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: 2020.12.10 at 10:15:41 AM 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" />
178 * </complexContent>
182 * <attGroup ref="{www.jalview.org}swingwindow"/>
183 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
184 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
186 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
187 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
188 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
189 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
190 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
191 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
192 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
193 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
194 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
195 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
196 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
197 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
198 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
199 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
200 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
201 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
202 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
203 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
204 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
205 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
206 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
207 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
208 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
209 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
210 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
211 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
212 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
213 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
214 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
215 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
216 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
217 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
218 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
219 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
220 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
221 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
222 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
223 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
224 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
225 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
227 * </complexContent>
230 * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
232 * <complexContent>
233 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
235 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
237 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
239 * </complexContent>
242 * <element name="tree" maxOccurs="unbounded" minOccurs="0">
244 * <complexContent>
245 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
246 * <sequence minOccurs="0">
247 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
248 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
250 * <attGroup ref="{www.jalview.org}swingwindow"/>
251 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
252 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
253 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
254 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
255 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
256 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
257 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
258 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
259 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
260 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
261 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
263 * </complexContent>
266 * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
268 * <complexContent>
269 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
271 * <element name="sequencePoint" maxOccurs="unbounded">
273 * <complexContent>
274 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
275 * <attGroup ref="{www.jalview.org}position"/>
276 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
278 * </complexContent>
281 * <element name="axis" maxOccurs="3" minOccurs="3">
283 * <complexContent>
284 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
285 * <attGroup ref="{www.jalview.org}position"/>
287 * </complexContent>
290 * <element name="seqPointMin">
292 * <complexContent>
293 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
294 * <attGroup ref="{www.jalview.org}position"/>
296 * </complexContent>
299 * <element name="seqPointMax">
301 * <complexContent>
302 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
303 * <attGroup ref="{www.jalview.org}position"/>
305 * </complexContent>
308 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
310 * <attGroup ref="{www.jalview.org}swingwindow"/>
311 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
312 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
313 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
314 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
315 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
316 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
317 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
318 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
319 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
320 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
322 * </complexContent>
325 * <element name="FeatureSettings" minOccurs="0">
327 * <complexContent>
328 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
330 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
332 * <complexContent>
333 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
335 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
336 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
338 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
339 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
340 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
341 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
342 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
343 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
344 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
345 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
346 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
347 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
348 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
349 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
351 * </complexContent>
354 * <element name="group" maxOccurs="unbounded" minOccurs="0">
356 * <complexContent>
357 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
358 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
359 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
361 * </complexContent>
366 * </complexContent>
372 * </complexContent>
378 @XmlAccessorType(XmlAccessType.FIELD)
379 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
391 public class JalviewModel {
393 @XmlElement(required = true)
394 @XmlSchemaType(name = "dateTime")
395 protected XMLGregorianCalendar creationDate;
396 @XmlElement(required = true)
397 protected String version;
398 @XmlElement(required = true)
399 protected VAMSAS vamsasModel;
400 @XmlElement(name = "JSeq")
401 protected List<JalviewModel.JSeq> jSeq;
402 @XmlElement(name = "JGroup")
403 protected List<JalviewModel.JGroup> jGroup;
404 @XmlElement(name = "Viewport")
405 protected List<JalviewModel.Viewport> viewport;
406 @XmlElement(name = "UserColours")
407 protected List<JalviewModel.UserColours> userColours;
408 protected List<JalviewModel.Tree> tree;
409 @XmlElement(name = "PcaViewer")
410 protected List<JalviewModel.PcaViewer> pcaViewer;
411 @XmlElement(name = "FeatureSettings")
412 protected JalviewModel.FeatureSettings featureSettings;
415 * Gets the value of the creationDate property.
419 * {@link XMLGregorianCalendar }
422 public XMLGregorianCalendar getCreationDate() {
427 * Sets the value of the creationDate property.
431 * {@link XMLGregorianCalendar }
434 public void setCreationDate(XMLGregorianCalendar value) {
435 this.creationDate = value;
439 * Gets the value of the version property.
446 public String getVersion() {
451 * Sets the value of the version property.
458 public void setVersion(String value) {
459 this.version = value;
463 * Gets the value of the vamsasModel property.
470 public VAMSAS getVamsasModel() {
475 * Sets the value of the vamsasModel property.
482 public void setVamsasModel(VAMSAS value) {
483 this.vamsasModel = value;
487 * Gets the value of the jSeq property.
490 * This accessor method returns a reference to the live list,
491 * not a snapshot. Therefore any modification you make to the
492 * returned list will be present inside the JAXB object.
493 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
496 * For example, to add a new item, do as follows:
498 * getJSeq().add(newItem);
503 * Objects of the following type(s) are allowed in the list
504 * {@link JalviewModel.JSeq }
508 public List<JalviewModel.JSeq> getJSeq() {
510 jSeq = new ArrayList<JalviewModel.JSeq>();
516 * Gets the value of the jGroup property.
519 * This accessor method returns a reference to the live list,
520 * not a snapshot. Therefore any modification you make to the
521 * returned list will be present inside the JAXB object.
522 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
525 * For example, to add a new item, do as follows:
527 * getJGroup().add(newItem);
532 * Objects of the following type(s) are allowed in the list
533 * {@link JalviewModel.JGroup }
537 public List<JalviewModel.JGroup> getJGroup() {
538 if (jGroup == null) {
539 jGroup = new ArrayList<JalviewModel.JGroup>();
545 * Gets the value of the viewport property.
548 * This accessor method returns a reference to the live list,
549 * not a snapshot. Therefore any modification you make to the
550 * returned list will be present inside the JAXB object.
551 * This is why there is not a <CODE>set</CODE> method for the viewport property.
554 * For example, to add a new item, do as follows:
556 * getViewport().add(newItem);
561 * Objects of the following type(s) are allowed in the list
562 * {@link JalviewModel.Viewport }
566 public List<JalviewModel.Viewport> getViewport() {
567 if (viewport == null) {
568 viewport = new ArrayList<JalviewModel.Viewport>();
570 return this.viewport;
574 * Gets the value of the userColours property.
577 * This accessor method returns a reference to the live list,
578 * not a snapshot. Therefore any modification you make to the
579 * returned list will be present inside the JAXB object.
580 * This is why there is not a <CODE>set</CODE> method for the userColours property.
583 * For example, to add a new item, do as follows:
585 * getUserColours().add(newItem);
590 * Objects of the following type(s) are allowed in the list
591 * {@link JalviewModel.UserColours }
595 public List<JalviewModel.UserColours> getUserColours() {
596 if (userColours == null) {
597 userColours = new ArrayList<JalviewModel.UserColours>();
599 return this.userColours;
603 * Gets the value of the tree property.
