2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
4 // Any modifications to this file will be lost upon recompilation of the source schema.
5 // Generated on: 2023.01.31 at 04:07:08 PM GMT
9 package jalview.xml.binding.jalview;
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
27 * <p>Java class for JalviewModel complex type.
29 * <p>The following schema fragment specifies the expected content contained within this class.
32 * <complexType name="JalviewModel">
34 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
36 * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
37 * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
38 * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
40 * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
43 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
45 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
46 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
49 * <extension base="{www.jalview.org}pdbentry">
51 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
54 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
55 * <attGroup ref="{www.jalview.org}swingwindow"/>
56 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
57 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
58 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
59 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
60 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
68 * </complexContent>
71 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
72 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
75 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
77 * <element name="secondaryStructure" maxOccurs="unbounded">
80 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
81 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
82 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
83 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
84 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
86 * </complexContent>
90 * <attGroup ref="{www.jalview.org}swingwindow"/>
91 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
92 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
93 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
94 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
96 * </complexContent>
100 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
101 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
102 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
104 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
105 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
107 * </complexContent>
110 * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
112 * <complexContent>
113 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
115 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
116 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
118 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
119 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
120 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
121 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
122 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
123 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
125 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
126 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
129 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
130 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
131 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
132 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
133 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
135 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
138 * </complexContent>
141 * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
143 * <complexContent>
144 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
146 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
149 * <complexContent>
150 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
151 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
154 * </complexContent>
157 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
159 * <complexContent>
160 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
161 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
162 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
163 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
165 * </complexContent>
168 * <element name="overview" minOccurs="0">
170 * <complexContent>
171 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
172 * <attGroup ref="{www.jalview.org}swingwindow"/>
173 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
174 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
175 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
176 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
177 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
179 * </complexContent>
183 * <attGroup ref="{www.jalview.org}swingwindow"/>
184 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
187 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
188 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
189 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
190 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
191 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
192 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
193 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
194 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
195 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
196 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
197 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
198 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
199 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
200 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
201 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
202 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
203 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
204 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
205 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
206 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
207 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
208 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
209 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
210 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
211 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
212 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
213 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
214 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
215 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
216 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
217 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
218 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
219 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
220 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
221 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
222 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
223 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
224 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
225 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
226 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
228 * </complexContent>
231 * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
233 * <complexContent>
234 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
236 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
238 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
240 * </complexContent>
243 * <element name="tree" maxOccurs="unbounded" minOccurs="0">
245 * <complexContent>
246 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
247 * <sequence minOccurs="0">
248 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
249 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
251 * <attGroup ref="{www.jalview.org}swingwindow"/>
252 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
253 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
254 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
255 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
256 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
257 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
258 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
259 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
260 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
261 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
262 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
264 * </complexContent>
267 * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
269 * <complexContent>
270 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
272 * <element name="sequencePoint" maxOccurs="unbounded">
274 * <complexContent>
275 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
276 * <attGroup ref="{www.jalview.org}position"/>
277 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
279 * </complexContent>
282 * <element name="axis" maxOccurs="3" minOccurs="3">
284 * <complexContent>
285 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
286 * <attGroup ref="{www.jalview.org}position"/>
288 * </complexContent>
291 * <element name="seqPointMin">
293 * <complexContent>
294 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
295 * <attGroup ref="{www.jalview.org}position"/>
297 * </complexContent>
300 * <element name="seqPointMax">
302 * <complexContent>
303 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
304 * <attGroup ref="{www.jalview.org}position"/>
306 * </complexContent>
309 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
311 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
312 * <attGroup ref="{www.jalview.org}swingwindow"/>
313 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
314 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
315 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
316 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
317 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
318 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
319 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
320 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
321 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
323 * </complexContent>
326 * <element name="FeatureSettings" minOccurs="0">
328 * <complexContent>
329 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
331 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
333 * <complexContent>
334 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
336 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
337 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
339 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
340 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
341 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
342 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
343 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
344 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
345 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
346 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
347 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
348 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
349 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
350 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
352 * </complexContent>
355 * <element name="group" maxOccurs="unbounded" minOccurs="0">
357 * <complexContent>
358 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
359 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
360 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
362 * </complexContent>
367 * </complexContent>
373 * </complexContent>
379 @XmlAccessorType(XmlAccessType.FIELD)
380 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
392 public class JalviewModel {
394 @XmlElement(required = true)
395 @XmlSchemaType(name = "dateTime")
396 protected XMLGregorianCalendar creationDate;
397 @XmlElement(required = true)
398 protected String version;
399 @XmlElement(required = true)
400 protected VAMSAS vamsasModel;
401 @XmlElement(name = "JSeq")
402 protected List<JalviewModel.JSeq> jSeq;
403 @XmlElement(name = "JGroup")
404 protected List<JalviewModel.JGroup> jGroup;
405 @XmlElement(name = "Viewport")
406 protected List<JalviewModel.Viewport> viewport;
407 @XmlElement(name = "UserColours")
408 protected List<JalviewModel.UserColours> userColours;
409 protected List<JalviewModel.Tree> tree;
410 @XmlElement(name = "PcaViewer")
411 protected List<JalviewModel.PcaViewer> pcaViewer;
412 @XmlElement(name = "FeatureSettings")
413 protected JalviewModel.FeatureSettings featureSettings;
416 * Gets the value of the creationDate property.
420 * {@link XMLGregorianCalendar }
423 public XMLGregorianCalendar getCreationDate() {
428 * Sets the value of the creationDate property.
432 * {@link XMLGregorianCalendar }
435 public void setCreationDate(XMLGregorianCalendar value) {
436 this.creationDate = value;
440 * Gets the value of the version property.
447 public String getVersion() {
452 * Sets the value of the version property.
459 public void setVersion(String value) {
460 this.version = value;
464 * Gets the value of the vamsasModel property.
471 public VAMSAS getVamsasModel() {
476 * Sets the value of the vamsasModel property.
483 public void setVamsasModel(VAMSAS value) {
484 this.vamsasModel = value;
488 * Gets the value of the jSeq property.
491 * This accessor method returns a reference to the live list,
492 * not a snapshot. Therefore any modification you make to the
493 * returned list will be present inside the JAXB object.
494 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
497 * For example, to add a new item, do as follows:
499 * getJSeq().add(newItem);
504 * Objects of the following type(s) are allowed in the list
505 * {@link JalviewModel.JSeq }
509 public List<JalviewModel.JSeq> getJSeq() {
511 jSeq = new ArrayList<JalviewModel.JSeq>();
517 * Gets the value of the jGroup property.
520 * This accessor method returns a reference to the live list,
521 * not a snapshot. Therefore any modification you make to the
522 * returned list will be present inside the JAXB object.
523 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
526 * For example, to add a new item, do as follows:
528 * getJGroup().add(newItem);
533 * Objects of the following type(s) are allowed in the list
534 * {@link JalviewModel.JGroup }
538 public List<JalviewModel.JGroup> getJGroup() {
539 if (jGroup == null) {
540 jGroup = new ArrayList<JalviewModel.JGroup>();
546 * Gets the value of the viewport property.
549 * This accessor method returns a reference to the live list,
550 * not a snapshot. Therefore any modification you make to the
551 * returned list will be present inside the JAXB object.
552 * This is why there is not a <CODE>set</CODE> method for the viewport property.
555 * For example, to add a new item, do as follows:
557 * getViewport().add(newItem);
562 * Objects of the following type(s) are allowed in the list
563 * {@link JalviewModel.Viewport }
567 public List<JalviewModel.Viewport> getViewport() {
568 if (viewport == null) {
569 viewport = new ArrayList<JalviewModel.Viewport>();
571 return this.viewport;
575 * Gets the value of the userColours property.
578 * This accessor method returns a reference to the live list,
579 * not a snapshot. Therefore any modification you make to the
580 * returned list will be present inside the JAXB object.
581 * This is why there is not a <CODE>set</CODE> method for the userColours property.
584 * For example, to add a new item, do as follows:
586 * getUserColours().add(newItem);
591 * Objects of the following type(s) are allowed in the list
592 * {@link JalviewModel.UserColours }
596 public List<JalviewModel.UserColours> getUserColours() {
597 if (userColours == null) {
598 userColours = new ArrayList<JalviewModel.UserColours>();
600 return this.userColours;
604 * Gets the value of the tree property.
607 * This accessor method returns a reference to the live list,
608 * not a snapshot. Therefore any modification you make to the
609 * returned list will be present inside the JAXB object.
610 * This is why there is not a <CODE>set</CODE> method for the tree property.
613 * For example, to add a new item, do as follows:
615 * getTree().add(newItem);
620 * Objects of the following type(s) are allowed in the list
621 * {@link JalviewModel.Tree }
625 public List<JalviewModel.Tree> getTree() {
627 tree = new ArrayList<JalviewModel.Tree>();
633 * Gets the value of the pcaViewer property.
636 * This accessor method returns a reference to the live list,
637 * not a snapshot. Therefore any modification you make to the
638 * returned list will be present inside the JAXB object.
639 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
642 * For example, to add a new item, do as follows:
644 * getPcaViewer().add(newItem);
649 * Objects of the following type(s) are allowed in the list
650 * {@link JalviewModel.PcaViewer }
654 public List<JalviewModel.PcaViewer> getPcaViewer() {
655 if (pcaViewer == null) {
656 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
658 return this.pcaViewer;
662 * Gets the value of the featureSettings property.
666 * {@link JalviewModel.FeatureSettings }
669 public JalviewModel.FeatureSettings getFeatureSettings() {
670 return featureSettings;
674 * Sets the value of the featureSettings property.
678 * {@link JalviewModel.FeatureSettings }
681 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
682 this.featureSettings = value;
687 * <p>Java class for anonymous complex type.
689 * <p>The following schema fragment specifies the expected content contained within this class.
693 * <complexContent>
694 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
696 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
698 * <complexContent>
699 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
701 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
702 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
704 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
705 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
706 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
707 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
708 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
709 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
710 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
711 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
712 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
713 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
714 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
715 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
717 * </complexContent>
720 * <element name="group" maxOccurs="unbounded" minOccurs="0">
722 * <complexContent>
723 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
724 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
725 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
727 * </complexContent>
732 * </complexContent>
738 @XmlAccessorType(XmlAccessType.FIELD)
739 @XmlType(name = "", propOrder = {
743 public static class FeatureSettings {
745 @XmlElement(namespace = "www.jalview.org")
746 protected List<JalviewModel.FeatureSettings.Setting> setting;
747 @XmlElement(namespace = "www.jalview.org")
748 protected List<JalviewModel.FeatureSettings.Group> group;
751 * Gets the value of the setting property.
754 * This accessor method returns a reference to the live list,
755 * not a snapshot. Therefore any modification you make to the
756 * returned list will be present inside the JAXB object.
757 * This is why there is not a <CODE>set</CODE> method for the setting property.
