *
3500    */
 
3501  1 toggle public Boolean isShowLabels()
3502    {
3503  1 return showLabels;
3504    }
3505   
3506    /**
3507    * Sets the value of the showLabels property.
3508    *
3509    * @param value
3510    * allowed object is {@link Boolean }
3511    *
3512    */
 
3513  1 toggle public void setShowLabels(Boolean value)
3514    {
3515  1 this.showLabels = value;
3516    }
3517   
3518    /**
3519    * Gets the value of the linkToAllViews property.
3520    *
3521    * @return possible object is {@link Boolean }
3522    *
3523    */
 
3524  1 toggle public Boolean isLinkToAllViews()
3525    {
3526  1 return linkToAllViews;
3527    }
3528   
3529    /**
3530    * Sets the value of the linkToAllViews property.
3531    *
3532    * @param value
3533    * allowed object is {@link Boolean }
3534    *
3535    */
 
3536  1 toggle public void setLinkToAllViews(Boolean value)
3537    {
3538  1 this.linkToAllViews = value;
3539    }
3540   
3541    /**
3542    * Gets the value of the includeGaps property.
3543    *
3544    * @return possible object is {@link Boolean }
3545    *
3546    */
 
3547  1 toggle public Boolean isIncludeGaps()
3548    {
3549  1 return includeGaps;
3550    }
3551   
3552    /**
3553    * Sets the value of the includeGaps property.
3554    *
3555    * @param value
3556    * allowed object is {@link Boolean }
3557    *
3558    */
 
3559  1 toggle public void setIncludeGaps(Boolean value)
3560    {
3561  1 this.includeGaps = value;
3562    }
3563   
3564    /**
3565    * Gets the value of the matchGaps property.
3566    *
3567    * @return possible object is {@link Boolean }
3568    *
3569    */
 
3570  1 toggle public Boolean isMatchGaps()
3571    {
3572  1 return matchGaps;
3573    }
3574   
3575    /**
3576    * Sets the value of the matchGaps property.
3577    *
3578    * @param value
3579    * allowed object is {@link Boolean }
3580    *
3581    */
 
3582  1 toggle public void setMatchGaps(Boolean value)
3583    {
3584  1 this.matchGaps = value;
3585    }
3586   
3587    /**
3588    * Gets the value of the includeGappedColumns property.
3589    *
3590    * @return possible object is {@link Boolean }
3591    *
3592    */
 
3593  1 toggle public Boolean isIncludeGappedColumns()
3594    {
3595  1 return includeGappedColumns;
3596    }
3597   
3598    /**
3599    * Sets the value of the includeGappedColumns property.
3600    *
3601    * @param value
3602    * allowed object is {@link Boolean }
3603    *
3604    */
 
3605  1 toggle public void setIncludeGappedColumns(Boolean value)
3606    {
3607  1 this.includeGappedColumns = value;
3608    }
3609   
3610    /**
3611    * Gets the value of the denominateByShortestLength property.
3612    *
3613    * @return possible object is {@link Boolean }
3614    *
3615    */
 
3616  1 toggle public Boolean isDenominateByShortestLength()
3617    {
3618  1 return denominateByShortestLength;
3619    }
3620   
3621    /**
3622    * Sets the value of the denominateByShortestLength property.
3623    *
3624    * @param value
3625    * allowed object is {@link Boolean }
3626    *
3627    */
 
3628  1 toggle public void setDenominateByShortestLength(Boolean value)
3629    {
3630  1 this.denominateByShortestLength = value;
3631    }
3632   
3633    /**
3634    * Gets the value of the width property.
3635    *
3636    * @return possible object is {@link Integer }
3637    *
3638    */
 
3639  1 toggle public Integer getWidth()
3640    {
3641  1 return width;
3642    }
3643   
3644    /**
3645    * Sets the value of the width property.
3646    *
3647    * @param value
3648    * allowed object is {@link Integer }
3649    *
3650    */
 
3651  1 toggle public void setWidth(Integer value)
3652    {
3653  1 this.width = value;
3654    }
3655   
3656    /**
3657    * Gets the value of the height property.
3658    *
3659    * @return possible object is {@link Integer }
3660    *
3661    */
 
3662  1 toggle public Integer getHeight()
3663    {
3664  1 return height;
3665    }
3666   
3667    /**
3668    * Sets the value of the height property.
3669    *
3670    * @param value
3671    * allowed object is {@link Integer }
3672    *
3673    */
 
3674  1 toggle public void setHeight(Integer value)
3675    {
3676  1 this.height = value;
3677    }
3678   
3679    /**
3680    * Gets the value of the xpos property.
3681    *
3682    * @return possible object is {@link Integer }
3683    *
3684    */
 
3685  1 toggle public Integer getXpos()
3686    {
3687  1 return xpos;
3688    }
3689   
3690    /**
3691    * Sets the value of the xpos property.
3692    *
3693    * @param value
3694    * allowed object is {@link Integer }
3695    *
3696    */
 
3697  1 toggle public void setXpos(Integer value)
3698    {
3699  1 this.xpos = value;
3700    }
3701   
3702    /**
3703    * Gets the value of the ypos property.
3704    *
3705    * @return possible object is {@link Integer }
3706    *
3707    */
 
3708  1 toggle public Integer getYpos()
3709    {
3710  1 return ypos;
3711    }
3712   
3713    /**
3714    * Sets the value of the ypos property.
3715    *
3716    * @param value
3717    * allowed object is {@link Integer }
3718    *
3719    */
 
3720  1 toggle public void setYpos(Integer value)
3721    {
3722  1 this.ypos = value;
3723    }
3724   
3725    /**
3726    * &lt;p&gt;Java class for anonymous complex type.
3727    *
3728    * &lt;p&gt;The following schema fragment specifies the expected content
3729    * contained within this class.
3730    *
3731    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3732    * &amp;lt;restriction
3733    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3734    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3735    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3736    *
3737    *
3738    */
3739    @XmlAccessorType(XmlAccessType.FIELD)
3740    @XmlType(name = "")
 
3741    public static class Axis
3742    {
3743   
3744    @XmlAttribute(name = "xPos")
3745    protected Float xPos;
3746   
3747    @XmlAttribute(name = "yPos")
3748    protected Float yPos;
3749   
3750    @XmlAttribute(name = "zPos")
3751    protected Float zPos;
3752   
3753    /**
3754    * Gets the value of the xPos property.
3755    *
3756    * @return possible object is {@link Float }
3757    *
3758    */
 
3759  3 toggle public Float getXPos()
3760    {
3761  3 return xPos;
3762    }
3763   
3764    /**
3765    * Sets the value of the xPos property.
3766    *
3767    * @param value
3768    * allowed object is {@link Float }
3769    *
3770    */
 
3771  3 toggle public void setXPos(Float value)
3772    {
3773  3 this.xPos = value;
3774    }
3775   
3776    /**
3777    * Gets the value of the yPos property.
3778    *
3779    * @return possible object is {@link Float }
3780    *
3781    */
 
3782  3 toggle public Float getYPos()
3783    {
3784  3 return yPos;
3785    }
3786   
3787    /**
3788    * Sets the value of the yPos property.
3789    *
3790    * @param value
3791    * allowed object is {@link Float }
3792    *
3793    */
 
3794  3 toggle public void setYPos(Float value)
3795    {
3796  3 this.yPos = value;
3797    }
3798   
3799    /**
3800    * Gets the value of the zPos property.
3801    *
3802    * @return possible object is {@link Float }
3803    *
3804    */
 
3805  3 toggle public Float getZPos()
3806    {
3807  3 return zPos;
3808    }
3809   
3810    /**
3811    * Sets the value of the zPos property.
3812    *
3813    * @param value
3814    * allowed object is {@link Float }
3815    *
3816    */
 
3817  3 toggle public void setZPos(Float value)
3818    {
3819  3 this.zPos = value;
3820    }
3821   
3822    }
3823   
3824    /**
3825    * &lt;p&gt;Java class for anonymous complex type.
3826    *
3827    * &lt;p&gt;The following schema fragment specifies the expected content
3828    * contained within this class.
3829    *
3830    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3831    * &amp;lt;restriction
3832    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3833    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3834    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3835    *
3836    *
3837    */
3838    @XmlAccessorType(XmlAccessType.FIELD)
3839    @XmlType(name = "")
 
3840    public static class SeqPointMax
3841    {
3842   
3843    @XmlAttribute(name = "xPos")
3844    protected Float xPos;
3845   
3846    @XmlAttribute(name = "yPos")
3847    protected Float yPos;
3848   
3849    @XmlAttribute(name = "zPos")
3850    protected Float zPos;
3851   
3852    /**
3853    * Gets the value of the xPos property.
3854    *
3855    * @return possible object is {@link Float }
3856    *
3857    */
 
3858  1 toggle public Float getXPos()
3859    {
3860  1 return xPos;
3861    }
3862   
3863    /**
3864    * Sets the value of the xPos property.
3865    *
3866    * @param value
3867    * allowed object is {@link Float }
3868    *
3869    */
 
3870  1 toggle public void setXPos(Float value)
3871    {
3872  1 this.xPos = value;
3873    }
3874   
3875    /**
3876    * Gets the value of the yPos property.
3877    *
3878    * @return possible object is {@link Float }
3879    *
3880    */
 
3881  1 toggle public Float getYPos()
3882    {
3883  1 return yPos;
3884    }
3885   
3886    /**
3887    * Sets the value of the yPos property.
3888    *
3889    * @param value
3890    * allowed object is {@link Float }
3891    *
3892    */
 
3893  1 toggle public void setYPos(Float value)
3894    {
3895  1 this.yPos = value;
3896    }
3897   
3898    /**
3899    * Gets the value of the zPos property.
3900    *
3901    * @return possible object is {@link Float }
3902    *
3903    */
 
3904  1 toggle public Float getZPos()
3905    {
3906  1 return zPos;
3907    }
3908   
3909    /**
3910    * Sets the value of the zPos property.
3911    *
3912    * @param value
3913    * allowed object is {@link Float }
3914    *
3915    */
 
3916  1 toggle public void setZPos(Float value)
3917    {
3918  1 this.zPos = value;
3919    }
3920   
3921    }
3922   
3923    /**
3924    * &lt;p&gt;Java class for anonymous complex type.
3925    *
3926    * &lt;p&gt;The following schema fragment specifies the expected content
3927    * contained within this class.
3928    *
3929    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
3930    * &amp;lt;restriction
3931    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
3932    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;/restriction&amp;gt;
3933    * &amp;lt;/complexContent&amp;gt; &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
3934    *
3935    *
3936    */
3937    @XmlAccessorType(XmlAccessType.FIELD)
3938    @XmlType(name = "")
 