606 * This accessor method returns a reference to the live list,
607 * not a snapshot. Therefore any modification you make to the
608 * returned list will be present inside the JAXB object.
609 * This is why there is not a <CODE>set</CODE> method for the tree property.
612 * For example, to add a new item, do as follows:
614 * getTree().add(newItem);
619 * Objects of the following type(s) are allowed in the list
620 * {@link JalviewModel.Tree }
624 public List<JalviewModel.Tree> getTree() {
626 tree = new ArrayList<JalviewModel.Tree>();
632 * Gets the value of the pcaViewer property.
635 * This accessor method returns a reference to the live list,
636 * not a snapshot. Therefore any modification you make to the
637 * returned list will be present inside the JAXB object.
638 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
641 * For example, to add a new item, do as follows:
643 * getPcaViewer().add(newItem);
648 * Objects of the following type(s) are allowed in the list
649 * {@link JalviewModel.PcaViewer }
653 public List<JalviewModel.PcaViewer> getPcaViewer() {
654 if (pcaViewer == null) {
655 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
657 return this.pcaViewer;
661 * Gets the value of the featureSettings property.
665 * {@link JalviewModel.FeatureSettings }
668 public JalviewModel.FeatureSettings getFeatureSettings() {
669 return featureSettings;
673 * Sets the value of the featureSettings property.
677 * {@link JalviewModel.FeatureSettings }
680 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
681 this.featureSettings = value;
686 * <p>Java class for anonymous complex type.
688 * <p>The following schema fragment specifies the expected content contained within this class.
692 * <complexContent>
693 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
695 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
697 * <complexContent>
698 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
700 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
701 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
703 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
704 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
705 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
706 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
707 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
708 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
709 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
710 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
711 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
712 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
713 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
714 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
716 * </complexContent>
719 * <element name="group" maxOccurs="unbounded" minOccurs="0">
721 * <complexContent>
722 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
723 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
724 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
726 * </complexContent>
731 * </complexContent>
737 @XmlAccessorType(XmlAccessType.FIELD)
738 @XmlType(name = "", propOrder = {
742 public static class FeatureSettings {
744 @XmlElement(namespace = "www.jalview.org")
745 protected List<JalviewModel.FeatureSettings.Setting> setting;
746 @XmlElement(namespace = "www.jalview.org")
747 protected List<JalviewModel.FeatureSettings.Group> group;
750 * Gets the value of the setting property.
753 * This accessor method returns a reference to the live list,
754 * not a snapshot. Therefore any modification you make to the
755 * returned list will be present inside the JAXB object.
756 * This is why there is not a <CODE>set</CODE> method for the setting property.
759 * For example, to add a new item, do as follows:
761 * getSetting().add(newItem);
766 * Objects of the following type(s) are allowed in the list
767 * {@link JalviewModel.FeatureSettings.Setting }
771 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
772 if (setting == null) {
773 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
779 * Gets the value of the group property.
782 * This accessor method returns a reference to the live list,
783 * not a snapshot. Therefore any modification you make to the
784 * returned list will be present inside the JAXB object.
785 * This is why there is not a <CODE>set</CODE> method for the group property.
788 * For example, to add a new item, do as follows:
790 * getGroup().add(newItem);
795 * Objects of the following type(s) are allowed in the list
796 * {@link JalviewModel.FeatureSettings.Group }
800 public List<JalviewModel.FeatureSettings.Group> getGroup() {
802 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
809 * <p>Java class for anonymous complex type.
811 * <p>The following schema fragment specifies the expected content contained within this class.
815 * <complexContent>
816 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
817 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
818 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
820 * </complexContent>
826 @XmlAccessorType(XmlAccessType.FIELD)
828 public static class Group {
830 @XmlAttribute(name = "name", required = true)
831 protected String name;
832 @XmlAttribute(name = "display", required = true)
833 protected boolean display;
836 * Gets the value of the name property.
843 public String getName() {
848 * Sets the value of the name property.
855 public void setName(String value) {
860 * Gets the value of the display property.
863 public boolean isDisplay() {
868 * Sets the value of the display property.
871 public void setDisplay(boolean value) {
872 this.display = value;
879 * <p>Java class for anonymous complex type.
881 * <p>The following schema fragment specifies the expected content contained within this class.
885 * <complexContent>
886 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
888 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
889 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
891 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
892 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
893 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
894 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
895 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
896 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
897 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
898 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
899 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
900 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
901 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
902 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
904 * </complexContent>
910 @XmlAccessorType(XmlAccessType.FIELD)
911 @XmlType(name = "", propOrder = {
915 public static class Setting {
917 @XmlElement(namespace = "www.jalview.org")
918 protected List<String> attributeName;
919 @XmlElement(namespace = "www.jalview.org")
920 protected FeatureMatcherSet matcherSet;
921 @XmlAttribute(name = "type", required = true)
922 protected String type;
923 @XmlAttribute(name = "colour", required = true)
924 protected int colour;
925 @XmlAttribute(name = "display", required = true)
926 protected boolean display;
927 @XmlAttribute(name = "order")
928 protected Float order;
929 @XmlAttribute(name = "mincolour")
930 protected Integer mincolour;
931 @XmlAttribute(name = "noValueColour")
932 protected NoValueColour noValueColour;
933 @XmlAttribute(name = "threshold")
934 protected Float threshold;
935 @XmlAttribute(name = "threshstate")
936 protected Integer threshstate;
937 @XmlAttribute(name = "max")
939 @XmlAttribute(name = "min")
941 @XmlAttribute(name = "colourByLabel")
942 protected Boolean colourByLabel;
943 @XmlAttribute(name = "autoScale")
944 protected Boolean autoScale;
947 * Gets the value of the attributeName property.
950 * This accessor method returns a reference to the live list,
951 * not a snapshot. Therefore any modification you make to the
952 * returned list will be present inside the JAXB object.
953 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
956 * For example, to add a new item, do as follows:
958 * getAttributeName().add(newItem);
963 * Objects of the following type(s) are allowed in the list
968 public List<String> getAttributeName() {
969 if (attributeName == null) {
970 attributeName = new ArrayList<String>();
972 return this.attributeName;
976 * Gets the value of the matcherSet property.
980 * {@link FeatureMatcherSet }
983 public FeatureMatcherSet getMatcherSet() {
988 * Sets the value of the matcherSet property.
992 * {@link FeatureMatcherSet }
995 public void setMatcherSet(FeatureMatcherSet value) {
996 this.matcherSet = value;
1000 * Gets the value of the type property.
1003 * possible object is
1007 public String getType() {
1012 * Sets the value of the type property.