760 * For example, to add a new item, do as follows:
762 * getSetting().add(newItem);
767 * Objects of the following type(s) are allowed in the list
768 * {@link JalviewModel.FeatureSettings.Setting }
772 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
773 if (setting == null) {
774 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
780 * Gets the value of the group property.
783 * This accessor method returns a reference to the live list,
784 * not a snapshot. Therefore any modification you make to the
785 * returned list will be present inside the JAXB object.
786 * This is why there is not a <CODE>set</CODE> method for the group property.
789 * For example, to add a new item, do as follows:
791 * getGroup().add(newItem);
796 * Objects of the following type(s) are allowed in the list
797 * {@link JalviewModel.FeatureSettings.Group }
801 public List<JalviewModel.FeatureSettings.Group> getGroup() {
803 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
810 * <p>Java class for anonymous complex type.
812 * <p>The following schema fragment specifies the expected content contained within this class.
816 * <complexContent>
817 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
818 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
819 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
821 * </complexContent>
827 @XmlAccessorType(XmlAccessType.FIELD)
829 public static class Group {
831 @XmlAttribute(name = "name", required = true)
832 protected String name;
833 @XmlAttribute(name = "display", required = true)
834 protected boolean display;
837 * Gets the value of the name property.
844 public String getName() {
849 * Sets the value of the name property.
856 public void setName(String value) {
861 * Gets the value of the display property.
864 public boolean isDisplay() {
869 * Sets the value of the display property.
872 public void setDisplay(boolean value) {
873 this.display = value;
880 * <p>Java class for anonymous complex type.
882 * <p>The following schema fragment specifies the expected content contained within this class.
886 * <complexContent>
887 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
889 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
890 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
892 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
893 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
894 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
895 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
896 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
897 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
898 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
899 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
900 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
901 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
902 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
903 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
905 * </complexContent>
911 @XmlAccessorType(XmlAccessType.FIELD)
912 @XmlType(name = "", propOrder = {
916 public static class Setting {
918 @XmlElement(namespace = "www.jalview.org")
919 protected List<String> attributeName;
920 @XmlElement(namespace = "www.jalview.org")
921 protected FeatureMatcherSet matcherSet;
922 @XmlAttribute(name = "type", required = true)
923 protected String type;
924 @XmlAttribute(name = "colour", required = true)
925 protected int colour;
926 @XmlAttribute(name = "display", required = true)
927 protected boolean display;
928 @XmlAttribute(name = "order")
929 protected Float order;
930 @XmlAttribute(name = "mincolour")
931 protected Integer mincolour;
932 @XmlAttribute(name = "noValueColour")
933 protected NoValueColour noValueColour;
934 @XmlAttribute(name = "threshold")
935 protected Float threshold;
936 @XmlAttribute(name = "threshstate")
937 protected Integer threshstate;
938 @XmlAttribute(name = "max")
940 @XmlAttribute(name = "min")
942 @XmlAttribute(name = "colourByLabel")
943 protected Boolean colourByLabel;
944 @XmlAttribute(name = "autoScale")
945 protected Boolean autoScale;
948 * Gets the value of the attributeName property.
951 * This accessor method returns a reference to the live list,
952 * not a snapshot. Therefore any modification you make to the
953 * returned list will be present inside the JAXB object.
954 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
957 * For example, to add a new item, do as follows:
959 * getAttributeName().add(newItem);
964 * Objects of the following type(s) are allowed in the list
969 public List<String> getAttributeName() {
970 if (attributeName == null) {
971 attributeName = new ArrayList<String>();
973 return this.attributeName;
977 * Gets the value of the matcherSet property.
981 * {@link FeatureMatcherSet }
984 public FeatureMatcherSet getMatcherSet() {
989 * Sets the value of the matcherSet property.
993 * {@link FeatureMatcherSet }
996 public void setMatcherSet(FeatureMatcherSet value) {
997 this.matcherSet = value;
1001 * Gets the value of the type property.
1004 * possible object is
1008 public String getType() {
1013 * Sets the value of the type property.
1020 public void setType(String value) {
1025 * Gets the value of the colour property.
1028 public int getColour() {
1033 * Sets the value of the colour property.
1036 public void setColour(int value) {
1037 this.colour = value;
1041 * Gets the value of the display property.
1044 public boolean isDisplay() {
1049 * Sets the value of the display property.
1052 public void setDisplay(boolean value) {
1053 this.display = value;
1057 * Gets the value of the order property.
1060 * possible object is
1064 public Float getOrder() {
1069 * Sets the value of the order property.
1076 public void setOrder(Float value) {
1081 * Gets the value of the mincolour property.
1084 * possible object is
1088 public Integer getMincolour() {
1093 * Sets the value of the mincolour property.
1100 public void setMincolour(Integer value) {
1101 this.mincolour = value;
1105 * Gets the value of the noValueColour property.
1108 * possible object is
1109 * {@link NoValueColour }
1112 public NoValueColour getNoValueColour() {
1113 if (noValueColour == null) {
1114 return NoValueColour.MIN;
1116 return noValueColour;
1121 * Sets the value of the noValueColour property.
1125 * {@link NoValueColour }
1128 public void setNoValueColour(NoValueColour value) {
1129 this.noValueColour = value;
1133 * Gets the value of the threshold property.
1136 * possible object is
1140 public Float getThreshold() {
1145 * Sets the value of the threshold property.
1152 public void setThreshold(Float value) {
1153 this.threshold = value;
1157 * Gets the value of the threshstate property.
1160 * possible object is
1164 public Integer getThreshstate() {
1169 * Sets the value of the threshstate property.
1176 public void setThreshstate(Integer value) {
1177 this.threshstate = value;
1181 * Gets the value of the max property.
1184 * possible object is
1188 public Float getMax() {
1193 * Sets the value of the max property.
1200 public void setMax(Float value) {
1205 * Gets the value of the min property.
1208 * possible object is
1212 public Float getMin() {
1217 * Sets the value of the min property.
1224 public void setMin(Float value) {
1229 * Gets the value of the colourByLabel property.
1232 * possible object is
1236 public Boolean isColourByLabel() {
1237 return colourByLabel;
1241 * Sets the value of the colourByLabel property.
1248 public void setColourByLabel(Boolean value) {
1249 this.colourByLabel = value;
1253 * Gets the value of the autoScale property.
1256 * possible object is
1260 public Boolean isAutoScale() {
1265 * Sets the value of the autoScale property.
1272 public void setAutoScale(Boolean value) {
1273 this.autoScale = value;
1282 * <p>Java class for anonymous complex type.
1284 * <p>The following schema fragment specifies the expected content contained within this class.
1288 * <complexContent>
1289 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1291 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1292 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1294 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1295 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1296 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1297 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1298 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1299 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1300 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1301 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1302 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1303 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1304 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1305 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1306 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1307 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1308 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1309 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1310 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1311 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1312 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1314 * </complexContent>
1320 @XmlAccessorType(XmlAccessType.FIELD)
1321 @XmlType(name = "", propOrder = {
1325 public static class JGroup {
1327 @XmlElement(namespace = "www.jalview.org", required = true)
1328 protected List<String> seq;
1329 @XmlElement(namespace = "www.jalview.org")
1330 protected AnnotationColourScheme annotationColours;
1331 @XmlAttribute(name = "start")
1332 protected Integer start;
1333 @XmlAttribute(name = "end")
1334 protected Integer end;
1335 @XmlAttribute(name = "name")
1336 protected String name;
1337 @XmlAttribute(name = "colour")
1338 protected String colour;
1339 @XmlAttribute(name = "consThreshold")
1340 protected Integer consThreshold;
1341 @XmlAttribute(name = "pidThreshold")
1342 protected Integer pidThreshold;
1343 @XmlAttribute(name = "outlineColour")
1344 protected Integer outlineColour;
1345 @XmlAttribute(name = "displayBoxes")
1346 protected Boolean displayBoxes;
1347 @XmlAttribute(name = "displayText")
1348 protected Boolean displayText;
1349 @XmlAttribute(name = "colourText")
1350 protected Boolean colourText;
1351 @XmlAttribute(name = "textCol1")
1352 protected Integer textCol1;
1353 @XmlAttribute(name = "textCol2")
1354 protected Integer textCol2;
1355 @XmlAttribute(name = "textColThreshold")
1356 protected Integer textColThreshold;
1357 @XmlAttribute(name = "showUnconserved")
1358 protected Boolean showUnconserved;
1359 @XmlAttribute(name = "ignoreGapsinConsensus")
1360 protected Boolean ignoreGapsinConsensus;
1361 @XmlAttribute(name = "showConsensusHistogram")
1362 protected Boolean showConsensusHistogram;
1363 @XmlAttribute(name = "showSequenceLogo")
1364 protected Boolean showSequenceLogo;
1365 @XmlAttribute(name = "normaliseSequenceLogo")
1366 protected Boolean normaliseSequenceLogo;
1367 @XmlAttribute(name = "id")
1368 protected String id;
1371 * Gets the value of the seq property.
1374 * This accessor method returns a reference to the live list,
1375 * not a snapshot. Therefore any modification you make to the
1376 * returned list will be present inside the JAXB object.
1377 * This is why there is not a <CODE>set</CODE> method for the seq property.
1380 * For example, to add a new item, do as follows:
1382 * getSeq().add(newItem);
1387 * Objects of the following type(s) are allowed in the list
1392 public List<String> getSeq() {
1394 seq = new ArrayList<String>();
1400 * Gets the value of the annotationColours property.
1403 * possible object is
1404 * {@link AnnotationColourScheme }
1407 public AnnotationColourScheme getAnnotationColours() {
1408 return annotationColours;
1412 * Sets the value of the annotationColours property.
1416 * {@link AnnotationColourScheme }
1419 public void setAnnotationColours(AnnotationColourScheme value) {
1420 this.annotationColours = value;
1424 * Gets the value of the start property.
1427 * possible object is
1431 public Integer getStart() {
1436 * Sets the value of the start property.
1443 public void setStart(Integer value) {
1448 * Gets the value of the end property.
1451 * possible object is
1455 public Integer getEnd() {
1460 * Sets the value of the end property.
1467 public void setEnd(Integer value) {
1472 * Gets the value of the name property.
1475 * possible object is
1479 public String getName() {
1484 * Sets the value of the name property.
1491 public void setName(String value) {
1496 * Gets the value of the colour property.
1499 * possible object is
1503 public String getColour() {
1508 * Sets the value of the colour property.
1515 public void setColour(String value) {
1516 this.colour = value;
1520 * Gets the value of the consThreshold property.
1523 * possible object is
1527 public Integer getConsThreshold() {
1528 return consThreshold;
1532 * Sets the value of the consThreshold property.
1539 public void setConsThreshold(Integer value) {
1540 this.consThreshold = value;
1544 * Gets the value of the pidThreshold property.
1547 * possible object is
1551 public Integer getPidThreshold() {
1552 return pidThreshold;
1556 * Sets the value of the pidThreshold property.
1563 public void setPidThreshold(Integer value) {
1564 this.pidThreshold = value;
1568 * Gets the value of the outlineColour property.