3939    public static class SeqPointMin
3940    {
3941   
3942    @XmlAttribute(name = "xPos")
3943    protected Float xPos;
3944   
3945    @XmlAttribute(name = "yPos")
3946    protected Float yPos;
3947   
3948    @XmlAttribute(name = "zPos")
3949    protected Float zPos;
3950   
3951    /**
3952    * Gets the value of the xPos property.
3953    *
3954    * @return possible object is {@link Float }
3955    *
3956    */
 
3957  1 toggle public Float getXPos()
3958    {
3959  1 return xPos;
3960    }
3961   
3962    /**
3963    * Sets the value of the xPos property.
3964    *
3965    * @param value
3966    * allowed object is {@link Float }
3967    *
3968    */
 
3969  1 toggle public void setXPos(Float value)
3970    {
3971  1 this.xPos = value;
3972    }
3973   
3974    /**
3975    * Gets the value of the yPos property.
3976    *
3977    * @return possible object is {@link Float }
3978    *
3979    */
 
3980  1 toggle public Float getYPos()
3981    {
3982  1 return yPos;
3983    }
3984   
3985    /**
3986    * Sets the value of the yPos property.
3987    *
3988    * @param value
3989    * allowed object is {@link Float }
3990    *
3991    */
 
3992  1 toggle public void setYPos(Float value)
3993    {
3994  1 this.yPos = value;
3995    }
3996   
3997    /**
3998    * Gets the value of the zPos property.
3999    *
4000    * @return possible object is {@link Float }
4001    *
4002    */
 
4003  1 toggle public Float getZPos()
4004    {
4005  1 return zPos;
4006    }
4007   
4008    /**
4009    * Sets the value of the zPos property.
4010    *
4011    * @param value
4012    * allowed object is {@link Float }
4013    *
4014    */
 
4015  1 toggle public void setZPos(Float value)
4016    {
4017  1 this.zPos = value;
4018    }
4019   
4020    }
4021   
4022    /**
4023    * &lt;p&gt;Java class for anonymous complex type.
4024    *
4025    * &lt;p&gt;The following schema fragment specifies the expected content
4026    * contained within this class.
4027    *
4028    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4029    * &amp;lt;restriction
4030    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
4031    * ref="{www.jalview.org}position"/&amp;gt; &amp;lt;attribute
4032    * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
4033    * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4034    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4035    *
4036    *
4037    */
4038    @XmlAccessorType(XmlAccessType.FIELD)
4039    @XmlType(name = "")
 
4040    public static class SequencePoint
4041    {
4042   
4043    @XmlAttribute(name = "sequenceRef")
4044    protected String sequenceRef;
4045   
4046    @XmlAttribute(name = "xPos")
4047    protected Float xPos;
4048   
4049    @XmlAttribute(name = "yPos")
4050    protected Float yPos;
4051   
4052    @XmlAttribute(name = "zPos")
4053    protected Float zPos;
4054   
4055    /**
4056    * Gets the value of the sequenceRef property.
4057    *
4058    * @return possible object is {@link String }
4059    *
4060    */
 
4061  15 toggle public String getSequenceRef()
4062    {
4063  15 return sequenceRef;
4064    }
4065   
4066    /**
4067    * Sets the value of the sequenceRef property.
4068    *
4069    * @param value
4070    * allowed object is {@link String }
4071    *
4072    */
 
4073  15 toggle public void setSequenceRef(String value)
4074    {
4075  15 this.sequenceRef = value;
4076    }
4077   
4078    /**
4079    * Gets the value of the xPos property.
4080    *
4081    * @return possible object is {@link Float }
4082    *
4083    */
 
4084  15 toggle public Float getXPos()
4085    {
4086  15 return xPos;
4087    }
4088   
4089    /**
4090    * Sets the value of the xPos property.
4091    *
4092    * @param value
4093    * allowed object is {@link Float }
4094    *
4095    */
 
4096  15 toggle public void setXPos(Float value)
4097    {
4098  15 this.xPos = value;
4099    }
4100   
4101    /**
4102    * Gets the value of the yPos property.
4103    *
4104    * @return possible object is {@link Float }
4105    *
4106    */
 
4107  15 toggle public Float getYPos()
4108    {
4109  15 return yPos;
4110    }
4111   
4112    /**
4113    * Sets the value of the yPos property.
4114    *
4115    * @param value
4116    * allowed object is {@link Float }
4117    *
4118    */
 
4119  15 toggle public void setYPos(Float value)
4120    {
4121  15 this.yPos = value;
4122    }
4123   
4124    /**
4125    * Gets the value of the zPos property.
4126    *
4127    * @return possible object is {@link Float }
4128    *
4129    */
 
4130  15 toggle public Float getZPos()
4131    {
4132  15 return zPos;
4133    }
4134   
4135    /**
4136    * Sets the value of the zPos property.
4137    *
4138    * @param value
4139    * allowed object is {@link Float }
4140    *
4141    */
 
4142  15 toggle public void setZPos(Float value)
4143    {
4144  15 this.zPos = value;
4145    }
4146   
4147    }
4148   
4149    }
4150   
4151    /**
4152    * &lt;p&gt;Java class for anonymous complex type.
4153    *
4154    * &lt;p&gt;The following schema fragment specifies the expected content
4155    * contained within this class.
4156    *
4157    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4158    * &amp;lt;restriction
4159    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;sequence
4160    * minOccurs="0"&amp;gt; &amp;lt;element name="title"
4161    * type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt; &amp;lt;element
4162    * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
4163    * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
4164    * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
4165    * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4166    * &amp;lt;attribute name="fontSize"
4167    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4168    * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4169    * &amp;lt;attribute name="threshold"
4170    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
4171    * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
4172    * /&amp;gt; &amp;lt;attribute name="showDistances"
4173    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4174    * &amp;lt;attribute name="markUnlinked"
4175    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4176    * &amp;lt;attribute name="fitToWindow"
4177    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4178    * &amp;lt;attribute name="currentTree"
4179    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4180    * &amp;lt;attribute name="columnWise"
4181    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4182    * &amp;lt;attribute name="columnReference"
4183    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4184    * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4185    * &amp;lt;attribute name="linkToAllViews"
4186    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4187    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4188    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4189    *
4190    *
4191    */
4192    @XmlAccessorType(XmlAccessType.FIELD)
4193    @XmlType(name = "", propOrder = { "title", "newick" })
 
4194    public static class Tree
4195    {
4196   
4197    @XmlElement(namespace = "www.jalview.org")
4198    protected String title;
4199   
4200    @XmlElement(namespace = "www.jalview.org")
4201    protected String newick;
4202   
4203    @XmlAttribute(name = "fontName")
4204    protected String fontName;
4205   
4206    @XmlAttribute(name = "fontSize")
4207    protected Integer fontSize;
4208   
4209    @XmlAttribute(name = "fontStyle")
4210    protected Integer fontStyle;
4211   
4212    @XmlAttribute(name = "threshold")
4213    protected Float threshold;
4214   
4215    @XmlAttribute(name = "showBootstrap")
4216    protected Boolean showBootstrap;
4217   
4218    @XmlAttribute(name = "showDistances")
4219    protected Boolean showDistances;
4220   
4221    @XmlAttribute(name = "markUnlinked")
4222    protected Boolean markUnlinked;
4223   
4224    @XmlAttribute(name = "fitToWindow")
4225    protected Boolean fitToWindow;
4226   
4227    @XmlAttribute(name = "currentTree")
4228    protected Boolean currentTree;
4229   
4230    @XmlAttribute(name = "columnWise")
4231    protected Boolean columnWise;
4232   
4233    @XmlAttribute(name = "columnReference")
4234    protected String columnReference;
4235   
4236    @XmlAttribute(name = "id")
4237    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4238    @XmlID
4239    @XmlSchemaType(name = "ID")
4240    protected String id;
4241   
4242    @XmlAttribute(name = "linkToAllViews")
4243    protected Boolean linkToAllViews;
4244   
4245    @XmlAttribute(name = "width")
4246    protected Integer width;
4247   
4248    @XmlAttribute(name = "height")
4249    protected Integer height;
4250   
4251    @XmlAttribute(name = "xpos")
4252    protected Integer xpos;
4253   
4254    @XmlAttribute(name = "ypos")
4255    protected Integer ypos;
4256   
4257    /**
4258    * Gets the value of the title property.
4259    *
4260    * @return possible object is {@link String }
4261    *
4262    */
 
4263  12 toggle public String getTitle()
4264    {
4265  12 return title;
4266    }
4267   
4268    /**
4269    * Sets the value of the title property.
4270    *
4271    * @param value
4272    * allowed object is {@link String }
4273    *
4274    */
 
4275  4 toggle public void setTitle(String value)
4276    {
4277  4 this.title = value;
4278    }
4279   
4280    /**
4281    * Gets the value of the newick property.
4282    *
4283    * @return possible object is {@link String }
4284    *
4285    */
 
4286  12 toggle public String getNewick()
4287    {
4288  12 return newick;
4289    }
4290   
4291    /**
4292    * Sets the value of the newick property.
4293    *
4294    * @param value
4295    * allowed object is {@link String }
4296    *
4297    */
 
4298  4 toggle public void setNewick(String value)
4299    {
4300  4 this.newick = value;
4301    }
4302   
4303    /**
4304    * Gets the value of the fontName property.
4305    *
4306    * @return possible object is {@link String }
4307    *
4308    */
 
4309  24 toggle public String getFontName()
4310    {
4311  24 return fontName;
4312    }
4313   
4314    /**
4315    * Sets the value of the fontName property.
4316    *
4317    * @param value
4318    * allowed object is {@link String }
4319    *
4320    */
 
4321  4 toggle public void setFontName(String value)
4322    {
4323  4 this.fontName = value;
4324    }
4325   
4326    /**
4327    * Gets the value of the fontSize property.
4328    *
4329    * @return possible object is {@link Integer }
4330    *
4331    */
 
4332  12 toggle public Integer getFontSize()
4333    {
4334  12 return fontSize;
4335    }
4336   
4337    /**
4338    * Sets the value of the fontSize property.
4339    *
4340    * @param value
4341    * allowed object is {@link Integer }
4342    *
4343    */
 
4344  4 toggle public void setFontSize(Integer value)
4345    {
4346  4 this.fontSize = value;
4347    }
4348   
4349    /**
4350    * Gets the value of the fontStyle property.
4351    *
4352    * @return possible object is {@link Integer }
4353    *
4354    */
 
4355  12 toggle public Integer getFontStyle()
4356    {
4357  12 return fontStyle;
4358    }
4359   
4360    /**
4361    * Sets the value of the fontStyle property.
4362    *
4363    * @param value
4364    * allowed object is {@link Integer }
4365    *
4366    */
 
4367  4 toggle public void setFontStyle(Integer value)
4368    {
4369  4 this.fontStyle = value;
4370    }
4371   
4372    /**
4373    * Gets the value of the threshold property.
4374    *
4375    * @return possible object is {@link Float }
4376    *
4377    */
 