1019 public void setType(String value) {
1024 * Gets the value of the colour property.
1027 public int getColour() {
1032 * Sets the value of the colour property.
1035 public void setColour(int value) {
1036 this.colour = value;
1040 * Gets the value of the display property.
1043 public boolean isDisplay() {
1048 * Sets the value of the display property.
1051 public void setDisplay(boolean value) {
1052 this.display = value;
1056 * Gets the value of the order property.
1059 * possible object is
1063 public Float getOrder() {
1068 * Sets the value of the order property.
1075 public void setOrder(Float value) {
1080 * Gets the value of the mincolour property.
1083 * possible object is
1087 public Integer getMincolour() {
1092 * Sets the value of the mincolour property.
1099 public void setMincolour(Integer value) {
1100 this.mincolour = value;
1104 * Gets the value of the noValueColour property.
1107 * possible object is
1108 * {@link NoValueColour }
1111 public NoValueColour getNoValueColour() {
1112 if (noValueColour == null) {
1113 return NoValueColour.MIN;
1115 return noValueColour;
1120 * Sets the value of the noValueColour property.
1124 * {@link NoValueColour }
1127 public void setNoValueColour(NoValueColour value) {
1128 this.noValueColour = value;
1132 * Gets the value of the threshold property.
1135 * possible object is
1139 public Float getThreshold() {
1144 * Sets the value of the threshold property.
1151 public void setThreshold(Float value) {
1152 this.threshold = value;
1156 * Gets the value of the threshstate property.
1159 * possible object is
1163 public Integer getThreshstate() {
1168 * Sets the value of the threshstate property.
1175 public void setThreshstate(Integer value) {
1176 this.threshstate = value;
1180 * Gets the value of the max property.
1183 * possible object is
1187 public Float getMax() {
1192 * Sets the value of the max property.
1199 public void setMax(Float value) {
1204 * Gets the value of the min property.
1207 * possible object is
1211 public Float getMin() {
1216 * Sets the value of the min property.
1223 public void setMin(Float value) {
1228 * Gets the value of the colourByLabel property.
1231 * possible object is
1235 public Boolean isColourByLabel() {
1236 return colourByLabel;
1240 * Sets the value of the colourByLabel property.
1247 public void setColourByLabel(Boolean value) {
1248 this.colourByLabel = value;
1252 * Gets the value of the autoScale property.
1255 * possible object is
1259 public Boolean isAutoScale() {
1264 * Sets the value of the autoScale property.
1271 public void setAutoScale(Boolean value) {
1272 this.autoScale = value;
1281 * <p>Java class for anonymous complex type.
1283 * <p>The following schema fragment specifies the expected content contained within this class.
1287 * <complexContent>
1288 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1290 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1291 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1293 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1294 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1295 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1296 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1297 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1298 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1299 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1300 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1301 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1302 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1303 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1304 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1305 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1306 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1307 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1308 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1309 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1310 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1311 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1313 * </complexContent>
1319 @XmlAccessorType(XmlAccessType.FIELD)
1320 @XmlType(name = "", propOrder = {
1324 public static class JGroup {
1326 @XmlElement(namespace = "www.jalview.org", required = true)
1327 protected List<String> seq;
1328 @XmlElement(namespace = "www.jalview.org")
1329 protected AnnotationColourScheme annotationColours;
1330 @XmlAttribute(name = "start")
1331 protected Integer start;
1332 @XmlAttribute(name = "end")
1333 protected Integer end;
1334 @XmlAttribute(name = "name")
1335 protected String name;
1336 @XmlAttribute(name = "colour")
1337 protected String colour;
1338 @XmlAttribute(name = "consThreshold")
1339 protected Integer consThreshold;
1340 @XmlAttribute(name = "pidThreshold")
1341 protected Integer pidThreshold;
1342 @XmlAttribute(name = "outlineColour")
1343 protected Integer outlineColour;
1344 @XmlAttribute(name = "displayBoxes")
1345 protected Boolean displayBoxes;
1346 @XmlAttribute(name = "displayText")
1347 protected Boolean displayText;
1348 @XmlAttribute(name = "colourText")
1349 protected Boolean colourText;
1350 @XmlAttribute(name = "textCol1")
1351 protected Integer textCol1;
1352 @XmlAttribute(name = "textCol2")
1353 protected Integer textCol2;
1354 @XmlAttribute(name = "textColThreshold")
1355 protected Integer textColThreshold;
1356 @XmlAttribute(name = "showUnconserved")
1357 protected Boolean showUnconserved;
1358 @XmlAttribute(name = "ignoreGapsinConsensus")
1359 protected Boolean ignoreGapsinConsensus;
1360 @XmlAttribute(name = "showConsensusHistogram")
1361 protected Boolean showConsensusHistogram;
1362 @XmlAttribute(name = "showSequenceLogo")
1363 protected Boolean showSequenceLogo;
1364 @XmlAttribute(name = "normaliseSequenceLogo")
1365 protected Boolean normaliseSequenceLogo;
1366 @XmlAttribute(name = "id")
1367 protected String id;
1370 * Gets the value of the seq property.
1373 * This accessor method returns a reference to the live list,
1374 * not a snapshot. Therefore any modification you make to the
1375 * returned list will be present inside the JAXB object.
1376 * This is why there is not a <CODE>set</CODE> method for the seq property.
1379 * For example, to add a new item, do as follows:
1381 * getSeq().add(newItem);
1386 * Objects of the following type(s) are allowed in the list
1391 public List<String> getSeq() {
1393 seq = new ArrayList<String>();
1399 * Gets the value of the annotationColours property.
1402 * possible object is
1403 * {@link AnnotationColourScheme }
1406 public AnnotationColourScheme getAnnotationColours() {
1407 return annotationColours;
1411 * Sets the value of the annotationColours property.
1415 * {@link AnnotationColourScheme }
1418 public void setAnnotationColours(AnnotationColourScheme value) {
1419 this.annotationColours = value;
1423 * Gets the value of the start property.
1426 * possible object is
1430 public Integer getStart() {
1435 * Sets the value of the start property.
1442 public void setStart(Integer value) {
1447 * Gets the value of the end property.
1450 * possible object is
1454 public Integer getEnd() {
1459 * Sets the value of the end property.
1466 public void setEnd(Integer value) {
1471 * Gets the value of the name property.
1474 * possible object is
1478 public String getName() {
1483 * Sets the value of the name property.
1490 public void setName(String value) {
1495 * Gets the value of the colour property.
1498 * possible object is
1502 public String getColour() {
1507 * Sets the value of the colour property.