1571 * possible object is
1575 public Integer getOutlineColour() {
1576 return outlineColour;
1580 * Sets the value of the outlineColour property.
1587 public void setOutlineColour(Integer value) {
1588 this.outlineColour = value;
1592 * Gets the value of the displayBoxes property.
1595 * possible object is
1599 public Boolean isDisplayBoxes() {
1600 return displayBoxes;
1604 * Sets the value of the displayBoxes property.
1611 public void setDisplayBoxes(Boolean value) {
1612 this.displayBoxes = value;
1616 * Gets the value of the displayText property.
1619 * possible object is
1623 public Boolean isDisplayText() {
1628 * Sets the value of the displayText property.
1635 public void setDisplayText(Boolean value) {
1636 this.displayText = value;
1640 * Gets the value of the colourText property.
1643 * possible object is
1647 public Boolean isColourText() {
1652 * Sets the value of the colourText property.
1659 public void setColourText(Boolean value) {
1660 this.colourText = value;
1664 * Gets the value of the textCol1 property.
1667 * possible object is
1671 public Integer getTextCol1() {
1676 * Sets the value of the textCol1 property.
1683 public void setTextCol1(Integer value) {
1684 this.textCol1 = value;
1688 * Gets the value of the textCol2 property.
1691 * possible object is
1695 public Integer getTextCol2() {
1700 * Sets the value of the textCol2 property.
1707 public void setTextCol2(Integer value) {
1708 this.textCol2 = value;
1712 * Gets the value of the textColThreshold property.
1715 * possible object is
1719 public Integer getTextColThreshold() {
1720 return textColThreshold;
1724 * Sets the value of the textColThreshold property.
1731 public void setTextColThreshold(Integer value) {
1732 this.textColThreshold = value;
1736 * Gets the value of the showUnconserved property.
1739 * possible object is
1743 public Boolean isShowUnconserved() {
1744 return showUnconserved;
1748 * Sets the value of the showUnconserved property.
1755 public void setShowUnconserved(Boolean value) {
1756 this.showUnconserved = value;
1760 * Gets the value of the ignoreGapsinConsensus property.
1763 * possible object is
1767 public boolean isIgnoreGapsinConsensus() {
1768 if (ignoreGapsinConsensus == null) {
1771 return ignoreGapsinConsensus;
1776 * Sets the value of the ignoreGapsinConsensus property.
1783 public void setIgnoreGapsinConsensus(Boolean value) {
1784 this.ignoreGapsinConsensus = value;
1788 * Gets the value of the showConsensusHistogram property.
1791 * possible object is
1795 public boolean isShowConsensusHistogram() {
1796 if (showConsensusHistogram == null) {
1799 return showConsensusHistogram;
1804 * Sets the value of the showConsensusHistogram property.
1811 public void setShowConsensusHistogram(Boolean value) {
1812 this.showConsensusHistogram = value;
1816 * Gets the value of the showSequenceLogo property.
1819 * possible object is
1823 public boolean isShowSequenceLogo() {
1824 if (showSequenceLogo == null) {
1827 return showSequenceLogo;
1832 * Sets the value of the showSequenceLogo property.
1839 public void setShowSequenceLogo(Boolean value) {
1840 this.showSequenceLogo = value;
1844 * Gets the value of the normaliseSequenceLogo property.
1847 * possible object is
1851 public boolean isNormaliseSequenceLogo() {
1852 if (normaliseSequenceLogo == null) {
1855 return normaliseSequenceLogo;
1860 * Sets the value of the normaliseSequenceLogo property.
1867 public void setNormaliseSequenceLogo(Boolean value) {
1868 this.normaliseSequenceLogo = value;
1872 * Gets the value of the id property.
1875 * possible object is
1879 public String getId() {
1884 * Sets the value of the id property.
1891 public void setId(String value) {
1899 * <p>Java class for anonymous complex type.
1901 * <p>The following schema fragment specifies the expected content contained within this class.
1905 * <complexContent>
1906 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1908 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1909 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1911 * <complexContent>
1912 * <extension base="{www.jalview.org}pdbentry">
1914 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1916 * <simpleContent>
1917 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1918 * <attGroup ref="{www.jalview.org}swingwindow"/>
1919 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1920 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1921 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1922 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1923 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1924 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1926 * </simpleContent>
1931 * </complexContent>
1934 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1935 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1937 * <complexContent>
1938 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1940 * <element name="secondaryStructure" maxOccurs="unbounded">
1942 * <complexContent>
1943 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1944 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1945 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1946 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1947 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1949 * </complexContent>
1953 * <attGroup ref="{www.jalview.org}swingwindow"/>
1954 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1955 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1956 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1957 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1959 * </complexContent>
1963 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1964 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1965 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1966 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1967 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1968 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1970 * </complexContent>
1976 @XmlAccessorType(XmlAccessType.FIELD)
1977 @XmlType(name = "", propOrder = {
1983 public static class JSeq {
1985 @XmlElement(namespace = "www.jalview.org")
1986 protected List<Feature> features;
1987 @XmlElement(namespace = "www.jalview.org")
1988 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1989 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1990 protected List<Integer> hiddenSequences;
1991 @XmlElement(namespace = "www.jalview.org")
1992 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1993 @XmlAttribute(name = "colour")
1994 protected Integer colour;
1995 @XmlAttribute(name = "start", required = true)
1996 protected int start;
1997 @XmlAttribute(name = "end", required = true)
1999 @XmlAttribute(name = "id", required = true)
2000 protected String id;
2001 @XmlAttribute(name = "hidden")
2002 protected Boolean hidden;
2003 @XmlAttribute(name = "viewreference")
2004 protected Boolean viewreference;
2007 * Gets the value of the features property.
2010 * This accessor method returns a reference to the live list,
2011 * not a snapshot. Therefore any modification you make to the
2012 * returned list will be present inside the JAXB object.
2013 * This is why there is not a <CODE>set</CODE> method for the features property.
2016 * For example, to add a new item, do as follows:
2018 * getFeatures().add(newItem);
2023 * Objects of the following type(s) are allowed in the list
2028 public List<Feature> getFeatures() {
2029 if (features == null) {
2030 features = new ArrayList<Feature>();
2032 return this.features;
2036 * Gets the value of the pdbids property.
2039 * This accessor method returns a reference to the live list,
2040 * not a snapshot. Therefore any modification you make to the
2041 * returned list will be present inside the JAXB object.
2042 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2045 * For example, to add a new item, do as follows:
2047 * getPdbids().add(newItem);
2052 * Objects of the following type(s) are allowed in the list
2053 * {@link JalviewModel.JSeq.Pdbids }
2057 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2058 if (pdbids == null) {
2059 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2065 * Gets the value of the hiddenSequences property.
2068 * This accessor method returns a reference to the live list,
2069 * not a snapshot. Therefore any modification you make to the
2070 * returned list will be present inside the JAXB object.
2071 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2074 * For example, to add a new item, do as follows:
2076 * getHiddenSequences().add(newItem);
2081 * Objects of the following type(s) are allowed in the list
2086 public List<Integer> getHiddenSequences() {
2087 if (hiddenSequences == null) {
2088 hiddenSequences = new ArrayList<Integer>();
2090 return this.hiddenSequences;
2094 * Gets the value of the rnaViewer property.
2097 * This accessor method returns a reference to the live list,
2098 * not a snapshot. Therefore any modification you make to the
2099 * returned list will be present inside the JAXB object.
2100 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2103 * For example, to add a new item, do as follows:
2105 * getRnaViewer().add(newItem);
2110 * Objects of the following type(s) are allowed in the list
2111 * {@link JalviewModel.JSeq.RnaViewer }
2115 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2116 if (rnaViewer == null) {
2117 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2119 return this.rnaViewer;
2123 * Gets the value of the colour property.
2126 * possible object is
2130 public Integer getColour() {
2135 * Sets the value of the colour property.
2142 public void setColour(Integer value) {
2143 this.colour = value;
2147 * Gets the value of the start property.
2150 public int getStart() {
2155 * Sets the value of the start property.
2158 public void setStart(int value) {
2163 * Gets the value of the end property.
2166 public int getEnd() {
2171 * Sets the value of the end property.
2174 public void setEnd(int value) {
2179 * Gets the value of the id property.
2182 * possible object is
2186 public String getId() {
2191 * Sets the value of the id property.
2198 public void setId(String value) {
2203 * Gets the value of the hidden property.
2206 * possible object is
2210 public Boolean isHidden() {
2215 * Sets the value of the hidden property.
2222 public void setHidden(Boolean value) {
2223 this.hidden = value;
2227 * Gets the value of the viewreference property.
2230 * possible object is
2234 public Boolean isViewreference() {
2235 return viewreference;
2239 * Sets the value of the viewreference property.
2246 public void setViewreference(Boolean value) {
2247 this.viewreference = value;
2252 * <p>Java class for anonymous complex type.
2254 * <p>The following schema fragment specifies the expected content contained within this class.
2258 * <complexContent>
2259 * <extension base="{www.jalview.org}pdbentry">
2261 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2263 * <simpleContent>
2264 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2265 * <attGroup ref="{www.jalview.org}swingwindow"/>
2266 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2267 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2268 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2269 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2270 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2271 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2273 * </simpleContent>
2278 * </complexContent>
2284 @XmlAccessorType(XmlAccessType.FIELD)
2285 @XmlType(name = "", propOrder = {
2288 public static class Pdbids
2292 @XmlElement(namespace = "www.jalview.org")
2293 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2296 * Gets the value of the structureState property.
2299 * This accessor method returns a reference to the live list,
2300 * not a snapshot. Therefore any modification you make to the
2301 * returned list will be present inside the JAXB object.
2302 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2305 * For example, to add a new item, do as follows:
2307 * getStructureState().add(newItem);
2312 * Objects of the following type(s) are allowed in the list
2313 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2317 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2318 if (structureState == null) {
2319 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2321 return this.structureState;
2326 * <p>Java class for anonymous complex type.
2328 * <p>The following schema fragment specifies the expected content contained within this class.
2332 * <simpleContent>
2333 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2334 * <attGroup ref="{www.jalview.org}swingwindow"/>
2335 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2336 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2337 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2338 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2339 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2340 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2342 * </simpleContent>
2348 @XmlAccessorType(XmlAccessType.FIELD)
2349 @XmlType(name = "", propOrder = {
2352 public static class StructureState {
2355 protected String value;
2356 @XmlAttribute(name = "visible")
2357 protected Boolean visible;
2358 @XmlAttribute(name = "viewId")
2359 protected String viewId;
2360 @XmlAttribute(name = "alignwithAlignPanel")
2361 protected Boolean alignwithAlignPanel;
2362 @XmlAttribute(name = "colourwithAlignPanel")
2363 protected Boolean colourwithAlignPanel;
2364 @XmlAttribute(name = "colourByJmol")
2365 protected Boolean colourByJmol;
2366 @XmlAttribute(name = "type")
2367 protected String type;
2368 @XmlAttribute(name = "width")
2369 protected Integer width;
2370 @XmlAttribute(name = "height")
2371 protected Integer height;
2372 @XmlAttribute(name = "xpos")
2373 protected Integer xpos;
2374 @XmlAttribute(name = "ypos")
2375 protected Integer ypos;
2378 * Gets the value of the value property.