4378  12 toggle public Float getThreshold()
4379    {
4380  12 return threshold;
4381    }
4382   
4383    /**
4384    * Sets the value of the threshold property.
4385    *
4386    * @param value
4387    * allowed object is {@link Float }
4388    *
4389    */
 
4390  4 toggle public void setThreshold(Float value)
4391    {
4392  4 this.threshold = value;
4393    }
4394   
4395    /**
4396    * Gets the value of the showBootstrap property.
4397    *
4398    * @return possible object is {@link Boolean }
4399    *
4400    */
 
4401  12 toggle public Boolean isShowBootstrap()
4402    {
4403  12 return showBootstrap;
4404    }
4405   
4406    /**
4407    * Sets the value of the showBootstrap property.
4408    *
4409    * @param value
4410    * allowed object is {@link Boolean }
4411    *
4412    */
 
4413  4 toggle public void setShowBootstrap(Boolean value)
4414    {
4415  4 this.showBootstrap = value;
4416    }
4417   
4418    /**
4419    * Gets the value of the showDistances property.
4420    *
4421    * @return possible object is {@link Boolean }
4422    *
4423    */
 
4424  12 toggle public Boolean isShowDistances()
4425    {
4426  12 return showDistances;
4427    }
4428   
4429    /**
4430    * Sets the value of the showDistances property.
4431    *
4432    * @param value
4433    * allowed object is {@link Boolean }
4434    *
4435    */
 
4436  4 toggle public void setShowDistances(Boolean value)
4437    {
4438  4 this.showDistances = value;
4439    }
4440   
4441    /**
4442    * Gets the value of the markUnlinked property.
4443    *
4444    * @return possible object is {@link Boolean }
4445    *
4446    */
 
4447  12 toggle public Boolean isMarkUnlinked()
4448    {
4449  12 return markUnlinked;
4450    }
4451   
4452    /**
4453    * Sets the value of the markUnlinked property.
4454    *
4455    * @param value
4456    * allowed object is {@link Boolean }
4457    *
4458    */
 
4459  4 toggle public void setMarkUnlinked(Boolean value)
4460    {
4461  4 this.markUnlinked = value;
4462    }
4463   
4464    /**
4465    * Gets the value of the fitToWindow property.
4466    *
4467    * @return possible object is {@link Boolean }
4468    *
4469    */
 
4470  12 toggle public Boolean isFitToWindow()
4471    {
4472  12 return fitToWindow;
4473    }
4474   
4475    /**
4476    * Sets the value of the fitToWindow property.
4477    *
4478    * @param value
4479    * allowed object is {@link Boolean }
4480    *
4481    */
 
4482  4 toggle public void setFitToWindow(Boolean value)
4483    {
4484  4 this.fitToWindow = value;
4485    }
4486   
4487    /**
4488    * Gets the value of the currentTree property.
4489    *
4490    * @return possible object is {@link Boolean }
4491    *
4492    */
 
4493  12 toggle public Boolean isCurrentTree()
4494    {
4495  12 return currentTree;
4496    }
4497   
4498    /**
4499    * Sets the value of the currentTree property.
4500    *
4501    * @param value
4502    * allowed object is {@link Boolean }
4503    *
4504    */
 
4505  4 toggle public void setCurrentTree(Boolean value)
4506    {
4507  4 this.currentTree = value;
4508    }
4509   
4510    /**
4511    * Gets the value of the columnWise property.
4512    *
4513    * @return possible object is {@link Boolean }
4514    *
4515    */
 
4516  12 toggle public boolean isColumnWise()
4517    {
4518  12 if (columnWise == null)
4519    {
4520  12 return false;
4521    }
4522    else
4523    {
4524  0 return columnWise;
4525    }
4526    }
4527   
4528    /**
4529    * Sets the value of the columnWise property.
4530    *
4531    * @param value
4532    * allowed object is {@link Boolean }
4533    *
4534    */
 
4535  0 toggle public void setColumnWise(Boolean value)
4536    {
4537  0 this.columnWise = value;
4538    }
4539   
4540    /**
4541    * Gets the value of the columnReference property.
4542    *
4543    * @return possible object is {@link String }
4544    *
4545    */
 
4546  0 toggle public String getColumnReference()
4547    {
4548  0 return columnReference;
4549    }
4550   
4551    /**
4552    * Sets the value of the columnReference property.
4553    *
4554    * @param value
4555    * allowed object is {@link String }
4556    *
4557    */
 
4558  0 toggle public void setColumnReference(String value)
4559    {
4560  0 this.columnReference = value;
4561    }
4562   
4563    /**
4564    * Gets the value of the id property.
4565    *
4566    * @return possible object is {@link String }
4567    *
4568    */
 
4569  24 toggle public String getId()
4570    {
4571  24 return id;
4572    }
4573   
4574    /**
4575    * Sets the value of the id property.
4576    *
4577    * @param value
4578    * allowed object is {@link String }
4579    *
4580    */
 
4581  4 toggle public void setId(String value)
4582    {
4583  4 this.id = value;
4584    }
4585   
4586    /**
4587    * Gets the value of the linkToAllViews property.
4588    *
4589    * @return possible object is {@link Boolean }
4590    *
4591    */
 
4592  12 toggle public boolean isLinkToAllViews()
4593    {
4594  12 if (linkToAllViews == null)
4595    {
4596  8 return false;
4597    }
4598    else
4599    {
4600  4 return linkToAllViews;
4601    }
4602    }
4603   
4604    /**
4605    * Sets the value of the linkToAllViews property.
4606    *
4607    * @param value
4608    * allowed object is {@link Boolean }
4609    *
4610    */
 
4611  4 toggle public void setLinkToAllViews(Boolean value)
4612    {
4613  4 this.linkToAllViews = value;
4614    }
4615   
4616    /**
4617    * Gets the value of the width property.
4618    *
4619    * @return possible object is {@link Integer }
4620    *
4621    */
 
4622  12 toggle public Integer getWidth()
4623    {
4624  12 return width;
4625    }
4626   
4627    /**
4628    * Sets the value of the width property.
4629    *
4630    * @param value
4631    * allowed object is {@link Integer }
4632    *
4633    */
 
4634  4 toggle public void setWidth(Integer value)
4635    {
4636  4 this.width = value;
4637    }
4638   
4639    /**
4640    * Gets the value of the height property.
4641    *
4642    * @return possible object is {@link Integer }
4643    *
4644    */
 
4645  12 toggle public Integer getHeight()
4646    {
4647  12 return height;
4648    }
4649   
4650    /**
4651    * Sets the value of the height property.
4652    *
4653    * @param value
4654    * allowed object is {@link Integer }
4655    *
4656    */
 
4657  4 toggle public void setHeight(Integer value)
4658    {
4659  4 this.height = value;
4660    }
4661   
4662    /**
4663    * Gets the value of the xpos property.
4664    *
4665    * @return possible object is {@link Integer }
4666    *
4667    */
 
4668  12 toggle public Integer getXpos()
4669    {
4670  12 return xpos;
4671    }
4672   
4673    /**
4674    * Sets the value of the xpos property.
4675    *
4676    * @param value
4677    * allowed object is {@link Integer }
4678    *
4679    */
 
4680  4 toggle public void setXpos(Integer value)
4681    {
4682  4 this.xpos = value;
4683    }
4684   
4685    /**
4686    * Gets the value of the ypos property.
4687    *
4688    * @return possible object is {@link Integer }
4689    *
4690    */
 
4691  12 toggle public Integer getYpos()
4692    {
4693  12 return ypos;
4694    }
4695   
4696    /**
4697    * Sets the value of the ypos property.
4698    *
4699    * @param value
4700    * allowed object is {@link Integer }
4701    *
4702    */
 
4703  4 toggle public void setYpos(Integer value)
4704    {
4705  4 this.ypos = value;
4706    }
4707   
4708    }
4709   
4710    /**
4711    * &lt;p&gt;Java class for anonymous complex type.
4712    *
4713    * &lt;p&gt;The following schema fragment specifies the expected content
4714    * contained within this class.
4715    *
4716    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4717    * &amp;lt;restriction
4718    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4719    * &amp;lt;sequence&amp;gt; &amp;lt;element name="UserColourScheme"
4720    * type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
4721    * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="id"
4722    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4723    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4724    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4725    *
4726    *
4727    */
4728    @XmlAccessorType(XmlAccessType.FIELD)
4729    @XmlType(name = "", propOrder = { "userColourScheme" })
 
4730    public static class UserColours
4731    {
4732   
4733    @XmlElement(
4734    name = "UserColourScheme",
4735    namespace = "www.jalview.org",
4736    required = true)
4737    protected JalviewUserColours userColourScheme;
4738   
4739    @XmlAttribute(name = "id")
4740    protected String id;
4741   
4742    /**
4743    * Gets the value of the userColourScheme property.
4744    *
4745    * @return possible object is {@link JalviewUserColours }
4746    *
4747    */
 
4748  0 toggle public JalviewUserColours getUserColourScheme()
4749    {
4750  0 return userColourScheme;
4751    }
4752   
4753    /**
4754    * Sets the value of the userColourScheme property.
4755    *
4756    * @param value
4757    * allowed object is {@link JalviewUserColours }
4758    *
4759    */
 
4760  0 toggle public void setUserColourScheme(JalviewUserColours value)
4761    {
4762  0 this.userColourScheme = value;
4763    }
4764   
4765    /**
4766    * Gets the value of the id property.
4767    *
4768    * @return possible object is {@link String }
4769    *
4770    */
 
4771  0 toggle public String getId()
4772    {
4773  0 return id;
4774    }
4775   
4776    /**
4777    * Sets the value of the id property.
4778    *
4779    * @param value
4780    * allowed object is {@link String }
4781    *
4782    */
 