1514 public void setColour(String value) {
1515 this.colour = value;
1519 * Gets the value of the consThreshold property.
1522 * possible object is
1526 public Integer getConsThreshold() {
1527 return consThreshold;
1531 * Sets the value of the consThreshold property.
1538 public void setConsThreshold(Integer value) {
1539 this.consThreshold = value;
1543 * Gets the value of the pidThreshold property.
1546 * possible object is
1550 public Integer getPidThreshold() {
1551 return pidThreshold;
1555 * Sets the value of the pidThreshold property.
1562 public void setPidThreshold(Integer value) {
1563 this.pidThreshold = value;
1567 * Gets the value of the outlineColour property.
1570 * possible object is
1574 public Integer getOutlineColour() {
1575 return outlineColour;
1579 * Sets the value of the outlineColour property.
1586 public void setOutlineColour(Integer value) {
1587 this.outlineColour = value;
1591 * Gets the value of the displayBoxes property.
1594 * possible object is
1598 public Boolean isDisplayBoxes() {
1599 return displayBoxes;
1603 * Sets the value of the displayBoxes property.
1610 public void setDisplayBoxes(Boolean value) {
1611 this.displayBoxes = value;
1615 * Gets the value of the displayText property.
1618 * possible object is
1622 public Boolean isDisplayText() {
1627 * Sets the value of the displayText property.
1634 public void setDisplayText(Boolean value) {
1635 this.displayText = value;
1639 * Gets the value of the colourText property.
1642 * possible object is
1646 public Boolean isColourText() {
1651 * Sets the value of the colourText property.
1658 public void setColourText(Boolean value) {
1659 this.colourText = value;
1663 * Gets the value of the textCol1 property.
1666 * possible object is
1670 public Integer getTextCol1() {
1675 * Sets the value of the textCol1 property.
1682 public void setTextCol1(Integer value) {
1683 this.textCol1 = value;
1687 * Gets the value of the textCol2 property.
1690 * possible object is
1694 public Integer getTextCol2() {
1699 * Sets the value of the textCol2 property.
1706 public void setTextCol2(Integer value) {
1707 this.textCol2 = value;
1711 * Gets the value of the textColThreshold property.
1714 * possible object is
1718 public Integer getTextColThreshold() {
1719 return textColThreshold;
1723 * Sets the value of the textColThreshold property.
1730 public void setTextColThreshold(Integer value) {
1731 this.textColThreshold = value;
1735 * Gets the value of the showUnconserved property.
1738 * possible object is
1742 public Boolean isShowUnconserved() {
1743 return showUnconserved;
1747 * Sets the value of the showUnconserved property.
1754 public void setShowUnconserved(Boolean value) {
1755 this.showUnconserved = value;
1759 * Gets the value of the ignoreGapsinConsensus property.
1762 * possible object is
1766 public boolean isIgnoreGapsinConsensus() {
1767 if (ignoreGapsinConsensus == null) {
1770 return ignoreGapsinConsensus;
1775 * Sets the value of the ignoreGapsinConsensus property.
1782 public void setIgnoreGapsinConsensus(Boolean value) {
1783 this.ignoreGapsinConsensus = value;
1787 * Gets the value of the showConsensusHistogram property.
1790 * possible object is
1794 public boolean isShowConsensusHistogram() {
1795 if (showConsensusHistogram == null) {
1798 return showConsensusHistogram;
1803 * Sets the value of the showConsensusHistogram property.
1810 public void setShowConsensusHistogram(Boolean value) {
1811 this.showConsensusHistogram = value;
1815 * Gets the value of the showSequenceLogo property.
1818 * possible object is
1822 public boolean isShowSequenceLogo() {
1823 if (showSequenceLogo == null) {
1826 return showSequenceLogo;
1831 * Sets the value of the showSequenceLogo property.
1838 public void setShowSequenceLogo(Boolean value) {
1839 this.showSequenceLogo = value;
1843 * Gets the value of the normaliseSequenceLogo property.
1846 * possible object is
1850 public boolean isNormaliseSequenceLogo() {
1851 if (normaliseSequenceLogo == null) {
1854 return normaliseSequenceLogo;
1859 * Sets the value of the normaliseSequenceLogo property.
1866 public void setNormaliseSequenceLogo(Boolean value) {
1867 this.normaliseSequenceLogo = value;
1871 * Gets the value of the id property.
1874 * possible object is
1878 public String getId() {
1883 * Sets the value of the id property.
1890 public void setId(String value) {
1898 * <p>Java class for anonymous complex type.
1900 * <p>The following schema fragment specifies the expected content contained within this class.
1904 * <complexContent>
1905 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1907 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1908 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1910 * <complexContent>
1911 * <extension base="{www.jalview.org}pdbentry">
1913 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1915 * <simpleContent>
1916 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1917 * <attGroup ref="{www.jalview.org}swingwindow"/>
1918 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1919 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1920 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1921 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1922 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1923 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1925 * </simpleContent>
1930 * </complexContent>
1933 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1934 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1936 * <complexContent>
1937 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1939 * <element name="secondaryStructure" maxOccurs="unbounded">
1941 * <complexContent>
1942 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1943 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1944 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1945 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1946 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1948 * </complexContent>
1952 * <attGroup ref="{www.jalview.org}swingwindow"/>
1953 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1954 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1955 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1956 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1958 * </complexContent>
1962 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1963 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1964 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1965 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1966 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1967 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1969 * </complexContent>
1975 @XmlAccessorType(XmlAccessType.FIELD)
1976 @XmlType(name = "", propOrder = {
1982 public static class JSeq {
1984 @XmlElement(namespace = "www.jalview.org")
1985 protected List<Feature> features;
1986 @XmlElement(namespace = "www.jalview.org")
1987 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1988 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1989 protected List<Integer> hiddenSequences;
1990 @XmlElement(namespace = "www.jalview.org")
1991 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1992 @XmlAttribute(name = "colour")
1993 protected Integer colour;
1994 @XmlAttribute(name = "start", required = true)
1995 protected int start;
1996 @XmlAttribute(name = "end", required = true)
1998 @XmlAttribute(name = "id", required = true)
1999 protected String id;
2000 @XmlAttribute(name = "hidden")
2001 protected Boolean hidden;
2002 @XmlAttribute(name = "viewreference")
2003 protected Boolean viewreference;
2006 * Gets the value of the features property.
2009 * This accessor method returns a reference to the live list,
2010 * not a snapshot. Therefore any modification you make to the
2011 * returned list will be present inside the JAXB object.
2012 * This is why there is not a <CODE>set</CODE> method for the features property.