2381 * possible object is
2385 public String getValue() {
2390 * Sets the value of the value property.
2397 public void setValue(String value) {
2402 * Gets the value of the visible property.
2405 * possible object is
2409 public Boolean isVisible() {
2414 * Sets the value of the visible property.
2421 public void setVisible(Boolean value) {
2422 this.visible = value;
2426 * Gets the value of the viewId property.
2429 * possible object is
2433 public String getViewId() {
2438 * Sets the value of the viewId property.
2445 public void setViewId(String value) {
2446 this.viewId = value;
2450 * Gets the value of the alignwithAlignPanel property.
2453 * possible object is
2457 public boolean isAlignwithAlignPanel() {
2458 if (alignwithAlignPanel == null) {
2461 return alignwithAlignPanel;
2466 * Sets the value of the alignwithAlignPanel property.
2473 public void setAlignwithAlignPanel(Boolean value) {
2474 this.alignwithAlignPanel = value;
2478 * Gets the value of the colourwithAlignPanel property.
2481 * possible object is
2485 public boolean isColourwithAlignPanel() {
2486 if (colourwithAlignPanel == null) {
2489 return colourwithAlignPanel;
2494 * Sets the value of the colourwithAlignPanel property.
2501 public void setColourwithAlignPanel(Boolean value) {
2502 this.colourwithAlignPanel = value;
2506 * Gets the value of the colourByJmol property.
2509 * possible object is
2513 public boolean isColourByJmol() {
2514 if (colourByJmol == null) {
2517 return colourByJmol;
2522 * Sets the value of the colourByJmol property.
2529 public void setColourByJmol(Boolean value) {
2530 this.colourByJmol = value;
2534 * Gets the value of the type property.
2537 * possible object is
2541 public String getType() {
2546 * Sets the value of the type property.
2553 public void setType(String value) {
2558 * Gets the value of the width property.
2561 * possible object is
2565 public Integer getWidth() {
2570 * Sets the value of the width property.
2577 public void setWidth(Integer value) {
2582 * Gets the value of the height property.
2585 * possible object is
2589 public Integer getHeight() {
2594 * Sets the value of the height property.
2601 public void setHeight(Integer value) {
2602 this.height = value;
2606 * Gets the value of the xpos property.
2609 * possible object is
2613 public Integer getXpos() {
2618 * Sets the value of the xpos property.
2625 public void setXpos(Integer value) {
2630 * Gets the value of the ypos property.
2633 * possible object is
2637 public Integer getYpos() {
2642 * Sets the value of the ypos property.
2649 public void setYpos(Integer value) {
2659 * <p>Java class for anonymous complex type.
2661 * <p>The following schema fragment specifies the expected content contained within this class.
2665 * <complexContent>
2666 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2668 * <element name="secondaryStructure" maxOccurs="unbounded">
2670 * <complexContent>
2671 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2672 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2673 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2674 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2675 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2677 * </complexContent>
2681 * <attGroup ref="{www.jalview.org}swingwindow"/>
2682 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2683 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2684 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2685 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2687 * </complexContent>
2693 @XmlAccessorType(XmlAccessType.FIELD)
2694 @XmlType(name = "", propOrder = {
2695 "secondaryStructure"
2697 public static class RnaViewer {
2699 @XmlElement(namespace = "www.jalview.org", required = true)
2700 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2701 @XmlAttribute(name = "title")
2702 protected String title;
2703 @XmlAttribute(name = "viewId")
2704 protected String viewId;
2705 @XmlAttribute(name = "dividerLocation")
2706 protected Integer dividerLocation;
2707 @XmlAttribute(name = "selectedRna")
2708 protected Integer selectedRna;
2709 @XmlAttribute(name = "width")
2710 protected Integer width;
2711 @XmlAttribute(name = "height")
2712 protected Integer height;
2713 @XmlAttribute(name = "xpos")
2714 protected Integer xpos;
2715 @XmlAttribute(name = "ypos")
2716 protected Integer ypos;
2719 * Gets the value of the secondaryStructure property.
2722 * This accessor method returns a reference to the live list,
2723 * not a snapshot. Therefore any modification you make to the
2724 * returned list will be present inside the JAXB object.
2725 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2728 * For example, to add a new item, do as follows:
2730 * getSecondaryStructure().add(newItem);
2735 * Objects of the following type(s) are allowed in the list
2736 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2740 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2741 if (secondaryStructure == null) {
2742 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2744 return this.secondaryStructure;
2748 * Gets the value of the title property.
2751 * possible object is
2755 public String getTitle() {
2760 * Sets the value of the title property.
2767 public void setTitle(String value) {
2772 * Gets the value of the viewId property.
2775 * possible object is
2779 public String getViewId() {
2784 * Sets the value of the viewId property.
2791 public void setViewId(String value) {
2792 this.viewId = value;
2796 * Gets the value of the dividerLocation property.
2799 * possible object is
2803 public Integer getDividerLocation() {
2804 return dividerLocation;
2808 * Sets the value of the dividerLocation property.
2815 public void setDividerLocation(Integer value) {
2816 this.dividerLocation = value;
2820 * Gets the value of the selectedRna property.
2823 * possible object is
2827 public Integer getSelectedRna() {
2832 * Sets the value of the selectedRna property.
2839 public void setSelectedRna(Integer value) {
2840 this.selectedRna = value;
2844 * Gets the value of the width property.
2847 * possible object is
2851 public Integer getWidth() {
2856 * Sets the value of the width property.
2863 public void setWidth(Integer value) {
2868 * Gets the value of the height property.
2871 * possible object is
2875 public Integer getHeight() {
2880 * Sets the value of the height property.
2887 public void setHeight(Integer value) {
2888 this.height = value;
2892 * Gets the value of the xpos property.
2895 * possible object is
2899 public Integer getXpos() {
2904 * Sets the value of the xpos property.
2911 public void setXpos(Integer value) {
2916 * Gets the value of the ypos property.
2919 * possible object is
2923 public Integer getYpos() {
2928 * Sets the value of the ypos property.
2935 public void setYpos(Integer value) {
2941 * <p>Java class for anonymous complex type.
2943 * <p>The following schema fragment specifies the expected content contained within this class.
2947 * <complexContent>
2948 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2949 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2950 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2951 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2952 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2954 * </complexContent>
2960 @XmlAccessorType(XmlAccessType.FIELD)
2962 public static class SecondaryStructure {
2964 @XmlAttribute(name = "title")
2965 protected String title;
2966 @XmlAttribute(name = "annotationId", required = true)
2967 protected String annotationId;
2968 @XmlAttribute(name = "gapped")
2969 protected Boolean gapped;
2970 @XmlAttribute(name = "viewerState")
2971 protected String viewerState;
2974 * Gets the value of the title property.
2977 * possible object is
2981 public String getTitle() {
2986 * Sets the value of the title property.
2993 public void setTitle(String value) {
2998 * Gets the value of the annotationId property.
3001 * possible object is
3005 public String getAnnotationId() {
3006 return annotationId;
3010 * Sets the value of the annotationId property.
3017 public void setAnnotationId(String value) {
3018 this.annotationId = value;
3022 * Gets the value of the gapped property.
3025 * possible object is
3029 public Boolean isGapped() {
3034 * Sets the value of the gapped property.
3041 public void setGapped(Boolean value) {
3042 this.gapped = value;
3046 * Gets the value of the viewerState property.
3049 * possible object is
3053 public String getViewerState() {
3058 * Sets the value of the viewerState property.
3065 public void setViewerState(String value) {
3066 this.viewerState = value;
3077 * <p>Java class for anonymous complex type.
3079 * <p>The following schema fragment specifies the expected content contained within this class.
3083 * <complexContent>
3084 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3086 * <element name="sequencePoint" maxOccurs="unbounded">
3088 * <complexContent>
3089 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3090 * <attGroup ref="{www.jalview.org}position"/>
3091 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3093 * </complexContent>
3096 * <element name="axis" maxOccurs="3" minOccurs="3">
3098 * <complexContent>
3099 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3100 * <attGroup ref="{www.jalview.org}position"/>
3102 * </complexContent>
3105 * <element name="seqPointMin">
3107 * <complexContent>
3108 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3109 * <attGroup ref="{www.jalview.org}position"/>
3111 * </complexContent>
3114 * <element name="seqPointMax">
3116 * <complexContent>
3117 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3118 * <attGroup ref="{www.jalview.org}position"/>
3120 * </complexContent>
3123 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3125 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
3126 * <attGroup ref="{www.jalview.org}swingwindow"/>
3127 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3128 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3129 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3130 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3131 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3132 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3133 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3134 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3135 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3137 * </complexContent>
3143 @XmlAccessorType(XmlAccessType.FIELD)
3144 @XmlType(name = "", propOrder = {
3151 public static class PcaViewer {
3153 @XmlElement(namespace = "www.jalview.org", required = true)
3154 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3155 @XmlElement(namespace = "www.jalview.org", required = true)
3156 protected List<JalviewModel.PcaViewer.Axis> axis;
3157 @XmlElement(namespace = "www.jalview.org", required = true)
3158 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3159 @XmlElement(namespace = "www.jalview.org", required = true)
3160 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3161 @XmlElement(namespace = "www.jalview.org", required = true)
3162 protected PcaDataType pcaData;
3163 @XmlAttribute(name = "title")
3164 protected String title;
3165 @XmlAttribute(name = "scoreModelName")
3166 protected String scoreModelName;
3167 @XmlAttribute(name = "xDim")
3168 protected Integer xDim;
3169 @XmlAttribute(name = "yDim")
3170 protected Integer yDim;
3171 @XmlAttribute(name = "zDim")
3172 protected Integer zDim;
3173 @XmlAttribute(name = "bgColour")
3174 protected Integer bgColour;
3175 @XmlAttribute(name = "scaleFactor")
3176 protected Float scaleFactor;
3177 @XmlAttribute(name = "showLabels")
3178 protected Boolean showLabels;
3179 @XmlAttribute(name = "linkToAllViews")
3180 protected Boolean linkToAllViews;
3181 @XmlAttribute(name = "includeGaps")
3182 protected Boolean includeGaps;
3183 @XmlAttribute(name = "matchGaps")
3184 protected Boolean matchGaps;
3185 @XmlAttribute(name = "includeGappedColumns")
3186 protected Boolean includeGappedColumns;
3187 @XmlAttribute(name = "denominateByShortestLength")
3188 protected Boolean denominateByShortestLength;
3189 @XmlAttribute(name = "width")
3190 protected Integer width;
3191 @XmlAttribute(name = "height")
3192 protected Integer height;
3193 @XmlAttribute(name = "xpos")
3194 protected Integer xpos;
3195 @XmlAttribute(name = "ypos")
3196 protected Integer ypos;
3199 * Gets the value of the sequencePoint property.