4783  0 toggle public void setId(String value)
4784    {
4785  0 this.id = value;
4786    }
4787   
4788    }
4789   
4790    /**
4791    * &lt;p&gt;Java class for anonymous complex type.
4792    *
4793    * &lt;p&gt;The following schema fragment specifies the expected content
4794    * contained within this class.
4795    *
4796    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4797    * &amp;lt;restriction
4798    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
4799    * &amp;lt;sequence&amp;gt; &amp;lt;element name="AnnotationColours"
4800    * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
4801    * &amp;lt;element name="hiddenColumns" maxOccurs="unbounded"
4802    * minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
4803    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
4804    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
4805    * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4806    * &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
4807    * /&amp;gt; &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4808    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
4809    * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
4810    * &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
4811    * &amp;lt;extension
4812    * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
4813    * &amp;lt;attribute name="calcId" use="required"
4814    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4815    * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
4816    * default="false" /&amp;gt; &amp;lt;attribute name="autoUpdate"
4817    * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4818    * &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
4819    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt; &amp;lt;element
4820    * name="overview" minOccurs="0"&amp;gt; &amp;lt;complexType&amp;gt;
4821    * &amp;lt;complexContent&amp;gt; &amp;lt;restriction
4822    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
4823    * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
4824    * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
4825    * /&amp;gt; &amp;lt;attribute name="residueColour"
4826    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4827    * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4828    * &amp;lt;attribute name="hiddenColour"
4829    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4830    * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4831    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4832    * &amp;lt;/complexType&amp;gt; &amp;lt;/element&amp;gt;
4833    * &amp;lt;/sequence&amp;gt; &amp;lt;attGroup
4834    * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
4835    * name="conservationSelected"
4836    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4837    * &amp;lt;attribute name="pidSelected"
4838    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4839    * &amp;lt;attribute name="bgColour"
4840    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4841    * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4842    * &amp;lt;attribute name="pidThreshold"
4843    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4844    * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
4845    * &amp;lt;attribute name="showFullId"
4846    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4847    * &amp;lt;attribute name="rightAlignIds"
4848    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4849    * &amp;lt;attribute name="showText"
4850    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4851    * &amp;lt;attribute name="showColourText"
4852    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4853    * &amp;lt;attribute name="showUnconserved"
4854    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4855    * &amp;lt;attribute name="showBoxes"
4856    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4857    * &amp;lt;attribute name="wrapAlignment"
4858    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4859    * &amp;lt;attribute name="renderGaps"
4860    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4861    * &amp;lt;attribute name="showSequenceFeatures"
4862    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4863    * &amp;lt;attribute name="showNPfeatureTooltip"
4864    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4865    * &amp;lt;attribute name="showDbRefTooltip"
4866    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4867    * &amp;lt;attribute name="followHighlight"
4868    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4869    * &amp;lt;attribute name="followSelection"
4870    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4871    * &amp;lt;attribute name="showAnnotation"
4872    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4873    * &amp;lt;attribute name="centreColumnLabels"
4874    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4875    * &amp;lt;attribute name="showGroupConservation"
4876    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4877    * &amp;lt;attribute name="showGroupConsensus"
4878    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4879    * &amp;lt;attribute name="showConsensusHistogram"
4880    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4881    * &amp;lt;attribute name="showSequenceLogo"
4882    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4883    * &amp;lt;attribute name="normaliseSequenceLogo"
4884    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4885    * &amp;lt;attribute name="ignoreGapsinConsensus"
4886    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4887    * &amp;lt;attribute name="startRes"
4888    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4889    * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4890    * &amp;lt;attribute name="charWidth"
4891    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4892    * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4893    * &amp;lt;attribute name="fontName"
4894    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4895    * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4896    * &amp;lt;attribute name="fontStyle"
4897    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4898    * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4899    * &amp;lt;attribute name="idWidthManuallyAdjusted"
4900    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4901    * &amp;lt;attribute name="scaleProteinAsCdna"
4902    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
4903    * &amp;lt;attribute name="viewName"
4904    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4905    * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
4906    * /&amp;gt; &amp;lt;attribute name="gatheredViews"
4907    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
4908    * &amp;lt;attribute name="textCol1"
4909    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4910    * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
4911    * &amp;lt;attribute name="textColThreshold"
4912    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
4913    * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
4914    * &amp;lt;attribute name="complementId"
4915    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
4916    * name="showComplementFeatures"
4917    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4918    * &amp;lt;attribute name="showComplementFeaturesOnTop"
4919    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
4920    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
4921    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
4922    *
4923    *
4924    */
4925    @XmlAccessorType(XmlAccessType.FIELD)
4926    @XmlType(
4927    name = "",
4928    propOrder =
4929    { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
 
4930    public static class Viewport
4931    {
4932   
4933    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4934    protected AnnotationColourScheme annotationColours;
4935   
4936    @XmlElement(namespace = "www.jalview.org")
4937    protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4938   
4939    @XmlElement(namespace = "www.jalview.org")
4940    protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4941   
4942    @XmlElement(namespace = "www.jalview.org")
4943    protected JalviewModel.Viewport.Overview overview;
4944   
4945    @XmlAttribute(name = "conservationSelected")
4946    protected Boolean conservationSelected;
4947   
4948    @XmlAttribute(name = "pidSelected")
4949    protected Boolean pidSelected;
4950   
4951    @XmlAttribute(name = "bgColour")
4952    protected String bgColour;
4953   
4954    @XmlAttribute(name = "consThreshold")
4955    protected Integer consThreshold;
4956   
4957    @XmlAttribute(name = "pidThreshold")
4958    protected Integer pidThreshold;
4959   
4960    @XmlAttribute(name = "title")
4961    protected String title;
4962   
4963    @XmlAttribute(name = "showFullId")
4964    protected Boolean showFullId;
4965   
4966    @XmlAttribute(name = "rightAlignIds")
4967    protected Boolean rightAlignIds;
4968   
4969    @XmlAttribute(name = "showText")
4970    protected Boolean showText;
4971   
4972    @XmlAttribute(name = "showColourText")
4973    protected Boolean showColourText;
4974   
4975    @XmlAttribute(name = "showUnconserved")
4976    protected Boolean showUnconserved;
4977   
4978    @XmlAttribute(name = "showBoxes")
4979    protected Boolean showBoxes;
4980   
4981    @XmlAttribute(name = "wrapAlignment")
4982    protected Boolean wrapAlignment;
4983   
4984    @XmlAttribute(name = "renderGaps")
4985    protected Boolean renderGaps;
4986   
4987    @XmlAttribute(name = "showSequenceFeatures")
4988    protected Boolean showSequenceFeatures;
4989   
4990    @XmlAttribute(name = "showNPfeatureTooltip")
4991    protected Boolean showNPfeatureTooltip;
4992   
4993    @XmlAttribute(name = "showDbRefTooltip")
4994    protected Boolean showDbRefTooltip;
4995   
4996    @XmlAttribute(name = "followHighlight")
4997    protected Boolean followHighlight;
4998   
4999    @XmlAttribute(name = "followSelection")
5000    protected Boolean followSelection;
5001   
5002    @XmlAttribute(name = "showAnnotation")
5003    protected Boolean showAnnotation;
5004   
5005    @XmlAttribute(name = "centreColumnLabels")
5006    protected Boolean centreColumnLabels;
5007   
5008    @XmlAttribute(name = "showGroupConservation")
5009    protected Boolean showGroupConservation;
5010   
5011    @XmlAttribute(name = "showGroupConsensus")
5012    protected Boolean showGroupConsensus;
5013   
5014    @XmlAttribute(name = "showConsensusHistogram")
5015    protected Boolean showConsensusHistogram;
5016   
5017    @XmlAttribute(name = "showSequenceLogo")
5018    protected Boolean showSequenceLogo;
5019   
5020    @XmlAttribute(name = "normaliseSequenceLogo")
5021    protected Boolean normaliseSequenceLogo;
5022   
5023    @XmlAttribute(name = "ignoreGapsinConsensus")
5024    protected Boolean ignoreGapsinConsensus;
5025   
5026    @XmlAttribute(name = "startRes")
5027    protected Integer startRes;
5028   
5029    @XmlAttribute(name = "startSeq")
5030    protected Integer startSeq;
5031   
5032    @XmlAttribute(name = "charWidth")
5033    protected Integer charWidth;
5034   
5035    @XmlAttribute(name = "charHeight")
5036    protected Integer charHeight;
5037   
5038    @XmlAttribute(name = "fontName")
5039    protected String fontName;
5040   
5041    @XmlAttribute(name = "fontSize")
5042    protected Integer fontSize;
5043   
5044    @XmlAttribute(name = "fontStyle")
5045    protected Integer fontStyle;
5046   
5047    @XmlAttribute(name = "idWidth")
5048    protected Integer idWidth;
5049   
5050    @XmlAttribute(name = "idWidthManuallyAdjusted")
5051    protected Boolean idWidthManuallyAdjusted;
5052   
5053    @XmlAttribute(name = "scaleProteinAsCdna")
5054    protected Boolean scaleProteinAsCdna;
5055   
5056    @XmlAttribute(name = "viewName")
5057    protected String viewName;
5058   
5059    @XmlAttribute(name = "sequenceSetId")
5060    protected String sequenceSetId;
5061   
5062    @XmlAttribute(name = "gatheredViews")
5063    protected Boolean gatheredViews;
5064   
5065    @XmlAttribute(name = "textCol1")
5066    protected Integer textCol1;
5067   
5068    @XmlAttribute(name = "textCol2")
5069    protected Integer textCol2;
5070   
5071    @XmlAttribute(name = "textColThreshold")
5072    protected Integer textColThreshold;
5073   
5074    @XmlAttribute(name = "id")
5075    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5076    @XmlID
5077    @XmlSchemaType(name = "ID")
5078    protected String id;
5079   
5080    @XmlAttribute(name = "complementId")
5081    protected String complementId;
5082   
5083    @XmlAttribute(name = "showComplementFeatures")
5084    protected Boolean showComplementFeatures;
5085   
5086    @XmlAttribute(name = "showComplementFeaturesOnTop")
5087    protected Boolean showComplementFeaturesOnTop;
5088   
5089    @XmlAttribute(name = "width")
5090    protected Integer width;
5091   
5092    @XmlAttribute(name = "height")
5093    protected Integer height;
5094   
5095    @XmlAttribute(name = "xpos")
5096    protected Integer xpos;
5097   
5098    @XmlAttribute(name = "ypos")
5099    protected Integer ypos;
5100   
5101    /**
5102    * Gets the value of the annotationColours property.
5103    *
5104    * @return possible object is {@link AnnotationColourScheme }
5105    *
5106    */
 
5107  2 toggle public AnnotationColourScheme getAnnotationColours()
5108    {
5109  2 return annotationColours;
5110    }
5111   
5112    /**
5113    * Sets the value of the annotationColours property.
5114    *
5115    * @param value
5116    * allowed object is {@link AnnotationColourScheme }
5117    *
5118    */
 
5119  2 toggle public void setAnnotationColours(AnnotationColourScheme value)
5120    {
5121  2 this.annotationColours = value;
5122    }
5123   
5124    /**
5125    * Gets the value of the hiddenColumns property.
5126    *
5127    * &lt;p&gt; This accessor method returns a reference to the live list, not
5128    * a snapshot. Therefore any modification you make to the returned list will
5129    * be present inside the JAXB object. This is why there is not a
5130    * &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
5131    *
5132    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
5133    * getHiddenColumns().add(newItem); &lt;/pre&gt;
5134    *
5135    *
5136    * &lt;p&gt; Objects of the following type(s) are allowed in the list
5137    * {@link JalviewModel.Viewport.HiddenColumns }
5138    *
5139    *
5140    */
 