2015 * For example, to add a new item, do as follows:
2017 * getFeatures().add(newItem);
2022 * Objects of the following type(s) are allowed in the list
2027 public List<Feature> getFeatures() {
2028 if (features == null) {
2029 features = new ArrayList<Feature>();
2031 return this.features;
2035 * Gets the value of the pdbids property.
2038 * This accessor method returns a reference to the live list,
2039 * not a snapshot. Therefore any modification you make to the
2040 * returned list will be present inside the JAXB object.
2041 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2044 * For example, to add a new item, do as follows:
2046 * getPdbids().add(newItem);
2051 * Objects of the following type(s) are allowed in the list
2052 * {@link JalviewModel.JSeq.Pdbids }
2056 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2057 if (pdbids == null) {
2058 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2064 * Gets the value of the hiddenSequences property.
2067 * This accessor method returns a reference to the live list,
2068 * not a snapshot. Therefore any modification you make to the
2069 * returned list will be present inside the JAXB object.
2070 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2073 * For example, to add a new item, do as follows:
2075 * getHiddenSequences().add(newItem);
2080 * Objects of the following type(s) are allowed in the list
2085 public List<Integer> getHiddenSequences() {
2086 if (hiddenSequences == null) {
2087 hiddenSequences = new ArrayList<Integer>();
2089 return this.hiddenSequences;
2093 * Gets the value of the rnaViewer property.
2096 * This accessor method returns a reference to the live list,
2097 * not a snapshot. Therefore any modification you make to the
2098 * returned list will be present inside the JAXB object.
2099 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2102 * For example, to add a new item, do as follows:
2104 * getRnaViewer().add(newItem);
2109 * Objects of the following type(s) are allowed in the list
2110 * {@link JalviewModel.JSeq.RnaViewer }
2114 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2115 if (rnaViewer == null) {
2116 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2118 return this.rnaViewer;
2122 * Gets the value of the colour property.
2125 * possible object is
2129 public Integer getColour() {
2134 * Sets the value of the colour property.
2141 public void setColour(Integer value) {
2142 this.colour = value;
2146 * Gets the value of the start property.
2149 public int getStart() {
2154 * Sets the value of the start property.
2157 public void setStart(int value) {
2162 * Gets the value of the end property.
2165 public int getEnd() {
2170 * Sets the value of the end property.
2173 public void setEnd(int value) {
2178 * Gets the value of the id property.
2181 * possible object is
2185 public String getId() {
2190 * Sets the value of the id property.
2197 public void setId(String value) {
2202 * Gets the value of the hidden property.
2205 * possible object is
2209 public Boolean isHidden() {
2214 * Sets the value of the hidden property.
2221 public void setHidden(Boolean value) {
2222 this.hidden = value;
2226 * Gets the value of the viewreference property.
2229 * possible object is
2233 public Boolean isViewreference() {
2234 return viewreference;
2238 * Sets the value of the viewreference property.
2245 public void setViewreference(Boolean value) {
2246 this.viewreference = value;
2251 * <p>Java class for anonymous complex type.
2253 * <p>The following schema fragment specifies the expected content contained within this class.
2257 * <complexContent>
2258 * <extension base="{www.jalview.org}pdbentry">
2260 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2262 * <simpleContent>
2263 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2264 * <attGroup ref="{www.jalview.org}swingwindow"/>
2265 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2266 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2267 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2268 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2269 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2270 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2272 * </simpleContent>
2277 * </complexContent>
2283 @XmlAccessorType(XmlAccessType.FIELD)
2284 @XmlType(name = "", propOrder = {
2287 public static class Pdbids
2291 @XmlElement(namespace = "www.jalview.org")
2292 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2295 * Gets the value of the structureState property.
2298 * This accessor method returns a reference to the live list,
2299 * not a snapshot. Therefore any modification you make to the
2300 * returned list will be present inside the JAXB object.
2301 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2304 * For example, to add a new item, do as follows:
2306 * getStructureState().add(newItem);
2311 * Objects of the following type(s) are allowed in the list
2312 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2316 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2317 if (structureState == null) {
2318 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2320 return this.structureState;
2325 * <p>Java class for anonymous complex type.
2327 * <p>The following schema fragment specifies the expected content contained within this class.
2331 * <simpleContent>
2332 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2333 * <attGroup ref="{www.jalview.org}swingwindow"/>
2334 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2335 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2336 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2337 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2338 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2339 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2341 * </simpleContent>
2347 @XmlAccessorType(XmlAccessType.FIELD)
2348 @XmlType(name = "", propOrder = {
2351 public static class StructureState {
2354 protected String value;
2355 @XmlAttribute(name = "visible")
2356 protected Boolean visible;
2357 @XmlAttribute(name = "viewId")
2358 protected String viewId;
2359 @XmlAttribute(name = "alignwithAlignPanel")
2360 protected Boolean alignwithAlignPanel;
2361 @XmlAttribute(name = "colourwithAlignPanel")
2362 protected Boolean colourwithAlignPanel;
2363 @XmlAttribute(name = "colourByJmol")
2364 protected Boolean colourByJmol;
2365 @XmlAttribute(name = "type")
2366 protected String type;
2367 @XmlAttribute(name = "width")
2368 protected Integer width;
2369 @XmlAttribute(name = "height")
2370 protected Integer height;
2371 @XmlAttribute(name = "xpos")
2372 protected Integer xpos;
2373 @XmlAttribute(name = "ypos")
2374 protected Integer ypos;
2377 * Gets the value of the value property.
2380 * possible object is
2384 public String getValue() {
2389 * Sets the value of the value property.
2396 public void setValue(String value) {
2401 * Gets the value of the visible property.
2404 * possible object is
2408 public Boolean isVisible() {
2413 * Sets the value of the visible property.
2420 public void setVisible(Boolean value) {
2421 this.visible = value;
2425 * Gets the value of the viewId property.
2428 * possible object is
2432 public String getViewId() {
2437 * Sets the value of the viewId property.
2444 public void setViewId(String value) {
2445 this.viewId = value;
2449 * Gets the value of the alignwithAlignPanel property.
2452 * possible object is
2456 public boolean isAlignwithAlignPanel() {
2457 if (alignwithAlignPanel == null) {
2460 return alignwithAlignPanel;
2465 * Sets the value of the alignwithAlignPanel property.
2472 public void setAlignwithAlignPanel(Boolean value) {
2473 this.alignwithAlignPanel = value;
2477 * Gets the value of the colourwithAlignPanel property.
2480 * possible object is
2484 public boolean isColourwithAlignPanel() {
2485 if (colourwithAlignPanel == null) {
2488 return colourwithAlignPanel;
2493 * Sets the value of the colourwithAlignPanel property.