3202 * This accessor method returns a reference to the live list,
3203 * not a snapshot. Therefore any modification you make to the
3204 * returned list will be present inside the JAXB object.
3205 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3208 * For example, to add a new item, do as follows:
3210 * getSequencePoint().add(newItem);
3215 * Objects of the following type(s) are allowed in the list
3216 * {@link JalviewModel.PcaViewer.SequencePoint }
3220 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3221 if (sequencePoint == null) {
3222 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3224 return this.sequencePoint;
3228 * Gets the value of the axis property.
3231 * This accessor method returns a reference to the live list,
3232 * not a snapshot. Therefore any modification you make to the
3233 * returned list will be present inside the JAXB object.
3234 * This is why there is not a <CODE>set</CODE> method for the axis property.
3237 * For example, to add a new item, do as follows:
3239 * getAxis().add(newItem);
3244 * Objects of the following type(s) are allowed in the list
3245 * {@link JalviewModel.PcaViewer.Axis }
3249 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3251 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3257 * Gets the value of the seqPointMin property.
3260 * possible object is
3261 * {@link JalviewModel.PcaViewer.SeqPointMin }
3264 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3269 * Sets the value of the seqPointMin property.
3273 * {@link JalviewModel.PcaViewer.SeqPointMin }
3276 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3277 this.seqPointMin = value;
3281 * Gets the value of the seqPointMax property.
3284 * possible object is
3285 * {@link JalviewModel.PcaViewer.SeqPointMax }
3288 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3293 * Sets the value of the seqPointMax property.
3297 * {@link JalviewModel.PcaViewer.SeqPointMax }
3300 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3301 this.seqPointMax = value;
3305 * Gets the value of the pcaData property.
3308 * possible object is
3309 * {@link PcaDataType }
3312 public PcaDataType getPcaData() {
3317 * Sets the value of the pcaData property.
3321 * {@link PcaDataType }
3324 public void setPcaData(PcaDataType value) {
3325 this.pcaData = value;
3329 * Gets the value of the title property.
3332 * possible object is
3336 public String getTitle() {
3341 * Sets the value of the title property.
3348 public void setTitle(String value) {
3353 * Gets the value of the scoreModelName property.
3356 * possible object is
3360 public String getScoreModelName() {
3361 return scoreModelName;
3365 * Sets the value of the scoreModelName property.
3372 public void setScoreModelName(String value) {
3373 this.scoreModelName = value;
3377 * Gets the value of the xDim property.
3380 * possible object is
3384 public Integer getXDim() {
3389 * Sets the value of the xDim property.
3396 public void setXDim(Integer value) {
3401 * Gets the value of the yDim property.
3404 * possible object is
3408 public Integer getYDim() {
3413 * Sets the value of the yDim property.
3420 public void setYDim(Integer value) {
3425 * Gets the value of the zDim property.
3428 * possible object is
3432 public Integer getZDim() {
3437 * Sets the value of the zDim property.
3444 public void setZDim(Integer value) {
3449 * Gets the value of the bgColour property.
3452 * possible object is
3456 public Integer getBgColour() {
3461 * Sets the value of the bgColour property.
3468 public void setBgColour(Integer value) {
3469 this.bgColour = value;
3473 * Gets the value of the scaleFactor property.
3476 * possible object is
3480 public Float getScaleFactor() {
3485 * Sets the value of the scaleFactor property.
3492 public void setScaleFactor(Float value) {
3493 this.scaleFactor = value;
3497 * Gets the value of the showLabels property.
3500 * possible object is
3504 public Boolean isShowLabels() {
3509 * Sets the value of the showLabels property.
3516 public void setShowLabels(Boolean value) {
3517 this.showLabels = value;
3521 * Gets the value of the linkToAllViews property.
3524 * possible object is
3528 public Boolean isLinkToAllViews() {
3529 return linkToAllViews;
3533 * Sets the value of the linkToAllViews property.
3540 public void setLinkToAllViews(Boolean value) {
3541 this.linkToAllViews = value;
3545 * Gets the value of the includeGaps property.
3548 * possible object is
3552 public Boolean isIncludeGaps() {
3557 * Sets the value of the includeGaps property.
3564 public void setIncludeGaps(Boolean value) {
3565 this.includeGaps = value;
3569 * Gets the value of the matchGaps property.
3572 * possible object is
3576 public Boolean isMatchGaps() {
3581 * Sets the value of the matchGaps property.
3588 public void setMatchGaps(Boolean value) {
3589 this.matchGaps = value;
3593 * Gets the value of the includeGappedColumns property.
3596 * possible object is
3600 public Boolean isIncludeGappedColumns() {
3601 return includeGappedColumns;
3605 * Sets the value of the includeGappedColumns property.
3612 public void setIncludeGappedColumns(Boolean value) {
3613 this.includeGappedColumns = value;
3617 * Gets the value of the denominateByShortestLength property.
3620 * possible object is
3624 public Boolean isDenominateByShortestLength() {
3625 return denominateByShortestLength;
3629 * Sets the value of the denominateByShortestLength property.
3636 public void setDenominateByShortestLength(Boolean value) {
3637 this.denominateByShortestLength = value;
3641 * Gets the value of the width property.
3644 * possible object is
3648 public Integer getWidth() {
3653 * Sets the value of the width property.
3660 public void setWidth(Integer value) {
3665 * Gets the value of the height property.
3668 * possible object is
3672 public Integer getHeight() {
3677 * Sets the value of the height property.
3684 public void setHeight(Integer value) {
3685 this.height = value;
3689 * Gets the value of the xpos property.
3692 * possible object is
3696 public Integer getXpos() {
3701 * Sets the value of the xpos property.
3708 public void setXpos(Integer value) {
3713 * Gets the value of the ypos property.
3716 * possible object is
3720 public Integer getYpos() {
3725 * Sets the value of the ypos property.
3732 public void setYpos(Integer value) {
3738 * <p>Java class for anonymous complex type.
3740 * <p>The following schema fragment specifies the expected content contained within this class.
3744 * <complexContent>
3745 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3746 * <attGroup ref="{www.jalview.org}position"/>
3748 * </complexContent>
3754 @XmlAccessorType(XmlAccessType.FIELD)
3756 public static class Axis {
3758 @XmlAttribute(name = "xPos")
3759 protected Float xPos;
3760 @XmlAttribute(name = "yPos")
3761 protected Float yPos;
3762 @XmlAttribute(name = "zPos")
3763 protected Float zPos;
3766 * Gets the value of the xPos property.
3769 * possible object is
3773 public Float getXPos() {
3778 * Sets the value of the xPos property.
3785 public void setXPos(Float value) {
3790 * Gets the value of the yPos property.
3793 * possible object is
3797 public Float getYPos() {
3802 * Sets the value of the yPos property.
3809 public void setYPos(Float value) {
3814 * Gets the value of the zPos property.
3817 * possible object is
3821 public Float getZPos() {
3826 * Sets the value of the zPos property.
3833 public void setZPos(Float value) {
3841 * <p>Java class for anonymous complex type.
3843 * <p>The following schema fragment specifies the expected content contained within this class.
3847 * <complexContent>
3848 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3849 * <attGroup ref="{www.jalview.org}position"/>
3851 * </complexContent>
3857 @XmlAccessorType(XmlAccessType.FIELD)
3859 public static class SeqPointMax {
3861 @XmlAttribute(name = "xPos")
3862 protected Float xPos;
3863 @XmlAttribute(name = "yPos")
3864 protected Float yPos;
3865 @XmlAttribute(name = "zPos")
3866 protected Float zPos;
3869 * Gets the value of the xPos property.
3872 * possible object is
3876 public Float getXPos() {
3881 * Sets the value of the xPos property.
3888 public void setXPos(Float value) {
3893 * Gets the value of the yPos property.
3896 * possible object is
3900 public Float getYPos() {
3905 * Sets the value of the yPos property.
3912 public void setYPos(Float value) {
3917 * Gets the value of the zPos property.
3920 * possible object is
3924 public Float getZPos() {
3929 * Sets the value of the zPos property.
3936 public void setZPos(Float value) {
3944 * <p>Java class for anonymous complex type.
3946 * <p>The following schema fragment specifies the expected content contained within this class.
3950 * <complexContent>
3951 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3952 * <attGroup ref="{www.jalview.org}position"/>
3954 * </complexContent>
3960 @XmlAccessorType(XmlAccessType.FIELD)
3962 public static class SeqPointMin {
3964 @XmlAttribute(name = "xPos")
3965 protected Float xPos;
3966 @XmlAttribute(name = "yPos")
3967 protected Float yPos;
3968 @XmlAttribute(name = "zPos")
3969 protected Float zPos;
3972 * Gets the value of the xPos property.
3975 * possible object is
3979 public Float getXPos() {
3984 * Sets the value of the xPos property.
3991 public void setXPos(Float value) {
3996 * Gets the value of the yPos property.
3999 * possible object is
4003 public Float getYPos() {
4008 * Sets the value of the yPos property.
4015 public void setYPos(Float value) {
4020 * Gets the value of the zPos property.
4023 * possible object is
4027 public Float getZPos() {
4032 * Sets the value of the zPos property.
4039 public void setZPos(Float value) {
4047 * <p>Java class for anonymous complex type.
4049 * <p>The following schema fragment specifies the expected content contained within this class.
4053 * <complexContent>
4054 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4055 * <attGroup ref="{www.jalview.org}position"/>
4056 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4058 * </complexContent>
4064 @XmlAccessorType(XmlAccessType.FIELD)
4066 public static class SequencePoint {
4068 @XmlAttribute(name = "sequenceRef")
4069 protected String sequenceRef;
4070 @XmlAttribute(name = "xPos")
4071 protected Float xPos;
4072 @XmlAttribute(name = "yPos")
4073 protected Float yPos;
4074 @XmlAttribute(name = "zPos")
4075 protected Float zPos;
4078 * Gets the value of the sequenceRef property.
4081 * possible object is
4085 public String getSequenceRef() {
4090 * Sets the value of the sequenceRef property.
4097 public void setSequenceRef(String value) {
4098 this.sequenceRef = value;
4102 * Gets the value of the xPos property.
4105 * possible object is
4109 public Float getXPos() {
4114 * Sets the value of the xPos property.
4121 public void setXPos(Float value) {
4126 * Gets the value of the yPos property.
4129 * possible object is
4133 public Float getYPos() {
4138 * Sets the value of the yPos property.
4145 public void setYPos(Float value) {
4150 * Gets the value of the zPos property.
4153 * possible object is
4157 public Float getZPos() {
4162 * Sets the value of the zPos property.
4169 public void setZPos(Float value) {
4179 * <p>Java class for anonymous complex type.
4181 * <p>The following schema fragment specifies the expected content contained within this class.