5141  221 toggle public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
5142    {
5143  221 if (hiddenColumns == null)
5144    {
5145  67 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5146    }
5147  221 return this.hiddenColumns;
5148    }
5149   
5150    /**
5151    * Gets the value of the calcIdParam property.
5152    *
5153    * &lt;p&gt; This accessor method returns a reference to the live list, not
5154    * a snapshot. Therefore any modification you make to the returned list will
5155    * be present inside the JAXB object. This is why there is not a
5156    * &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
5157    *
5158    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
5159    * getCalcIdParam().add(newItem); &lt;/pre&gt;
5160    *
5161    *
5162    * &lt;p&gt; Objects of the following type(s) are allowed in the list
5163    * {@link JalviewModel.Viewport.CalcIdParam }
5164    *
5165    *
5166    */
 
5167  170 toggle public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
5168    {
5169  170 if (calcIdParam == null)
5170    {
5171  85 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5172    }
5173  170 return this.calcIdParam;
5174    }
5175   
5176    /**
5177    * Gets the value of the overview property.
5178    *
5179    * @return possible object is {@link JalviewModel.Viewport.Overview }
5180    *
5181    */
 
5182  75 toggle public JalviewModel.Viewport.Overview getOverview()
5183    {
5184  75 return overview;
5185    }
5186   
5187    /**
5188    * Sets the value of the overview property.
5189    *
5190    * @param value
5191    * allowed object is {@link JalviewModel.Viewport.Overview }
5192    *
5193    */
 
5194  14 toggle public void setOverview(JalviewModel.Viewport.Overview value)
5195    {
5196  14 this.overview = value;
5197    }
5198   
5199    /**
5200    * Gets the value of the conservationSelected property.
5201    *
5202    * @return possible object is {@link Boolean }
5203    *
5204    */
 
5205  170 toggle public Boolean isConservationSelected()
5206    {
5207  170 return conservationSelected;
5208    }
5209   
5210    /**
5211    * Sets the value of the conservationSelected property.
5212    *
5213    * @param value
5214    * allowed object is {@link Boolean }
5215    *
5216    */
 
5217  46 toggle public void setConservationSelected(Boolean value)
5218    {
5219  46 this.conservationSelected = value;
5220    }
5221   
5222    /**
5223    * Gets the value of the pidSelected property.
5224    *
5225    * @return possible object is {@link Boolean }
5226    *
5227    */
 
5228  85 toggle public Boolean isPidSelected()
5229    {
5230  85 return pidSelected;
5231    }
5232   
5233    /**
5234    * Sets the value of the pidSelected property.
5235    *
5236    * @param value
5237    * allowed object is {@link Boolean }
5238    *
5239    */
 
5240  46 toggle public void setPidSelected(Boolean value)
5241    {
5242  46 this.pidSelected = value;
5243    }
5244   
5245    /**
5246    * Gets the value of the bgColour property.
5247    *
5248    * @return possible object is {@link String }
5249    *
5250    */
 
5251  338 toggle public String getBgColour()
5252    {
5253  338 return bgColour;
5254    }
5255   
5256    /**
5257    * Sets the value of the bgColour property.
5258    *
5259    * @param value
5260    * allowed object is {@link String }
5261    *
5262    */
 
5263  46 toggle public void setBgColour(String value)
5264    {
5265  46 this.bgColour = value;
5266    }
5267   
5268    /**
5269    * Gets the value of the consThreshold property.
5270    *
5271    * @return possible object is {@link Integer }
5272    *
5273    */
 
5274  87 toggle public Integer getConsThreshold()
5275    {
5276  87 return consThreshold;
5277    }
5278   
5279    /**
5280    * Sets the value of the consThreshold property.
5281    *
5282    * @param value
5283    * allowed object is {@link Integer }
5284    *
5285    */
 
5286  2 toggle public void setConsThreshold(Integer value)
5287    {
5288  2 this.consThreshold = value;
5289    }
5290   
5291    /**
5292    * Gets the value of the pidThreshold property.
5293    *
5294    * @return possible object is {@link Integer }
5295    *
5296    */
 
5297  85 toggle public Integer getPidThreshold()
5298    {
5299  85 return pidThreshold;
5300    }
5301   
5302    /**
5303    * Sets the value of the pidThreshold property.
5304    *
5305    * @param value
5306    * allowed object is {@link Integer }
5307    *
5308    */
 
5309  8 toggle public void setPidThreshold(Integer value)
5310    {
5311  8 this.pidThreshold = value;
5312    }
5313   
5314    /**
5315    * Gets the value of the title property.
5316    *
5317    * @return possible object is {@link String }
5318    *
5319    */
 
5320  170 toggle public String getTitle()
5321    {
5322  170 return title;
5323    }
5324   
5325    /**
5326    * Sets the value of the title property.
5327    *
5328    * @param value
5329    * allowed object is {@link String }
5330    *
5331    */
 
5332  46 toggle public void setTitle(String value)
5333    {
5334  46 this.title = value;
5335    }
5336   
5337    /**
5338    * Gets the value of the showFullId property.
5339    *
5340    * @return possible object is {@link Boolean }
5341    *
5342    */
 
5343  85 toggle public Boolean isShowFullId()
5344    {
5345  85 return showFullId;
5346    }
5347   
5348    /**
5349    * Sets the value of the showFullId property.
5350    *
5351    * @param value
5352    * allowed object is {@link Boolean }
5353    *
5354    */
 
5355  46 toggle public void setShowFullId(Boolean value)
5356    {
5357  46 this.showFullId = value;
5358    }
5359   
5360    /**
5361    * Gets the value of the rightAlignIds property.
5362    *
5363    * @return possible object is {@link Boolean }
5364    *
5365    */
 
5366  85 toggle public Boolean isRightAlignIds()
5367    {
5368  85 return rightAlignIds;
5369    }
5370   
5371    /**
5372    * Sets the value of the rightAlignIds property.
5373    *
5374    * @param value
5375    * allowed object is {@link Boolean }
5376    *
5377    */
 
5378  46 toggle public void setRightAlignIds(Boolean value)
5379    {
5380  46 this.rightAlignIds = value;
5381    }
5382   
5383    /**
5384    * Gets the value of the showText property.
5385    *
5386    * @return possible object is {@link Boolean }
5387    *
5388    */
 
5389  85 toggle public Boolean isShowText()
5390    {
5391  85 return showText;
5392    }
5393   
5394    /**
5395    * Sets the value of the showText property.
5396    *
5397    * @param value
5398    * allowed object is {@link Boolean }
5399    *
5400    */
 
5401  46 toggle public void setShowText(Boolean value)
5402    {
5403  46 this.showText = value;
5404    }
5405   
5406    /**
5407    * Gets the value of the showColourText property.
5408    *
5409    * @return possible object is {@link Boolean }
5410    *
5411    */
 
5412  85 toggle public Boolean isShowColourText()
5413    {
5414  85 return showColourText;
5415    }
5416   
5417    /**
5418    * Sets the value of the showColourText property.
5419    *
5420    * @param value
5421    * allowed object is {@link Boolean }
5422    *
5423    */
 
5424  46 toggle public void setShowColourText(Boolean value)
5425    {
5426  46 this.showColourText = value;
5427    }
5428   
5429    /**
5430    * Gets the value of the showUnconserved property.
5431    *
5432    * @return possible object is {@link Boolean }
5433    *
5434    */
 
5435  85 toggle public boolean isShowUnconserved()
5436    {
5437  85 if (showUnconserved == null)
5438    {
5439  0 return false;
5440    }
5441    else
5442    {
5443  85 return showUnconserved;
5444    }
5445    }
5446   
5447    /**
5448    * Sets the value of the showUnconserved property.
5449    *
5450    * @param value
5451    * allowed object is {@link Boolean }
5452    *
5453    */
 
5454  46 toggle public void setShowUnconserved(Boolean value)
5455    {
5456  46 this.showUnconserved = value;
5457    }
5458   
5459    /**
5460    * Gets the value of the showBoxes property.
5461    *
5462    * @return possible object is {@link Boolean }
5463    *
5464    */
 
5465  85 toggle public Boolean isShowBoxes()
5466    {
5467  85 return showBoxes;
5468    }
5469   
5470    /**
5471    * Sets the value of the showBoxes property.
5472    *
5473    * @param value
5474    * allowed object is {@link Boolean }
5475    *
5476    */
 
5477  46 toggle public void setShowBoxes(Boolean value)
5478    {
5479  46 this.showBoxes = value;
5480    }
5481   
5482    /**
5483    * Gets the value of the wrapAlignment property.
5484    *
5485    * @return possible object is {@link Boolean }
5486    *
5487    */
 
5488  85 toggle public Boolean isWrapAlignment()
5489    {
5490  85 return wrapAlignment;
5491    }
5492   
5493    /**
5494    * Sets the value of the wrapAlignment property.
5495    *
5496    * @param value
5497    * allowed object is {@link Boolean }
5498    *
5499    */
 
5500  46 toggle public void setWrapAlignment(Boolean value)
5501    {
5502  46 this.wrapAlignment = value;
5503    }
5504   
5505    /**
5506    * Gets the value of the renderGaps property.
5507    *
5508    * @return possible object is {@link Boolean }
5509    *
5510    */
 
5511  85 toggle public Boolean isRenderGaps()
5512    {
5513  85 return renderGaps;
5514    }
5515   
5516    /**
5517    * Sets the value of the renderGaps property.
5518    *
5519    * @param value
5520    * allowed object is {@link Boolean }
5521    *
5522    */
 
5523  46 toggle public void setRenderGaps(Boolean value)
5524    {
5525  46 this.renderGaps = value;
5526    }
5527   
5528    /**
5529    * Gets the value of the showSequenceFeatures property.
5530    *
5531    * @return possible object is {@link Boolean }
5532    *
5533    */
 
5534  85 toggle public Boolean isShowSequenceFeatures()
5535    {
5536  85 return showSequenceFeatures;
5537    }
5538   
5539    /**
5540    * Sets the value of the showSequenceFeatures property.
5541    *
5542    * @param value
5543    * allowed object is {@link Boolean }
5544    *
5545    */
 
5546  46 toggle public void setShowSequenceFeatures(Boolean value)
5547    {
5548  46 this.showSequenceFeatures = value;
5549    }
5550   
5551    /**
5552    * Gets the value of the showNPfeatureTooltip property.
5553    *
5554    * @return possible object is {@link Boolean }
5555    *
5556    */
 
5557  85 toggle public Boolean isShowNPfeatureTooltip()
5558    {
5559  85 return showNPfeatureTooltip;
5560    }
5561   
5562    /**
5563    * Sets the value of the showNPfeatureTooltip property.
5564    *
5565    * @param value
5566    * allowed object is {@link Boolean }
5567    *
5568    */
 
5569  46 toggle public void setShowNPfeatureTooltip(Boolean value)
5570    {
5571  46 this.showNPfeatureTooltip = value;
5572    }
5573   
5574    /**
5575    * Gets the value of the showDbRefTooltip property.
5576    *
5577    * @return possible object is {@link Boolean }
5578    *
5579    */
 