2500 public void setColourwithAlignPanel(Boolean value) {
2501 this.colourwithAlignPanel = value;
2505 * Gets the value of the colourByJmol property.
2508 * possible object is
2512 public boolean isColourByJmol() {
2513 if (colourByJmol == null) {
2516 return colourByJmol;
2521 * Sets the value of the colourByJmol property.
2528 public void setColourByJmol(Boolean value) {
2529 this.colourByJmol = value;
2533 * Gets the value of the type property.
2536 * possible object is
2540 public String getType() {
2545 * Sets the value of the type property.
2552 public void setType(String value) {
2557 * Gets the value of the width property.
2560 * possible object is
2564 public Integer getWidth() {
2569 * Sets the value of the width property.
2576 public void setWidth(Integer value) {
2581 * Gets the value of the height property.
2584 * possible object is
2588 public Integer getHeight() {
2593 * Sets the value of the height property.
2600 public void setHeight(Integer value) {
2601 this.height = value;
2605 * Gets the value of the xpos property.
2608 * possible object is
2612 public Integer getXpos() {
2617 * Sets the value of the xpos property.
2624 public void setXpos(Integer value) {
2629 * Gets the value of the ypos property.
2632 * possible object is
2636 public Integer getYpos() {
2641 * Sets the value of the ypos property.
2648 public void setYpos(Integer value) {
2658 * <p>Java class for anonymous complex type.
2660 * <p>The following schema fragment specifies the expected content contained within this class.
2664 * <complexContent>
2665 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2667 * <element name="secondaryStructure" maxOccurs="unbounded">
2669 * <complexContent>
2670 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2671 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2672 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2673 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2674 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2676 * </complexContent>
2680 * <attGroup ref="{www.jalview.org}swingwindow"/>
2681 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2682 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2683 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2684 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2686 * </complexContent>
2692 @XmlAccessorType(XmlAccessType.FIELD)
2693 @XmlType(name = "", propOrder = {
2694 "secondaryStructure"
2696 public static class RnaViewer {
2698 @XmlElement(namespace = "www.jalview.org", required = true)
2699 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2700 @XmlAttribute(name = "title")
2701 protected String title;
2702 @XmlAttribute(name = "viewId")
2703 protected String viewId;
2704 @XmlAttribute(name = "dividerLocation")
2705 protected Integer dividerLocation;
2706 @XmlAttribute(name = "selectedRna")
2707 protected Integer selectedRna;
2708 @XmlAttribute(name = "width")
2709 protected Integer width;
2710 @XmlAttribute(name = "height")
2711 protected Integer height;
2712 @XmlAttribute(name = "xpos")
2713 protected Integer xpos;
2714 @XmlAttribute(name = "ypos")
2715 protected Integer ypos;
2718 * Gets the value of the secondaryStructure property.
2721 * This accessor method returns a reference to the live list,
2722 * not a snapshot. Therefore any modification you make to the
2723 * returned list will be present inside the JAXB object.
2724 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2727 * For example, to add a new item, do as follows:
2729 * getSecondaryStructure().add(newItem);
2734 * Objects of the following type(s) are allowed in the list
2735 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2739 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2740 if (secondaryStructure == null) {
2741 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2743 return this.secondaryStructure;
2747 * Gets the value of the title property.
2750 * possible object is
2754 public String getTitle() {
2759 * Sets the value of the title property.
2766 public void setTitle(String value) {
2771 * Gets the value of the viewId property.
2774 * possible object is
2778 public String getViewId() {
2783 * Sets the value of the viewId property.
2790 public void setViewId(String value) {
2791 this.viewId = value;
2795 * Gets the value of the dividerLocation property.
2798 * possible object is
2802 public Integer getDividerLocation() {
2803 return dividerLocation;
2807 * Sets the value of the dividerLocation property.
2814 public void setDividerLocation(Integer value) {
2815 this.dividerLocation = value;
2819 * Gets the value of the selectedRna property.
2822 * possible object is
2826 public Integer getSelectedRna() {
2831 * Sets the value of the selectedRna property.
2838 public void setSelectedRna(Integer value) {
2839 this.selectedRna = value;
2843 * Gets the value of the width property.
2846 * possible object is
2850 public Integer getWidth() {
2855 * Sets the value of the width property.
2862 public void setWidth(Integer value) {
2867 * Gets the value of the height property.
2870 * possible object is
2874 public Integer getHeight() {
2879 * Sets the value of the height property.
2886 public void setHeight(Integer value) {
2887 this.height = value;
2891 * Gets the value of the xpos property.
2894 * possible object is
2898 public Integer getXpos() {
2903 * Sets the value of the xpos property.
2910 public void setXpos(Integer value) {
2915 * Gets the value of the ypos property.
2918 * possible object is
2922 public Integer getYpos() {
2927 * Sets the value of the ypos property.
2934 public void setYpos(Integer value) {
2940 * <p>Java class for anonymous complex type.
2942 * <p>The following schema fragment specifies the expected content contained within this class.
2946 * <complexContent>
2947 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2948 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2949 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2950 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2951 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2953 * </complexContent>
2959 @XmlAccessorType(XmlAccessType.FIELD)
2961 public static class SecondaryStructure {
2963 @XmlAttribute(name = "title")
2964 protected String title;
2965 @XmlAttribute(name = "annotationId", required = true)
2966 protected String annotationId;
2967 @XmlAttribute(name = "gapped")
2968 protected Boolean gapped;
2969 @XmlAttribute(name = "viewerState")
2970 protected String viewerState;
2973 * Gets the value of the title property.
2976 * possible object is
2980 public String getTitle() {
2985 * Sets the value of the title property.
2992 public void setTitle(String value) {
2997 * Gets the value of the annotationId property.
3000 * possible object is
3004 public String getAnnotationId() {
3005 return annotationId;
3009 * Sets the value of the annotationId property.
3016 public void setAnnotationId(String value) {
3017 this.annotationId = value;
3021 * Gets the value of the gapped property.
3024 * possible object is
3028 public Boolean isGapped() {
3033 * Sets the value of the gapped property.
3040 public void setGapped(Boolean value) {
3041 this.gapped = value;
3045 * Gets the value of the viewerState property.
3048 * possible object is
3052 public String getViewerState() {
3057 * Sets the value of the viewerState property.
3064 public void setViewerState(String value) {
3065 this.viewerState = value;
3076 * <p>Java class for anonymous complex type.
3078 * <p>The following schema fragment specifies the expected content contained within this class.