4185 * <complexContent>
4186 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4187 * <sequence minOccurs="0">
4188 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4189 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4191 * <attGroup ref="{www.jalview.org}swingwindow"/>
4192 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4193 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4194 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4195 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4196 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4197 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4198 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4199 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4200 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4201 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4202 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4204 * </complexContent>
4210 @XmlAccessorType(XmlAccessType.FIELD)
4211 @XmlType(name = "", propOrder = {
4215 public static class Tree {
4217 @XmlElement(namespace = "www.jalview.org")
4218 protected String title;
4219 @XmlElement(namespace = "www.jalview.org")
4220 protected String newick;
4221 @XmlAttribute(name = "fontName")
4222 protected String fontName;
4223 @XmlAttribute(name = "fontSize")
4224 protected Integer fontSize;
4225 @XmlAttribute(name = "fontStyle")
4226 protected Integer fontStyle;
4227 @XmlAttribute(name = "threshold")
4228 protected Float threshold;
4229 @XmlAttribute(name = "showBootstrap")
4230 protected Boolean showBootstrap;
4231 @XmlAttribute(name = "showDistances")
4232 protected Boolean showDistances;
4233 @XmlAttribute(name = "markUnlinked")
4234 protected Boolean markUnlinked;
4235 @XmlAttribute(name = "fitToWindow")
4236 protected Boolean fitToWindow;
4237 @XmlAttribute(name = "currentTree")
4238 protected Boolean currentTree;
4239 @XmlAttribute(name = "id")
4240 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4242 @XmlSchemaType(name = "ID")
4243 protected String id;
4244 @XmlAttribute(name = "linkToAllViews")
4245 protected Boolean linkToAllViews;
4246 @XmlAttribute(name = "width")
4247 protected Integer width;
4248 @XmlAttribute(name = "height")
4249 protected Integer height;
4250 @XmlAttribute(name = "xpos")
4251 protected Integer xpos;
4252 @XmlAttribute(name = "ypos")
4253 protected Integer ypos;
4256 * Gets the value of the title property.
4259 * possible object is
4263 public String getTitle() {
4268 * Sets the value of the title property.
4275 public void setTitle(String value) {
4280 * Gets the value of the newick property.
4283 * possible object is
4287 public String getNewick() {
4292 * Sets the value of the newick property.
4299 public void setNewick(String value) {
4300 this.newick = value;
4304 * Gets the value of the fontName property.
4307 * possible object is
4311 public String getFontName() {
4316 * Sets the value of the fontName property.
4323 public void setFontName(String value) {
4324 this.fontName = value;
4328 * Gets the value of the fontSize property.
4331 * possible object is
4335 public Integer getFontSize() {
4340 * Sets the value of the fontSize property.
4347 public void setFontSize(Integer value) {
4348 this.fontSize = value;
4352 * Gets the value of the fontStyle property.
4355 * possible object is
4359 public Integer getFontStyle() {
4364 * Sets the value of the fontStyle property.
4371 public void setFontStyle(Integer value) {
4372 this.fontStyle = value;
4376 * Gets the value of the threshold property.
4379 * possible object is
4383 public Float getThreshold() {
4388 * Sets the value of the threshold property.
4395 public void setThreshold(Float value) {
4396 this.threshold = value;
4400 * Gets the value of the showBootstrap property.
4403 * possible object is
4407 public Boolean isShowBootstrap() {
4408 return showBootstrap;
4412 * Sets the value of the showBootstrap property.
4419 public void setShowBootstrap(Boolean value) {
4420 this.showBootstrap = value;
4424 * Gets the value of the showDistances property.
4427 * possible object is
4431 public Boolean isShowDistances() {
4432 return showDistances;
4436 * Sets the value of the showDistances property.
4443 public void setShowDistances(Boolean value) {
4444 this.showDistances = value;
4448 * Gets the value of the markUnlinked property.
4451 * possible object is
4455 public Boolean isMarkUnlinked() {
4456 return markUnlinked;
4460 * Sets the value of the markUnlinked property.
4467 public void setMarkUnlinked(Boolean value) {
4468 this.markUnlinked = value;
4472 * Gets the value of the fitToWindow property.
4475 * possible object is
4479 public Boolean isFitToWindow() {
4484 * Sets the value of the fitToWindow property.
4491 public void setFitToWindow(Boolean value) {
4492 this.fitToWindow = value;
4496 * Gets the value of the currentTree property.
4499 * possible object is
4503 public Boolean isCurrentTree() {
4508 * Sets the value of the currentTree property.
4515 public void setCurrentTree(Boolean value) {
4516 this.currentTree = value;
4520 * Gets the value of the id property.
4523 * possible object is
4527 public String getId() {
4532 * Sets the value of the id property.
4539 public void setId(String value) {
4544 * Gets the value of the linkToAllViews property.
4547 * possible object is
4551 public boolean isLinkToAllViews() {
4552 if (linkToAllViews == null) {
4555 return linkToAllViews;
4560 * Sets the value of the linkToAllViews property.
4567 public void setLinkToAllViews(Boolean value) {
4568 this.linkToAllViews = value;
4572 * Gets the value of the width property.
4575 * possible object is
4579 public Integer getWidth() {
4584 * Sets the value of the width property.
4591 public void setWidth(Integer value) {
4596 * Gets the value of the height property.
4599 * possible object is
4603 public Integer getHeight() {
4608 * Sets the value of the height property.
4615 public void setHeight(Integer value) {
4616 this.height = value;
4620 * Gets the value of the xpos property.
4623 * possible object is
4627 public Integer getXpos() {
4632 * Sets the value of the xpos property.
4639 public void setXpos(Integer value) {
4644 * Gets the value of the ypos property.
4647 * possible object is
4651 public Integer getYpos() {
4656 * Sets the value of the ypos property.
4663 public void setYpos(Integer value) {
4671 * <p>Java class for anonymous complex type.
4673 * <p>The following schema fragment specifies the expected content contained within this class.
4677 * <complexContent>
4678 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4680 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4682 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4684 * </complexContent>
4690 @XmlAccessorType(XmlAccessType.FIELD)
4691 @XmlType(name = "", propOrder = {
4694 public static class UserColours {
4696 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4697 protected JalviewUserColours userColourScheme;
4698 @XmlAttribute(name = "id")
4699 protected String id;
4702 * Gets the value of the userColourScheme property.
4705 * possible object is
4706 * {@link JalviewUserColours }
4709 public JalviewUserColours getUserColourScheme() {
4710 return userColourScheme;
4714 * Sets the value of the userColourScheme property.
4718 * {@link JalviewUserColours }
4721 public void setUserColourScheme(JalviewUserColours value) {
4722 this.userColourScheme = value;
4726 * Gets the value of the id property.
4729 * possible object is
4733 public String getId() {
4738 * Sets the value of the id property.
4745 public void setId(String value) {
4753 * <p>Java class for anonymous complex type.
4755 * <p>The following schema fragment specifies the expected content contained within this class.
4759 * <complexContent>
4760 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4762 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4763 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4765 * <complexContent>
4766 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4767 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4768 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4770 * </complexContent>
4773 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4775 * <complexContent>
4776 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4777 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4778 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4779 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4781 * </complexContent>
4784 * <element name="overview" minOccurs="0">
4786 * <complexContent>
4787 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4788 * <attGroup ref="{www.jalview.org}swingwindow"/>
4789 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4790 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4791 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4792 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4793 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4795 * </complexContent>
4799 * <attGroup ref="{www.jalview.org}swingwindow"/>
4800 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4801 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4802 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4803 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4804 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4805 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4806 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4807 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4809 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4811 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4812 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4813 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4816 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4817 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4818 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4819 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4820 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4821 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4822 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4824 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4825 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4826 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4827 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4828 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4829 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4830 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4831 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4832 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4833 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4834 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4835 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4836 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4837 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4838 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4839 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4840 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4841 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4842 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4844 * </complexContent>
4850 @XmlAccessorType(XmlAccessType.FIELD)
4851 @XmlType(name = "", propOrder = {
4852 "annotationColours",
4857 public static class Viewport {
4859 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4860 protected AnnotationColourScheme annotationColours;
4861 @XmlElement(namespace = "www.jalview.org")
4862 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4863 @XmlElement(namespace = "www.jalview.org")
4864 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4865 @XmlElement(namespace = "www.jalview.org")
4866 protected JalviewModel.Viewport.Overview overview;
4867 @XmlAttribute(name = "conservationSelected")
4868 protected Boolean conservationSelected;
4869 @XmlAttribute(name = "pidSelected")
4870 protected Boolean pidSelected;
4871 @XmlAttribute(name = "bgColour")
4872 protected String bgColour;
4873 @XmlAttribute(name = "consThreshold")
4874 protected Integer consThreshold;
4875 @XmlAttribute(name = "pidThreshold")
4876 protected Integer pidThreshold;
4877 @XmlAttribute(name = "title")
4878 protected String title;
4879 @XmlAttribute(name = "showFullId")
4880 protected Boolean showFullId;
4881 @XmlAttribute(name = "rightAlignIds")
4882 protected Boolean rightAlignIds;
4883 @XmlAttribute(name = "showText")
4884 protected Boolean showText;
4885 @XmlAttribute(name = "showColourText")
4886 protected Boolean showColourText;
4887 @XmlAttribute(name = "showUnconserved")
4888 protected Boolean showUnconserved;
4889 @XmlAttribute(name = "showBoxes")
4890 protected Boolean showBoxes;
4891 @XmlAttribute(name = "wrapAlignment")
4892 protected Boolean wrapAlignment;
4893 @XmlAttribute(name = "renderGaps")
4894 protected Boolean renderGaps;
4895 @XmlAttribute(name = "showSequenceFeatures")
4896 protected Boolean showSequenceFeatures;
4897 @XmlAttribute(name = "showNPfeatureTooltip")
4898 protected Boolean showNPfeatureTooltip;
4899 @XmlAttribute(name = "showDbRefTooltip")
4900 protected Boolean showDbRefTooltip;
4901 @XmlAttribute(name = "followHighlight")
4902 protected Boolean followHighlight;
4903 @XmlAttribute(name = "followSelection")
4904 protected Boolean followSelection;
4905 @XmlAttribute(name = "showAnnotation")
4906 protected Boolean showAnnotation;
4907 @XmlAttribute(name = "centreColumnLabels")
4908 protected Boolean centreColumnLabels;
4909 @XmlAttribute(name = "showGroupConservation")
4910 protected Boolean showGroupConservation;
4911 @XmlAttribute(name = "showGroupConsensus")
4912 protected Boolean showGroupConsensus;
4913 @XmlAttribute(name = "showConsensusHistogram")
4914 protected Boolean showConsensusHistogram;
4915 @XmlAttribute(name = "showSequenceLogo")
4916 protected Boolean showSequenceLogo;
4917 @XmlAttribute(name = "normaliseSequenceLogo")
4918 protected Boolean normaliseSequenceLogo;
4919 @XmlAttribute(name = "ignoreGapsinConsensus")
4920 protected Boolean ignoreGapsinConsensus;
4921 @XmlAttribute(name = "startRes")
4922 protected Integer startRes;
4923 @XmlAttribute(name = "startSeq")
4924 protected Integer startSeq;
4925 @XmlAttribute(name = "fontName")
4926 protected String fontName;
4927 @XmlAttribute(name = "fontSize")
4928 protected Integer fontSize;
4929 @XmlAttribute(name = "fontStyle")
4930 protected Integer fontStyle;
4931 @XmlAttribute(name = "scaleProteinAsCdna")
4932 protected Boolean scaleProteinAsCdna;
4933 @XmlAttribute(name = "viewName")
4934 protected String viewName;
4935 @XmlAttribute(name = "sequenceSetId")
4936 protected String sequenceSetId;
4937 @XmlAttribute(name = "gatheredViews")
4938 protected Boolean gatheredViews;
4939 @XmlAttribute(name = "textCol1")
4940 protected Integer textCol1;
4941 @XmlAttribute(name = "textCol2")
4942 protected Integer textCol2;
4943 @XmlAttribute(name = "textColThreshold")
4944 protected Integer textColThreshold;
4945 @XmlAttribute(name = "id")
4946 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4948 @XmlSchemaType(name = "ID")
4949 protected String id;
4950 @XmlAttribute(name = "complementId")
4951 protected String complementId;
4952 @XmlAttribute(name = "showComplementFeatures")
4953 protected Boolean showComplementFeatures;
4954 @XmlAttribute(name = "showComplementFeaturesOnTop")
4955 protected Boolean showComplementFeaturesOnTop;
4956 @XmlAttribute(name = "width")
4957 protected Integer width;
4958 @XmlAttribute(name = "height")
4959 protected Integer height;
4960 @XmlAttribute(name = "xpos")
4961 protected Integer xpos;
4962 @XmlAttribute(name = "ypos")
4963 protected Integer ypos;
4966 * Gets the value of the annotationColours property.