5580  85 toggle public Boolean isShowDbRefTooltip()
5581    {
5582  85 return showDbRefTooltip;
5583    }
5584   
5585    /**
5586    * Sets the value of the showDbRefTooltip property.
5587    *
5588    * @param value
5589    * allowed object is {@link Boolean }
5590    *
5591    */
 
5592  46 toggle public void setShowDbRefTooltip(Boolean value)
5593    {
5594  46 this.showDbRefTooltip = value;
5595    }
5596   
5597    /**
5598    * Gets the value of the followHighlight property.
5599    *
5600    * @return possible object is {@link Boolean }
5601    *
5602    */
 
5603  85 toggle public boolean isFollowHighlight()
5604    {
5605  85 if (followHighlight == null)
5606    {
5607  0 return true;
5608    }
5609    else
5610    {
5611  85 return followHighlight;
5612    }
5613    }
5614   
5615    /**
5616    * Sets the value of the followHighlight property.
5617    *
5618    * @param value
5619    * allowed object is {@link Boolean }
5620    *
5621    */
 
5622  46 toggle public void setFollowHighlight(Boolean value)
5623    {
5624  46 this.followHighlight = value;
5625    }
5626   
5627    /**
5628    * Gets the value of the followSelection property.
5629    *
5630    * @return possible object is {@link Boolean }
5631    *
5632    */
 
5633  85 toggle public boolean isFollowSelection()
5634    {
5635  85 if (followSelection == null)
5636    {
5637  0 return true;
5638    }
5639    else
5640    {
5641  85 return followSelection;
5642    }
5643    }
5644   
5645    /**
5646    * Sets the value of the followSelection property.
5647    *
5648    * @param value
5649    * allowed object is {@link Boolean }
5650    *
5651    */
 
5652  46 toggle public void setFollowSelection(Boolean value)
5653    {
5654  46 this.followSelection = value;
5655    }
5656   
5657    /**
5658    * Gets the value of the showAnnotation property.
5659    *
5660    * @return possible object is {@link Boolean }
5661    *
5662    */
 
5663  170 toggle public Boolean isShowAnnotation()
5664    {
5665  170 return showAnnotation;
5666    }
5667   
5668    /**
5669    * Sets the value of the showAnnotation property.
5670    *
5671    * @param value
5672    * allowed object is {@link Boolean }
5673    *
5674    */
 
5675  46 toggle public void setShowAnnotation(Boolean value)
5676    {
5677  46 this.showAnnotation = value;
5678    }
5679   
5680    /**
5681    * Gets the value of the centreColumnLabels property.
5682    *
5683    * @return possible object is {@link Boolean }
5684    *
5685    */
 
5686  85 toggle public boolean isCentreColumnLabels()
5687    {
5688  85 if (centreColumnLabels == null)
5689    {
5690  85 return false;
5691    }
5692    else
5693    {
5694  0 return centreColumnLabels;
5695    }
5696    }
5697   
5698    /**
5699    * Sets the value of the centreColumnLabels property.
5700    *
5701    * @param value
5702    * allowed object is {@link Boolean }
5703    *
5704    */
 
5705  0 toggle public void setCentreColumnLabels(Boolean value)
5706    {
5707  0 this.centreColumnLabels = value;
5708    }
5709   
5710    /**
5711    * Gets the value of the showGroupConservation property.
5712    *
5713    * @return possible object is {@link Boolean }
5714    *
5715    */
 
5716  85 toggle public boolean isShowGroupConservation()
5717    {
5718  85 if (showGroupConservation == null)
5719    {
5720  0 return false;
5721    }
5722    else
5723    {
5724  85 return showGroupConservation;
5725    }
5726    }
5727   
5728    /**
5729    * Sets the value of the showGroupConservation property.
5730    *
5731    * @param value
5732    * allowed object is {@link Boolean }
5733    *
5734    */
 
5735  46 toggle public void setShowGroupConservation(Boolean value)
5736    {
5737  46 this.showGroupConservation = value;
5738    }
5739   
5740    /**
5741    * Gets the value of the showGroupConsensus property.
5742    *
5743    * @return possible object is {@link Boolean }
5744    *
5745    */
 
5746  85 toggle public boolean isShowGroupConsensus()
5747    {
5748  85 if (showGroupConsensus == null)
5749    {
5750  0 return false;
5751    }
5752    else
5753    {
5754  85 return showGroupConsensus;
5755    }
5756    }
5757   
5758    /**
5759    * Sets the value of the showGroupConsensus property.
5760    *
5761    * @param value
5762    * allowed object is {@link Boolean }
5763    *
5764    */
 
5765  46 toggle public void setShowGroupConsensus(Boolean value)
5766    {
5767  46 this.showGroupConsensus = value;
5768    }
5769   
5770    /**
5771    * Gets the value of the showConsensusHistogram property.
5772    *
5773    * @return possible object is {@link Boolean }
5774    *
5775    */
 
5776  85 toggle public boolean isShowConsensusHistogram()
5777    {
5778  85 if (showConsensusHistogram == null)
5779    {
5780  0 return true;
5781    }
5782    else
5783    {
5784  85 return showConsensusHistogram;
5785    }
5786    }
5787   
5788    /**
5789    * Sets the value of the showConsensusHistogram property.
5790    *
5791    * @param value
5792    * allowed object is {@link Boolean }
5793    *
5794    */
 
5795  46 toggle public void setShowConsensusHistogram(Boolean value)
5796    {
5797  46 this.showConsensusHistogram = value;
5798    }
5799   
5800    /**
5801    * Gets the value of the showSequenceLogo property.
5802    *
5803    * @return possible object is {@link Boolean }
5804    *
5805    */
 
5806  85 toggle public boolean isShowSequenceLogo()
5807    {
5808  85 if (showSequenceLogo == null)
5809    {
5810  0 return false;
5811    }
5812    else
5813    {
5814  85 return showSequenceLogo;
5815    }
5816    }
5817   
5818    /**
5819    * Sets the value of the showSequenceLogo property.
5820    *
5821    * @param value
5822    * allowed object is {@link Boolean }
5823    *
5824    */
 
5825  46 toggle public void setShowSequenceLogo(Boolean value)
5826    {
5827  46 this.showSequenceLogo = value;
5828    }
5829   
5830    /**
5831    * Gets the value of the normaliseSequenceLogo property.
5832    *
5833    * @return possible object is {@link Boolean }
5834    *
5835    */
 
5836  85 toggle public boolean isNormaliseSequenceLogo()
5837    {
5838  85 if (normaliseSequenceLogo == null)
5839    {
5840  30 return false;
5841    }
5842    else
5843    {
5844  55 return normaliseSequenceLogo;
5845    }
5846    }
5847   
5848    /**
5849    * Sets the value of the normaliseSequenceLogo property.
5850    *
5851    * @param value
5852    * allowed object is {@link Boolean }
5853    *
5854    */
 
5855  46 toggle public void setNormaliseSequenceLogo(Boolean value)
5856    {
5857  46 this.normaliseSequenceLogo = value;
5858    }
5859   
5860    /**
5861    * Gets the value of the ignoreGapsinConsensus property.
5862    *
5863    * @return possible object is {@link Boolean }
5864    *
5865    */
 
5866  170 toggle public boolean isIgnoreGapsinConsensus()
5867    {
5868  170 if (ignoreGapsinConsensus == null)
5869    {
5870  0 return true;
5871    }
5872    else
5873    {
5874  170 return ignoreGapsinConsensus;
5875    }
5876    }
5877   
5878    /**
5879    * Sets the value of the ignoreGapsinConsensus property.
5880    *
5881    * @param value
5882    * allowed object is {@link Boolean }
5883    *
5884    */
 
5885  46 toggle public void setIgnoreGapsinConsensus(Boolean value)
5886    {
5887  46 this.ignoreGapsinConsensus = value;
5888    }
5889   
5890    /**
5891    * Gets the value of the startRes property.
5892    *
5893    * @return possible object is {@link Integer }
5894    *
5895    */
 
5896  85 toggle public Integer getStartRes()
5897    {
5898  85 return startRes;
5899    }
5900   
5901    /**
5902    * Sets the value of the startRes property.
5903    *
5904    * @param value
5905    * allowed object is {@link Integer }
5906    *
5907    */
 
5908  46 toggle public void setStartRes(Integer value)
5909    {
5910  46 this.startRes = value;
5911    }
5912   
5913    /**
5914    * Gets the value of the startSeq property.
5915    *
5916    * @return possible object is {@link Integer }
5917    *
5918    */
 
5919  0 toggle public Integer getStartSeq()
5920    {
5921  0 return startSeq;
5922    }
5923   
5924    /**
5925    * Sets the value of the startSeq property.
5926    *
5927    * @param value
5928    * allowed object is {@link Integer }
5929    *
5930    */
 
5931  46 toggle public void setStartSeq(Integer value)
5932    {
5933  46 this.startSeq = value;
5934    }
5935   
5936    /**
5937    * Gets the value of the charWidth property.
5938    *
5939    * @return possible object is {@link Integer }
5940    *
5941    */
 
5942  212 toggle public Integer getCharWidth()
5943    {
5944  212 return charWidth;
5945    }
5946   
5947    /**
5948    * Sets the value of the charWidth property.
5949    *
5950    * @param value
5951    * allowed object is {@link Integer }
5952    *
5953    */
 
5954  46 toggle public void setCharWidth(Integer value)
5955    {
5956  46 this.charWidth = value;
5957    }
5958   
5959    /**
5960    * Gets the value of the charHeight property.
5961    *
5962    * @return possible object is {@link Integer }
5963    *
5964    */
 
5965  42 toggle public Integer getCharHeight()
5966    {
5967  42 return charHeight;
5968    }
5969   
5970    /**
5971    * Sets the value of the charHeight property.
5972    *
5973    * @param value
5974    * allowed object is {@link Integer }
5975    *
5976    */
 
5977  46 toggle public void setCharHeight(Integer value)
5978    {
5979  46 this.charHeight = value;
5980    }
5981   
5982    /**
5983    * Gets the value of the fontName property.
5984    *
5985    * @return possible object is {@link String }
5986    *
5987    */
 
5988  85 toggle public String getFontName()
5989    {
5990  85 return fontName;
5991    }
5992   
5993    /**
5994    * Sets the value of the fontName property.
5995    *
5996    * @param value
5997    * allowed object is {@link String }
5998    *
5999    */
 
6000  46 toggle public void setFontName(String value)
6001    {
6002  46 this.fontName = value;
6003    }
6004   
6005    /**
6006    * Gets the value of the fontSize property.
6007    *
6008    * @return possible object is {@link Integer }
6009    *
6010    */
 
6011  85 toggle public Integer getFontSize()
6012    {
6013  85 return fontSize;
6014    }
6015   
6016    /**
6017    * Sets the value of the fontSize property.
6018    *
6019    * @param value
6020    * allowed object is {@link Integer }
6021    *
6022    */
 