3082 * <complexContent>
3083 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3085 * <element name="sequencePoint" maxOccurs="unbounded">
3087 * <complexContent>
3088 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3089 * <attGroup ref="{www.jalview.org}position"/>
3090 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3092 * </complexContent>
3095 * <element name="axis" maxOccurs="3" minOccurs="3">
3097 * <complexContent>
3098 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3099 * <attGroup ref="{www.jalview.org}position"/>
3101 * </complexContent>
3104 * <element name="seqPointMin">
3106 * <complexContent>
3107 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3108 * <attGroup ref="{www.jalview.org}position"/>
3110 * </complexContent>
3113 * <element name="seqPointMax">
3115 * <complexContent>
3116 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3117 * <attGroup ref="{www.jalview.org}position"/>
3119 * </complexContent>
3122 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3124 * <attGroup ref="{www.jalview.org}swingwindow"/>
3125 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
3126 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3127 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3128 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3129 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3130 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3131 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3132 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3133 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3134 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3136 * </complexContent>
3142 @XmlAccessorType(XmlAccessType.FIELD)
3143 @XmlType(name = "", propOrder = {
3150 public static class PcaViewer {
3152 @XmlElement(namespace = "www.jalview.org", required = true)
3153 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3154 @XmlElement(namespace = "www.jalview.org", required = true)
3155 protected List<JalviewModel.PcaViewer.Axis> axis;
3156 @XmlElement(namespace = "www.jalview.org", required = true)
3157 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3158 @XmlElement(namespace = "www.jalview.org", required = true)
3159 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3160 @XmlElement(namespace = "www.jalview.org", required = true)
3161 protected PcaDataType pcaData;
3162 @XmlAttribute(name = "title")
3163 protected String title;
3164 @XmlAttribute(name = "scoreModelName")
3165 protected String scoreModelName;
3166 @XmlAttribute(name = "xDim")
3167 protected Integer xDim;
3168 @XmlAttribute(name = "yDim")
3169 protected Integer yDim;
3170 @XmlAttribute(name = "zDim")
3171 protected Integer zDim;
3172 @XmlAttribute(name = "bgColour")
3173 protected Integer bgColour;
3174 @XmlAttribute(name = "scaleFactor")
3175 protected Float scaleFactor;
3176 @XmlAttribute(name = "showLabels")
3177 protected Boolean showLabels;
3178 @XmlAttribute(name = "linkToAllViews")
3179 protected Boolean linkToAllViews;
3180 @XmlAttribute(name = "width")
3181 protected Integer width;
3182 @XmlAttribute(name = "height")
3183 protected Integer height;
3184 @XmlAttribute(name = "xpos")
3185 protected Integer xpos;
3186 @XmlAttribute(name = "ypos")
3187 protected Integer ypos;
3188 @XmlAttribute(name = "includeGaps")
3189 protected Boolean includeGaps;
3190 @XmlAttribute(name = "matchGaps")
3191 protected Boolean matchGaps;
3192 @XmlAttribute(name = "includeGappedColumns")
3193 protected Boolean includeGappedColumns;
3194 @XmlAttribute(name = "denominateByShortestLength")
3195 protected Boolean denominateByShortestLength;
3198 * Gets the value of the sequencePoint property.
3201 * This accessor method returns a reference to the live list,
3202 * not a snapshot. Therefore any modification you make to the
3203 * returned list will be present inside the JAXB object.
3204 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3207 * For example, to add a new item, do as follows:
3209 * getSequencePoint().add(newItem);
3214 * Objects of the following type(s) are allowed in the list
3215 * {@link JalviewModel.PcaViewer.SequencePoint }
3219 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3220 if (sequencePoint == null) {
3221 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3223 return this.sequencePoint;
3227 * Gets the value of the axis property.
3230 * This accessor method returns a reference to the live list,
3231 * not a snapshot. Therefore any modification you make to the
3232 * returned list will be present inside the JAXB object.
3233 * This is why there is not a <CODE>set</CODE> method for the axis property.
3236 * For example, to add a new item, do as follows:
3238 * getAxis().add(newItem);
3243 * Objects of the following type(s) are allowed in the list
3244 * {@link JalviewModel.PcaViewer.Axis }
3248 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3250 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3256 * Gets the value of the seqPointMin property.
3259 * possible object is
3260 * {@link JalviewModel.PcaViewer.SeqPointMin }
3263 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3268 * Sets the value of the seqPointMin property.
3272 * {@link JalviewModel.PcaViewer.SeqPointMin }
3275 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3276 this.seqPointMin = value;
3280 * Gets the value of the seqPointMax property.
3283 * possible object is
3284 * {@link JalviewModel.PcaViewer.SeqPointMax }
3287 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3292 * Sets the value of the seqPointMax property.
3296 * {@link JalviewModel.PcaViewer.SeqPointMax }
3299 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3300 this.seqPointMax = value;
3304 * Gets the value of the pcaData property.
3307 * possible object is
3308 * {@link PcaDataType }
3311 public PcaDataType getPcaData() {
3316 * Sets the value of the pcaData property.
3320 * {@link PcaDataType }
3323 public void setPcaData(PcaDataType value) {
3324 this.pcaData = value;
3328 * Gets the value of the title property.
3331 * possible object is
3335 public String getTitle() {
3340 * Sets the value of the title property.
3347 public void setTitle(String value) {
3352 * Gets the value of the scoreModelName property.
3355 * possible object is
3359 public String getScoreModelName() {
3360 return scoreModelName;
3364 * Sets the value of the scoreModelName property.
3371 public void setScoreModelName(String value) {
3372 this.scoreModelName = value;
3376 * Gets the value of the xDim property.
3379 * possible object is
3383 public Integer getXDim() {
3388 * Sets the value of the xDim property.
3395 public void setXDim(Integer value) {
3400 * Gets the value of the yDim property.
3403 * possible object is
3407 public Integer getYDim() {
3412 * Sets the value of the yDim property.
3419 public void setYDim(Integer value) {
3424 * Gets the value of the zDim property.
3427 * possible object is
3431 public Integer getZDim() {
3436 * Sets the value of the zDim property.
3443 public void setZDim(Integer value) {
3448 * Gets the value of the bgColour property.
3451 * possible object is
3455 public Integer getBgColour() {
3460 * Sets the value of the bgColour property.
3467 public void setBgColour(Integer value) {
3468 this.bgColour = value;
3472 * Gets the value of the scaleFactor property.
3475 * possible object is
3479 public Float getScaleFactor() {
3484 * Sets the value of the scaleFactor property.
3491 public void setScaleFactor(Float value) {
3492 this.scaleFactor = value;
3496 * Gets the value of the showLabels property.
3499 * possible object is
3503 public Boolean isShowLabels() {
3508 * Sets the value of the showLabels property.