4969 * possible object is
4970 * {@link AnnotationColourScheme }
4973 public AnnotationColourScheme getAnnotationColours() {
4974 return annotationColours;
4978 * Sets the value of the annotationColours property.
4982 * {@link AnnotationColourScheme }
4985 public void setAnnotationColours(AnnotationColourScheme value) {
4986 this.annotationColours = value;
4990 * Gets the value of the hiddenColumns property.
4993 * This accessor method returns a reference to the live list,
4994 * not a snapshot. Therefore any modification you make to the
4995 * returned list will be present inside the JAXB object.
4996 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4999 * For example, to add a new item, do as follows:
5001 * getHiddenColumns().add(newItem);
5006 * Objects of the following type(s) are allowed in the list
5007 * {@link JalviewModel.Viewport.HiddenColumns }
5011 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5012 if (hiddenColumns == null) {
5013 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5015 return this.hiddenColumns;
5019 * Gets the value of the calcIdParam property.
5022 * This accessor method returns a reference to the live list,
5023 * not a snapshot. Therefore any modification you make to the
5024 * returned list will be present inside the JAXB object.
5025 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5028 * For example, to add a new item, do as follows:
5030 * getCalcIdParam().add(newItem);
5035 * Objects of the following type(s) are allowed in the list
5036 * {@link JalviewModel.Viewport.CalcIdParam }
5040 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5041 if (calcIdParam == null) {
5042 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5044 return this.calcIdParam;
5048 * Gets the value of the overview property.
5051 * possible object is
5052 * {@link JalviewModel.Viewport.Overview }
5055 public JalviewModel.Viewport.Overview getOverview() {
5060 * Sets the value of the overview property.
5064 * {@link JalviewModel.Viewport.Overview }
5067 public void setOverview(JalviewModel.Viewport.Overview value) {
5068 this.overview = value;
5072 * Gets the value of the conservationSelected property.
5075 * possible object is
5079 public Boolean isConservationSelected() {
5080 return conservationSelected;
5084 * Sets the value of the conservationSelected property.
5091 public void setConservationSelected(Boolean value) {
5092 this.conservationSelected = value;
5096 * Gets the value of the pidSelected property.
5099 * possible object is
5103 public Boolean isPidSelected() {
5108 * Sets the value of the pidSelected property.
5115 public void setPidSelected(Boolean value) {
5116 this.pidSelected = value;
5120 * Gets the value of the bgColour property.
5123 * possible object is
5127 public String getBgColour() {
5132 * Sets the value of the bgColour property.
5139 public void setBgColour(String value) {
5140 this.bgColour = value;
5144 * Gets the value of the consThreshold property.
5147 * possible object is
5151 public Integer getConsThreshold() {
5152 return consThreshold;
5156 * Sets the value of the consThreshold property.
5163 public void setConsThreshold(Integer value) {
5164 this.consThreshold = value;
5168 * Gets the value of the pidThreshold property.
5171 * possible object is
5175 public Integer getPidThreshold() {
5176 return pidThreshold;
5180 * Sets the value of the pidThreshold property.
5187 public void setPidThreshold(Integer value) {
5188 this.pidThreshold = value;
5192 * Gets the value of the title property.
5195 * possible object is
5199 public String getTitle() {
5204 * Sets the value of the title property.
5211 public void setTitle(String value) {
5216 * Gets the value of the showFullId property.
5219 * possible object is
5223 public Boolean isShowFullId() {
5228 * Sets the value of the showFullId property.
5235 public void setShowFullId(Boolean value) {
5236 this.showFullId = value;
5240 * Gets the value of the rightAlignIds property.
5243 * possible object is
5247 public Boolean isRightAlignIds() {
5248 return rightAlignIds;
5252 * Sets the value of the rightAlignIds property.
5259 public void setRightAlignIds(Boolean value) {
5260 this.rightAlignIds = value;
5264 * Gets the value of the showText property.
5267 * possible object is
5271 public Boolean isShowText() {
5276 * Sets the value of the showText property.
5283 public void setShowText(Boolean value) {
5284 this.showText = value;
5288 * Gets the value of the showColourText property.
5291 * possible object is
5295 public Boolean isShowColourText() {
5296 return showColourText;
5300 * Sets the value of the showColourText property.
5307 public void setShowColourText(Boolean value) {
5308 this.showColourText = value;
5312 * Gets the value of the showUnconserved property.
5315 * possible object is
5319 public boolean isShowUnconserved() {
5320 if (showUnconserved == null) {
5323 return showUnconserved;
5328 * Sets the value of the showUnconserved property.
5335 public void setShowUnconserved(Boolean value) {
5336 this.showUnconserved = value;
5340 * Gets the value of the showBoxes property.
5343 * possible object is
5347 public Boolean isShowBoxes() {
5352 * Sets the value of the showBoxes property.
5359 public void setShowBoxes(Boolean value) {
5360 this.showBoxes = value;
5364 * Gets the value of the wrapAlignment property.
5367 * possible object is
5371 public Boolean isWrapAlignment() {
5372 return wrapAlignment;
5376 * Sets the value of the wrapAlignment property.
5383 public void setWrapAlignment(Boolean value) {
5384 this.wrapAlignment = value;
5388 * Gets the value of the renderGaps property.
5391 * possible object is
5395 public Boolean isRenderGaps() {
5400 * Sets the value of the renderGaps property.
5407 public void setRenderGaps(Boolean value) {
5408 this.renderGaps = value;
5412 * Gets the value of the showSequenceFeatures property.
5415 * possible object is
5419 public Boolean isShowSequenceFeatures() {
5420 return showSequenceFeatures;
5424 * Sets the value of the showSequenceFeatures property.
5431 public void setShowSequenceFeatures(Boolean value) {
5432 this.showSequenceFeatures = value;
5436 * Gets the value of the showNPfeatureTooltip property.
5439 * possible object is
5443 public Boolean isShowNPfeatureTooltip() {
5444 return showNPfeatureTooltip;
5448 * Sets the value of the showNPfeatureTooltip property.
5455 public void setShowNPfeatureTooltip(Boolean value) {
5456 this.showNPfeatureTooltip = value;
5460 * Gets the value of the showDbRefTooltip property.
5463 * possible object is
5467 public Boolean isShowDbRefTooltip() {
5468 return showDbRefTooltip;
5472 * Sets the value of the showDbRefTooltip property.
5479 public void setShowDbRefTooltip(Boolean value) {
5480 this.showDbRefTooltip = value;
5484 * Gets the value of the followHighlight property.
5487 * possible object is
5491 public boolean isFollowHighlight() {
5492 if (followHighlight == null) {
5495 return followHighlight;
5500 * Sets the value of the followHighlight property.
5507 public void setFollowHighlight(Boolean value) {
5508 this.followHighlight = value;
5512 * Gets the value of the followSelection property.
5515 * possible object is
5519 public boolean isFollowSelection() {
5520 if (followSelection == null) {
5523 return followSelection;
5528 * Sets the value of the followSelection property.
5535 public void setFollowSelection(Boolean value) {
5536 this.followSelection = value;
5540 * Gets the value of the showAnnotation property.
5543 * possible object is
5547 public Boolean isShowAnnotation() {
5548 return showAnnotation;
5552 * Sets the value of the showAnnotation property.
5559 public void setShowAnnotation(Boolean value) {
5560 this.showAnnotation = value;
5564 * Gets the value of the centreColumnLabels property.
5567 * possible object is
5571 public boolean isCentreColumnLabels() {
5572 if (centreColumnLabels == null) {
5575 return centreColumnLabels;
5580 * Sets the value of the centreColumnLabels property.
5587 public void setCentreColumnLabels(Boolean value) {
5588 this.centreColumnLabels = value;
5592 * Gets the value of the showGroupConservation property.
5595 * possible object is
5599 public boolean isShowGroupConservation() {
5600 if (showGroupConservation == null) {
5603 return showGroupConservation;
5608 * Sets the value of the showGroupConservation property.
5615 public void setShowGroupConservation(Boolean value) {
5616 this.showGroupConservation = value;
5620 * Gets the value of the showGroupConsensus property.
5623 * possible object is
5627 public boolean isShowGroupConsensus() {
5628 if (showGroupConsensus == null) {
5631 return showGroupConsensus;
5636 * Sets the value of the showGroupConsensus property.
5643 public void setShowGroupConsensus(Boolean value) {
5644 this.showGroupConsensus = value;
5648 * Gets the value of the showConsensusHistogram property.
5651 * possible object is
5655 public boolean isShowConsensusHistogram() {
5656 if (showConsensusHistogram == null) {
5659 return showConsensusHistogram;
5664 * Sets the value of the showConsensusHistogram property.
5671 public void setShowConsensusHistogram(Boolean value) {
5672 this.showConsensusHistogram = value;
5676 * Gets the value of the showSequenceLogo property.
5679 * possible object is
5683 public boolean isShowSequenceLogo() {
5684 if (showSequenceLogo == null) {
5687 return showSequenceLogo;
5692 * Sets the value of the showSequenceLogo property.
5699 public void setShowSequenceLogo(Boolean value) {
5700 this.showSequenceLogo = value;
5704 * Gets the value of the normaliseSequenceLogo property.