6023  46 toggle public void setFontSize(Integer value)
6024    {
6025  46 this.fontSize = value;
6026    }
6027   
6028    /**
6029    * Gets the value of the fontStyle property.
6030    *
6031    * @return possible object is {@link Integer }
6032    *
6033    */
 
6034  85 toggle public Integer getFontStyle()
6035    {
6036  85 return fontStyle;
6037    }
6038   
6039    /**
6040    * Sets the value of the fontStyle property.
6041    *
6042    * @param value
6043    * allowed object is {@link Integer }
6044    *
6045    */
 
6046  46 toggle public void setFontStyle(Integer value)
6047    {
6048  46 this.fontStyle = value;
6049    }
6050   
6051    /**
6052    * Gets the value of the idWidth property.
6053    *
6054    * @return possible object is {@link Integer }
6055    *
6056    */
 
6057  127 toggle public Integer getIdWidth()
6058    {
6059  127 return idWidth;
6060    }
6061   
6062    /**
6063    * Sets the value of the idWidth property.
6064    *
6065    * @param value
6066    * allowed object is {@link Integer }
6067    *
6068    */
 
6069  46 toggle public void setIdWidth(Integer value)
6070    {
6071  46 this.idWidth = value;
6072    }
6073   
6074    /**
6075    * Gets the value of the idWidthManuallyAdjusted property.
6076    *
6077    * @return possible object is {@link Boolean }
6078    *
6079    */
 
6080  42 toggle public Boolean isIdWidthManuallyAdjusted()
6081    {
6082  42 return idWidthManuallyAdjusted;
6083    }
6084   
6085    /**
6086    * Sets the value of the idWidthManuallyAdjusted property.
6087    *
6088    * @param value
6089    * allowed object is {@link Boolean }
6090    *
6091    */
 
6092  46 toggle public void setIdWidthManuallyAdjusted(Boolean value)
6093    {
6094  46 this.idWidthManuallyAdjusted = value;
6095    }
6096   
6097    /**
6098    * Gets the value of the scaleProteinAsCdna property.
6099    *
6100    * @return possible object is {@link Boolean }
6101    *
6102    */
 
6103  85 toggle public boolean isScaleProteinAsCdna()
6104    {
6105  85 if (scaleProteinAsCdna == null)
6106    {
6107  30 return true;
6108    }
6109    else
6110    {
6111  55 return scaleProteinAsCdna;
6112    }
6113    }
6114   
6115    /**
6116    * Sets the value of the scaleProteinAsCdna property.
6117    *
6118    * @param value
6119    * allowed object is {@link Boolean }
6120    *
6121    */
 
6122  46 toggle public void setScaleProteinAsCdna(Boolean value)
6123    {
6124  46 this.scaleProteinAsCdna = value;
6125    }
6126   
6127    /**
6128    * Gets the value of the viewName property.
6129    *
6130    * @return possible object is {@link String }
6131    *
6132    */
 
6133  144 toggle public String getViewName()
6134    {
6135  144 return viewName;
6136    }
6137   
6138    /**
6139    * Sets the value of the viewName property.
6140    *
6141    * @param value
6142    * allowed object is {@link String }
6143    *
6144    */
 
6145  46 toggle public void setViewName(String value)
6146    {
6147  46 this.viewName = value;
6148    }
6149   
6150    /**
6151    * Gets the value of the sequenceSetId property.
6152    *
6153    * @return possible object is {@link String }
6154    *
6155    */
 
6156  170 toggle public String getSequenceSetId()
6157    {
6158  170 return sequenceSetId;
6159    }
6160   
6161    /**
6162    * Sets the value of the sequenceSetId property.
6163    *
6164    * @param value
6165    * allowed object is {@link String }
6166    *
6167    */
 
6168  46 toggle public void setSequenceSetId(String value)
6169    {
6170  46 this.sequenceSetId = value;
6171    }
6172   
6173    /**
6174    * Gets the value of the gatheredViews property.
6175    *
6176    * @return possible object is {@link Boolean }
6177    *
6178    */
 
6179  85 toggle public Boolean isGatheredViews()
6180    {
6181  85 return gatheredViews;
6182    }
6183   
6184    /**
6185    * Sets the value of the gatheredViews property.
6186    *
6187    * @param value
6188    * allowed object is {@link Boolean }
6189    *
6190    */
 
6191  46 toggle public void setGatheredViews(Boolean value)
6192    {
6193  46 this.gatheredViews = value;
6194    }
6195   
6196    /**
6197    * Gets the value of the textCol1 property.
6198    *
6199    * @return possible object is {@link Integer }
6200    *
6201    */
 
6202  85 toggle public Integer getTextCol1()
6203    {
6204  85 return textCol1;
6205    }
6206   
6207    /**
6208    * Sets the value of the textCol1 property.
6209    *
6210    * @param value
6211    * allowed object is {@link Integer }
6212    *
6213    */
 
6214  46 toggle public void setTextCol1(Integer value)
6215    {
6216  46 this.textCol1 = value;
6217    }
6218   
6219    /**
6220    * Gets the value of the textCol2 property.
6221    *
6222    * @return possible object is {@link Integer }
6223    *
6224    */
 
6225  85 toggle public Integer getTextCol2()
6226    {
6227  85 return textCol2;
6228    }
6229   
6230    /**
6231    * Sets the value of the textCol2 property.
6232    *
6233    * @param value
6234    * allowed object is {@link Integer }
6235    *
6236    */
 
6237  46 toggle public void setTextCol2(Integer value)
6238    {
6239  46 this.textCol2 = value;
6240    }
6241   
6242    /**
6243    * Gets the value of the textColThreshold property.
6244    *
6245    * @return possible object is {@link Integer }
6246    *
6247    */
 
6248  85 toggle public Integer getTextColThreshold()
6249    {
6250  85 return textColThreshold;
6251    }
6252   
6253    /**
6254    * Sets the value of the textColThreshold property.
6255    *
6256    * @param value
6257    * allowed object is {@link Integer }
6258    *
6259    */
 
6260  46 toggle public void setTextColThreshold(Integer value)
6261    {
6262  46 this.textColThreshold = value;
6263    }
6264   
6265    /**
6266    * Gets the value of the id property.
6267    *
6268    * @return possible object is {@link String }
6269    *
6270    */
 
6271  160 toggle public String getId()
6272    {
6273  160 return id;
6274    }
6275   
6276    /**
6277    * Sets the value of the id property.
6278    *
6279    * @param value
6280    * allowed object is {@link String }
6281    *
6282    */
 
6283  56 toggle public void setId(String value)
6284    {
6285  56 this.id = value;
6286    }
6287   
6288    /**
6289    * Gets the value of the complementId property.
6290    *
6291    * @return possible object is {@link String }
6292    *
6293    */
 
6294  85 toggle public String getComplementId()
6295    {
6296  85 return complementId;
6297    }
6298   
6299    /**
6300    * Sets the value of the complementId property.
6301    *
6302    * @param value
6303    * allowed object is {@link String }
6304    *
6305    */
 
6306  0 toggle public void setComplementId(String value)
6307    {
6308  0 this.complementId = value;
6309    }
6310   
6311    /**
6312    * Gets the value of the showComplementFeatures property.
6313    *
6314    * @return possible object is {@link Boolean }
6315    *
6316    */
 
6317  85 toggle public boolean isShowComplementFeatures()
6318    {
6319  85 if (showComplementFeatures == null)
6320    {
6321  43 return false;
6322    }
6323    else
6324    {
6325  42 return showComplementFeatures;
6326    }
6327    }
6328   
6329    /**
6330    * Sets the value of the showComplementFeatures property.
6331    *
6332    * @param value
6333    * allowed object is {@link Boolean }
6334    *
6335    */
 
6336  46 toggle public void setShowComplementFeatures(Boolean value)
6337    {
6338  46 this.showComplementFeatures = value;
6339    }
6340   
6341    /**
6342    * Gets the value of the showComplementFeaturesOnTop property.
6343    *
6344    * @return possible object is {@link Boolean }
6345    *
6346    */
 
6347  85 toggle public boolean isShowComplementFeaturesOnTop()
6348    {
6349  85 if (showComplementFeaturesOnTop == null)
6350    {
6351  43 return false;
6352    }
6353    else
6354    {
6355  42 return showComplementFeaturesOnTop;
6356    }
6357    }
6358   
6359    /**
6360    * Sets the value of the showComplementFeaturesOnTop property.
6361    *
6362    * @param value
6363    * allowed object is {@link Boolean }
6364    *
6365    */
 
6366  46 toggle public void setShowComplementFeaturesOnTop(Boolean value)
6367    {
6368  46 this.showComplementFeaturesOnTop = value;
6369    }
6370   
6371    /**
6372    * Gets the value of the width property.
6373    *
6374    * @return possible object is {@link Integer }
6375    *
6376    */
 
6377  255 toggle public Integer getWidth()
6378    {
6379  255 return width;
6380    }
6381   
6382    /**
6383    * Sets the value of the width property.
6384    *
6385    * @param value
6386    * allowed object is {@link Integer }
6387    *
6388    */
 
6389  46 toggle public void setWidth(Integer value)
6390    {
6391  46 this.width = value;
6392    }
6393   
6394    /**
6395    * Gets the value of the height property.
6396    *
6397    * @return possible object is {@link Integer }
6398    *
6399    */
 
6400  255 toggle public Integer getHeight()
6401    {
6402  255 return height;
6403    }
6404   
6405    /**
6406    * Sets the value of the height property.
6407    *
6408    * @param value
6409    * allowed object is {@link Integer }
6410    *
6411    */
 
6412  46 toggle public void setHeight(Integer value)
6413    {
6414  46 this.height = value;
6415    }
6416   
6417    /**
6418    * Gets the value of the xpos property.
6419    *
6420    * @return possible object is {@link Integer }
6421    *
6422    */
 
6423  85 toggle public Integer getXpos()
6424    {
6425  85 return xpos;
6426    }
6427   
6428    /**
6429    * Sets the value of the xpos property.
6430    *
6431    * @param value
6432    * allowed object is {@link Integer }
6433    *
6434    */
 
6435  46 toggle public void setXpos(Integer value)
6436    {
6437  46 this.xpos = value;
6438    }
6439   
6440    /**
6441    * Gets the value of the ypos property.
6442    *
6443    * @return possible object is {@link Integer }
6444    *
6445    */
 
6446  85 toggle public Integer getYpos()
6447    {
6448  85 return ypos;
6449    }
6450   
6451    /**
6452    * Sets the value of the ypos property.
6453    *
6454    * @param value
6455    * allowed object is {@link Integer }
6456    *
6457    */
 
6458  46 toggle public void setYpos(Integer value)
6459    {
6460  46 this.ypos = value;
6461    }
6462   
6463    /**
6464    * &lt;p&gt;Java class for anonymous complex type.
6465    *
6466    * &lt;p&gt;The following schema fragment specifies the expected content
6467    * contained within this class.
6468    *
6469    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
6470    * &amp;lt;extension
6471    * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
6472    * &amp;lt;attribute name="calcId" use="required"
6473    * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6474    * &amp;lt;attribute name="needsUpdate"
6475    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
6476    * /&amp;gt; &amp;lt;attribute name="autoUpdate" use="required"
6477    * type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
6478    * &amp;lt;/extension&amp;gt; &amp;lt;/complexContent&amp;gt;
6479    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
6480    *
6481    *
6482    */
6483    @XmlAccessorType(XmlAccessType.FIELD)
6484    @XmlType(name = "")
 
6485    public static class CalcIdParam extends WebServiceParameterSet
6486    {
6487   
6488    @XmlAttribute(name = "calcId", required = true)
6489    protected String calcId;
6490   
6491    @XmlAttribute(name = "needsUpdate")
6492    protected Boolean needsUpdate;
6493   
6494    @XmlAttribute(name = "autoUpdate", required = true)
6495    protected boolean autoUpdate;
6496   
6497    /**
6498    * Gets the value of the calcId property.
6499    *
6500    * @return possible object is {@link String }
6501    *
6502    */
 
6503  0 toggle public String getCalcId()
6504    {
6505  0 return calcId;
6506    }
6507   
6508    /**
6509    * Sets the value of the calcId property.
6510    *
6511    * @param value
6512    * allowed object is {@link String }
6513    *
6514    */
 
6515  0 toggle public void setCalcId(String value)
6516    {
6517  0 this.calcId = value;
6518    }
6519   
6520    /**
6521    * Gets the value of the needsUpdate property.
6522    *
6523    * @return possible object is {@link Boolean }
6524    *
6525    */
 
6526  0 toggle public boolean isNeedsUpdate()
6527    {
6528  0 if (needsUpdate == null)
6529    {
6530  0 return false;
6531    }
6532    else
6533    {
6534  0 return needsUpdate;
6535    }
6536    }
6537   
6538    /**
6539    * Sets the value of the needsUpdate property.
6540    *
6541    * @param value
6542    * allowed object is {@link Boolean }
6543    *
6544    */
 
6545  0 toggle public void setNeedsUpdate(Boolean value)
6546    {
6547  0 this.needsUpdate = value;
6548    }
6549   
6550    /**
6551    * Gets the value of the autoUpdate property.
6552    *
6553    */
 
6554  0 toggle public boolean isAutoUpdate()
6555    {
6556  0 return autoUpdate;
6557    }
6558   
6559    /**
6560    * Sets the value of the autoUpdate property.
6561    *
6562    */
 
6563  0 toggle public void setAutoUpdate(boolean value)
6564    {
6565  0 this.autoUpdate = value;
6566    }
6567   
6568    }
6569   
6570    /**
6571    * &lt;p&gt;Java class for anonymous complex type.
6572    *
6573    * &lt;p&gt;The following schema fragment specifies the expected content
6574    * contained within this class.
6575    *
6576    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
6577    * &amp;lt;restriction
6578    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
6579    * &amp;lt;attribute name="start"
6580    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
6581    * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6582    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
6583    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
6584    *
6585    *
6586    */
6587    @XmlAccessorType(XmlAccessType.FIELD)
6588    @XmlType(name = "")
 
6589    public static class HiddenColumns
6590    {
6591   
6592    @XmlAttribute(name = "start")
6593    protected Integer start;
6594   
6595    @XmlAttribute(name = "end")
6596    protected Integer end;
6597   
6598    /**
6599    * Gets the value of the start property.
6600    *
6601    * @return possible object is {@link Integer }
6602    *
6603    */
 
6604  54 toggle public Integer getStart()
6605    {
6606  54 return start;
6607    }
6608   
6609    /**
6610    * Sets the value of the start property.
6611    *
6612    * @param value
6613    * allowed object is {@link Integer }
6614    *
6615    */
 
6616  6 toggle public void setStart(Integer value)
6617    {
6618  6 this.start = value;
6619    }
6620   
6621    /**
6622    * Gets the value of the end property.
6623    *
6624    * @return possible object is {@link Integer }
6625    *
6626    */
 
6627  54 toggle public Integer getEnd()
6628    {
6629  54 return end;
6630    }
6631   
6632    /**
6633    * Sets the value of the end property.
6634    *
6635    * @param value
6636    * allowed object is {@link Integer }
6637    *
6638    */
 
6639  6 toggle public void setEnd(Integer value)
6640    {
6641  6 this.end = value;
6642    }
6643   
6644    }
6645   
6646    /**
6647    * &lt;p&gt;Java class for anonymous complex type.
6648    *
6649    * &lt;p&gt;The following schema fragment specifies the expected content
6650    * contained within this class.
6651    *
6652    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
6653    * &amp;lt;restriction
6654    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attGroup
6655    * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
6656    * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
6657    * /&amp;gt; &amp;lt;attribute name="residueColour"
6658    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
6659    * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
6660    * &amp;lt;attribute name="hiddenColour"
6661    * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
6662    * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
6663    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
6664    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
6665    *
6666    *
6667    */
6668    @XmlAccessorType(XmlAccessType.FIELD)
6669    @XmlType(name = "")
 
6670    public static class Overview
6671    {
6672   
6673    @XmlAttribute(name = "showHidden")
6674    protected Boolean showHidden;
6675   
6676    @XmlAttribute(name = "residueColour")
6677    protected Integer residueColour;
6678   
6679    @XmlAttribute(name = "gapColour")
6680    protected Integer gapColour;
6681   
6682    @XmlAttribute(name = "hiddenColour")
6683    protected Integer hiddenColour;
6684   
6685    @XmlAttribute(name = "title")
6686    protected String title;
6687   
6688    @XmlAttribute(name = "width")
6689    protected Integer width;
6690   
6691    @XmlAttribute(name = "height")
6692    protected Integer height;
6693   
6694    @XmlAttribute(name = "xpos")
6695    protected Integer xpos;
6696   
6697    @XmlAttribute(name = "ypos")
6698    protected Integer ypos;
6699   
6700    /**
6701    * Gets the value of the showHidden property.
6702    *
6703    * @return possible object is {@link Boolean }
6704    *
6705    */
 
6706  11 toggle public Boolean isShowHidden()
6707    {
6708  11 return showHidden;
6709    }
6710   
6711    /**
6712    * Sets the value of the showHidden property.
6713    *
6714    * @param value
6715    * allowed object is {@link Boolean }
6716    *
6717    */
 
6718  14 toggle public void setShowHidden(Boolean value)
6719    {
6720  14 this.showHidden = value;
6721    }
6722   
6723    /**
6724    * Gets the value of the residueColour property.
6725    *
6726    * @return possible object is {@link Integer }
6727    *
6728    */
 
6729  11 toggle public Integer getResidueColour()
6730    {
6731  11 return residueColour;
6732    }
6733   
6734    /**
6735    * Sets the value of the residueColour property.
6736    *
6737    * @param value
6738    * allowed object is {@link Integer }
6739    *
6740    */
 
6741  14 toggle public void setResidueColour(Integer value)
6742    {
6743  14 this.residueColour = value;
6744    }
6745   
6746    /**
6747    * Gets the value of the gapColour property.
6748    *
6749    * @return possible object is {@link Integer }
6750    *
6751    */
 
6752  11 toggle public Integer getGapColour()
6753    {
6754  11 return gapColour;
6755    }
6756   
6757    /**
6758    * Sets the value of the gapColour property.
6759    *
6760    * @param value
6761    * allowed object is {@link Integer }
6762    *
6763    */
 
6764  14 toggle public void setGapColour(Integer value)
6765    {
6766  14 this.gapColour = value;
6767    }
6768   
6769    /**
6770    * Gets the value of the hiddenColour property.
6771    *
6772    * @return possible object is {@link Integer }
6773    *
6774    */
 
6775  11 toggle public Integer getHiddenColour()
6776    {
6777  11 return hiddenColour;
6778    }
6779   
6780    /**
6781    * Sets the value of the hiddenColour property.
6782    *
6783    * @param value
6784    * allowed object is {@link Integer }
6785    *
6786    */
 
6787  14 toggle public void setHiddenColour(Integer value)
6788    {
6789  14 this.hiddenColour = value;
6790    }
6791   
6792    /**
6793    * Gets the value of the title property.
6794    *
6795    * @return possible object is {@link String }
6796    *
6797    */
 
6798  11 toggle public String getTitle()
6799    {
6800  11 return title;
6801    }
6802   
6803    /**
6804    * Sets the value of the title property.
6805    *
6806    * @param value
6807    * allowed object is {@link String }
6808    *
6809    */
 
6810  14 toggle public void setTitle(String value)
6811    {
6812  14 this.title = value;
6813    }
6814   
6815    /**
6816    * Gets the value of the width property.
6817    *
6818    * @return possible object is {@link Integer }
6819    *
6820    */
 
6821  11 toggle public Integer getWidth()
6822    {
6823  11 return width;
6824    }
6825   
6826    /**
6827    * Sets the value of the width property.
6828    *
6829    * @param value
6830    * allowed object is {@link Integer }
6831    *
6832    */
 
6833  14 toggle public void setWidth(Integer value)
6834    {
6835  14 this.width = value;
6836    }
6837   
6838    /**
6839    * Gets the value of the height property.
6840    *
6841    * @return possible object is {@link Integer }
6842    *
6843    */
 
6844  11 toggle public Integer getHeight()
6845    {
6846  11 return height;
6847    }
6848   
6849    /**
6850    * Sets the value of the height property.
6851    *
6852    * @param value
6853    * allowed object is {@link Integer }
6854    *
6855    */
 
6856  14 toggle public void setHeight(Integer value)
6857    {
6858  14 this.height = value;
6859    }
6860   
6861    /**
6862    * Gets the value of the xpos property.
6863    *
6864    * @return possible object is {@link Integer }
6865    *
6866    */
 
6867  11 toggle public Integer getXpos()
6868    {
6869  11 return xpos;
6870    }
6871   
6872    /**
6873    * Sets the value of the xpos property.
6874    *
6875    * @param value
6876    * allowed object is {@link Integer }
6877    *
6878    */
 
6879  14 toggle public void setXpos(Integer value)
6880    {
6881  14 this.xpos = value;
6882    }
6883   
6884    /**
6885    * Gets the value of the ypos property.
6886    *
6887    * @return possible object is {@link Integer }
6888    *
6889    */
 
6890  11 toggle public Integer getYpos()
6891    {
6892  11 return ypos;
6893    }
6894   
6895    /**
6896    * Sets the value of the ypos property.
6897    *
6898    * @param value
6899    * allowed object is {@link Integer }
6900    *
6901    */
 
6902  14 toggle public void setYpos(Integer value)
6903    {
6904  14 this.ypos = value;
6905    }
6906   
6907    }
6908   
6909    }
6910   
6911    }