5707 * possible object is
5711 public boolean isNormaliseSequenceLogo() {
5712 if (normaliseSequenceLogo == null) {
5715 return normaliseSequenceLogo;
5720 * Sets the value of the normaliseSequenceLogo property.
5727 public void setNormaliseSequenceLogo(Boolean value) {
5728 this.normaliseSequenceLogo = value;
5732 * Gets the value of the ignoreGapsinConsensus property.
5735 * possible object is
5739 public boolean isIgnoreGapsinConsensus() {
5740 if (ignoreGapsinConsensus == null) {
5743 return ignoreGapsinConsensus;
5748 * Sets the value of the ignoreGapsinConsensus property.
5755 public void setIgnoreGapsinConsensus(Boolean value) {
5756 this.ignoreGapsinConsensus = value;
5760 * Gets the value of the startRes property.
5763 * possible object is
5767 public Integer getStartRes() {
5772 * Sets the value of the startRes property.
5779 public void setStartRes(Integer value) {
5780 this.startRes = value;
5784 * Gets the value of the startSeq property.
5787 * possible object is
5791 public Integer getStartSeq() {
5796 * Sets the value of the startSeq property.
5803 public void setStartSeq(Integer value) {
5804 this.startSeq = value;
5808 * Gets the value of the fontName property.
5811 * possible object is
5815 public String getFontName() {
5820 * Sets the value of the fontName property.
5827 public void setFontName(String value) {
5828 this.fontName = value;
5832 * Gets the value of the fontSize property.
5835 * possible object is
5839 public Integer getFontSize() {
5844 * Sets the value of the fontSize property.
5851 public void setFontSize(Integer value) {
5852 this.fontSize = value;
5856 * Gets the value of the fontStyle property.
5859 * possible object is
5863 public Integer getFontStyle() {
5868 * Sets the value of the fontStyle property.
5875 public void setFontStyle(Integer value) {
5876 this.fontStyle = value;
5880 * Gets the value of the scaleProteinAsCdna property.
5883 * possible object is
5887 public boolean isScaleProteinAsCdna() {
5888 if (scaleProteinAsCdna == null) {
5891 return scaleProteinAsCdna;
5896 * Sets the value of the scaleProteinAsCdna property.
5903 public void setScaleProteinAsCdna(Boolean value) {
5904 this.scaleProteinAsCdna = value;
5908 * Gets the value of the viewName property.
5911 * possible object is
5915 public String getViewName() {
5920 * Sets the value of the viewName property.
5927 public void setViewName(String value) {
5928 this.viewName = value;
5932 * Gets the value of the sequenceSetId property.
5935 * possible object is
5939 public String getSequenceSetId() {
5940 return sequenceSetId;
5944 * Sets the value of the sequenceSetId property.
5951 public void setSequenceSetId(String value) {
5952 this.sequenceSetId = value;
5956 * Gets the value of the gatheredViews property.
5959 * possible object is
5963 public Boolean isGatheredViews() {
5964 return gatheredViews;
5968 * Sets the value of the gatheredViews property.
5975 public void setGatheredViews(Boolean value) {
5976 this.gatheredViews = value;
5980 * Gets the value of the textCol1 property.
5983 * possible object is
5987 public Integer getTextCol1() {
5992 * Sets the value of the textCol1 property.
5999 public void setTextCol1(Integer value) {
6000 this.textCol1 = value;
6004 * Gets the value of the textCol2 property.
6007 * possible object is
6011 public Integer getTextCol2() {
6016 * Sets the value of the textCol2 property.
6023 public void setTextCol2(Integer value) {
6024 this.textCol2 = value;
6028 * Gets the value of the textColThreshold property.
6031 * possible object is
6035 public Integer getTextColThreshold() {
6036 return textColThreshold;
6040 * Sets the value of the textColThreshold property.
6047 public void setTextColThreshold(Integer value) {
6048 this.textColThreshold = value;
6052 * Gets the value of the id property.
6055 * possible object is
6059 public String getId() {
6064 * Sets the value of the id property.
6071 public void setId(String value) {
6076 * Gets the value of the complementId property.
6079 * possible object is
6083 public String getComplementId() {
6084 return complementId;
6088 * Sets the value of the complementId property.
6095 public void setComplementId(String value) {
6096 this.complementId = value;
6100 * Gets the value of the showComplementFeatures property.
6103 * possible object is
6107 public boolean isShowComplementFeatures() {
6108 if (showComplementFeatures == null) {
6111 return showComplementFeatures;
6116 * Sets the value of the showComplementFeatures property.
6123 public void setShowComplementFeatures(Boolean value) {
6124 this.showComplementFeatures = value;
6128 * Gets the value of the showComplementFeaturesOnTop property.
6131 * possible object is
6135 public boolean isShowComplementFeaturesOnTop() {
6136 if (showComplementFeaturesOnTop == null) {
6139 return showComplementFeaturesOnTop;
6144 * Sets the value of the showComplementFeaturesOnTop property.
6151 public void setShowComplementFeaturesOnTop(Boolean value) {
6152 this.showComplementFeaturesOnTop = value;
6156 * Gets the value of the width property.
6159 * possible object is
6163 public Integer getWidth() {
6168 * Sets the value of the width property.
6175 public void setWidth(Integer value) {
6180 * Gets the value of the height property.
6183 * possible object is
6187 public Integer getHeight() {
6192 * Sets the value of the height property.
6199 public void setHeight(Integer value) {
6200 this.height = value;
6204 * Gets the value of the xpos property.
6207 * possible object is
6211 public Integer getXpos() {
6216 * Sets the value of the xpos property.
6223 public void setXpos(Integer value) {
6228 * Gets the value of the ypos property.
6231 * possible object is
6235 public Integer getYpos() {
6240 * Sets the value of the ypos property.
6247 public void setYpos(Integer value) {
6253 * <p>Java class for anonymous complex type.
6255 * <p>The following schema fragment specifies the expected content contained within this class.
6259 * <complexContent>
6260 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6261 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6262 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6263 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6265 * </complexContent>
6271 @XmlAccessorType(XmlAccessType.FIELD)
6273 public static class CalcIdParam
6274 extends WebServiceParameterSet
6277 @XmlAttribute(name = "calcId", required = true)
6278 protected String calcId;
6279 @XmlAttribute(name = "needsUpdate")
6280 protected Boolean needsUpdate;
6281 @XmlAttribute(name = "autoUpdate", required = true)
6282 protected boolean autoUpdate;
6285 * Gets the value of the calcId property.
6288 * possible object is
6292 public String getCalcId() {
6297 * Sets the value of the calcId property.
6304 public void setCalcId(String value) {
6305 this.calcId = value;
6309 * Gets the value of the needsUpdate property.
6312 * possible object is
6316 public boolean isNeedsUpdate() {
6317 if (needsUpdate == null) {
6325 * Sets the value of the needsUpdate property.
6332 public void setNeedsUpdate(Boolean value) {
6333 this.needsUpdate = value;
6337 * Gets the value of the autoUpdate property.
6340 public boolean isAutoUpdate() {
6345 * Sets the value of the autoUpdate property.
6348 public void setAutoUpdate(boolean value) {
6349 this.autoUpdate = value;
6356 * <p>Java class for anonymous complex type.
6358 * <p>The following schema fragment specifies the expected content contained within this class.
6362 * <complexContent>
6363 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6364 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6365 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6367 * </complexContent>
6373 @XmlAccessorType(XmlAccessType.FIELD)
6375 public static class HiddenColumns {
6377 @XmlAttribute(name = "start")
6378 protected Integer start;
6379 @XmlAttribute(name = "end")
6380 protected Integer end;
6383 * Gets the value of the start property.
6386 * possible object is
6390 public Integer getStart() {
6395 * Sets the value of the start property.
6402 public void setStart(Integer value) {
6407 * Gets the value of the end property.
6410 * possible object is
6414 public Integer getEnd() {
6419 * Sets the value of the end property.
6426 public void setEnd(Integer value) {
6434 * <p>Java class for anonymous complex type.
6436 * <p>The following schema fragment specifies the expected content contained within this class.
6440 * <complexContent>
6441 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6442 * <attGroup ref="{www.jalview.org}swingwindow"/>
6443 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6444 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6445 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6446 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6447 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
6449 * </complexContent>
6455 @XmlAccessorType(XmlAccessType.FIELD)
6457 public static class Overview {
6459 @XmlAttribute(name = "showHidden")
6460 protected Boolean showHidden;
6461 @XmlAttribute(name = "residueColour")
6462 protected Integer residueColour;
6463 @XmlAttribute(name = "gapColour")
6464 protected Integer gapColour;
6465 @XmlAttribute(name = "hiddenColour")
6466 protected Integer hiddenColour;
6467 @XmlAttribute(name = "title")
6468 protected String title;
6469 @XmlAttribute(name = "width")
6470 protected Integer width;
6471 @XmlAttribute(name = "height")
6472 protected Integer height;
6473 @XmlAttribute(name = "xpos")
6474 protected Integer xpos;
6475 @XmlAttribute(name = "ypos")
6476 protected Integer ypos;
6479 * Gets the value of the showHidden property.
6482 * possible object is
6486 public Boolean isShowHidden() {
6491 * Sets the value of the showHidden property.
6498 public void setShowHidden(Boolean value) {
6499 this.showHidden = value;
6503 * Gets the value of the residueColour property.
6506 * possible object is
6510 public Integer getResidueColour() {
6511 return residueColour;
6515 * Sets the value of the residueColour property.
6522 public void setResidueColour(Integer value) {
6523 this.residueColour = value;
6527 * Gets the value of the gapColour property.
6530 * possible object is
6534 public Integer getGapColour() {
6539 * Sets the value of the gapColour property.
6546 public void setGapColour(Integer value) {
6547 this.gapColour = value;
6551 * Gets the value of the hiddenColour property.
6554 * possible object is
6558 public Integer getHiddenColour() {
6559 return hiddenColour;
6563 * Sets the value of the hiddenColour property.
6570 public void setHiddenColour(Integer value) {
6571 this.hiddenColour = value;
6575 * Gets the value of the title property.
6578 * possible object is
6582 public String getTitle() {
6587 * Sets the value of the title property.
6594 public void setTitle(String value) {
6599 * Gets the value of the width property.
6602 * possible object is
6606 public Integer getWidth() {
6611 * Sets the value of the width property.
6618 public void setWidth(Integer value) {
6623 * Gets the value of the height property.
6626 * possible object is
6630 public Integer getHeight() {
6635 * Sets the value of the height property.
6642 public void setHeight(Integer value) {
6643 this.height = value;
6647 * Gets the value of the xpos property.
6650 * possible object is
6654 public Integer getXpos() {
6659 * Sets the value of the xpos property.
6666 public void setXpos(Integer value) {
6671 * Gets the value of the ypos property.
6674 * possible object is
6678 public Integer getYpos() {
6683 * Sets the value of the ypos property.
6690 public void setYpos(Integer value) {