3515 public void setShowLabels(Boolean value) {
3516 this.showLabels = value;
3520 * Gets the value of the linkToAllViews property.
3523 * possible object is
3527 public Boolean isLinkToAllViews() {
3528 return linkToAllViews;
3532 * Sets the value of the linkToAllViews property.
3539 public void setLinkToAllViews(Boolean value) {
3540 this.linkToAllViews = value;
3544 * Gets the value of the width property.
3547 * possible object is
3551 public Integer getWidth() {
3556 * Sets the value of the width property.
3563 public void setWidth(Integer value) {
3568 * Gets the value of the height property.
3571 * possible object is
3575 public Integer getHeight() {
3580 * Sets the value of the height property.
3587 public void setHeight(Integer value) {
3588 this.height = value;
3592 * Gets the value of the xpos property.
3595 * possible object is
3599 public Integer getXpos() {
3604 * Sets the value of the xpos property.
3611 public void setXpos(Integer value) {
3616 * Gets the value of the ypos property.
3619 * possible object is
3623 public Integer getYpos() {
3628 * Sets the value of the ypos property.
3635 public void setYpos(Integer value) {
3640 * Gets the value of the includeGaps property.
3643 * possible object is
3647 public Boolean isIncludeGaps() {
3652 * Sets the value of the includeGaps property.
3659 public void setIncludeGaps(Boolean value) {
3660 this.includeGaps = value;
3664 * Gets the value of the matchGaps property.
3667 * possible object is
3671 public Boolean isMatchGaps() {
3676 * Sets the value of the matchGaps property.
3683 public void setMatchGaps(Boolean value) {
3684 this.matchGaps = value;
3688 * Gets the value of the includeGappedColumns property.
3691 * possible object is
3695 public Boolean isIncludeGappedColumns() {
3696 return includeGappedColumns;
3700 * Sets the value of the includeGappedColumns property.
3707 public void setIncludeGappedColumns(Boolean value) {
3708 this.includeGappedColumns = value;
3712 * Gets the value of the denominateByShortestLength property.
3715 * possible object is
3719 public Boolean isDenominateByShortestLength() {
3720 return denominateByShortestLength;
3724 * Sets the value of the denominateByShortestLength property.
3731 public void setDenominateByShortestLength(Boolean value) {
3732 this.denominateByShortestLength = value;
3737 * <p>Java class for anonymous complex type.
3739 * <p>The following schema fragment specifies the expected content contained within this class.
3743 * <complexContent>
3744 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3745 * <attGroup ref="{www.jalview.org}position"/>
3747 * </complexContent>
3753 @XmlAccessorType(XmlAccessType.FIELD)
3755 public static class Axis {
3757 @XmlAttribute(name = "xPos")
3758 protected Float xPos;
3759 @XmlAttribute(name = "yPos")
3760 protected Float yPos;
3761 @XmlAttribute(name = "zPos")
3762 protected Float zPos;
3765 * Gets the value of the xPos property.
3768 * possible object is
3772 public Float getXPos() {
3777 * Sets the value of the xPos property.
3784 public void setXPos(Float value) {
3789 * Gets the value of the yPos property.
3792 * possible object is
3796 public Float getYPos() {
3801 * Sets the value of the yPos property.
3808 public void setYPos(Float value) {
3813 * Gets the value of the zPos property.
3816 * possible object is
3820 public Float getZPos() {
3825 * Sets the value of the zPos property.
3832 public void setZPos(Float value) {
3840 * <p>Java class for anonymous complex type.
3842 * <p>The following schema fragment specifies the expected content contained within this class.
3846 * <complexContent>
3847 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3848 * <attGroup ref="{www.jalview.org}position"/>
3850 * </complexContent>
3856 @XmlAccessorType(XmlAccessType.FIELD)
3858 public static class SeqPointMax {
3860 @XmlAttribute(name = "xPos")
3861 protected Float xPos;
3862 @XmlAttribute(name = "yPos")
3863 protected Float yPos;
3864 @XmlAttribute(name = "zPos")
3865 protected Float zPos;
3868 * Gets the value of the xPos property.
3871 * possible object is
3875 public Float getXPos() {
3880 * Sets the value of the xPos property.
3887 public void setXPos(Float value) {
3892 * Gets the value of the yPos property.
3895 * possible object is
3899 public Float getYPos() {
3904 * Sets the value of the yPos property.
3911 public void setYPos(Float value) {
3916 * Gets the value of the zPos property.
3919 * possible object is
3923 public Float getZPos() {
3928 * Sets the value of the zPos property.
3935 public void setZPos(Float value) {
3943 * <p>Java class for anonymous complex type.
3945 * <p>The following schema fragment specifies the expected content contained within this class.
3949 * <complexContent>
3950 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3951 * <attGroup ref="{www.jalview.org}position"/>
3953 * </complexContent>
3959 @XmlAccessorType(XmlAccessType.FIELD)
3961 public static class SeqPointMin {
3963 @XmlAttribute(name = "xPos")
3964 protected Float xPos;
3965 @XmlAttribute(name = "yPos")
3966 protected Float yPos;
3967 @XmlAttribute(name = "zPos")
3968 protected Float zPos;
3971 * Gets the value of the xPos property.
3974 * possible object is
3978 public Float getXPos() {
3983 * Sets the value of the xPos property.
3990 public void setXPos(Float value) {
3995 * Gets the value of the yPos property.
3998 * possible object is
4002 public Float getYPos() {
4007 * Sets the value of the yPos property.
4014 public void setYPos(Float value) {
4019 * Gets the value of the zPos property.
4022 * possible object is
4026 public Float getZPos() {
4031 * Sets the value of the zPos property.
4038 public void setZPos(Float value) {
4046 * <p>Java class for anonymous complex type.
4048 * <p>The following schema fragment specifies the expected content contained within this class.
4052 * <complexContent>
4053 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4054 * <attGroup ref="{www.jalview.org}position"/>
4055 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4057 * </complexContent>
4063 @XmlAccessorType(XmlAccessType.FIELD)
4065 public static class SequencePoint {
4067 @XmlAttribute(name = "sequenceRef")
4068 protected String sequenceRef;
4069 @XmlAttribute(name = "xPos")
4070 protected Float xPos;
4071 @XmlAttribute(name = "yPos")
4072 protected Float yPos;
4073 @XmlAttribute(name = "zPos")
4074 protected Float zPos;
4077 * Gets the value of the sequenceRef property.
4080 * possible object is
4084 public String getSequenceRef() {
4089 * Sets the value of the sequenceRef property.
4096 public void setSequenceRef(String value) {
4097 this.sequenceRef = value;
4101 * Gets the value of the xPos property.
4104 * possible object is
4108 public Float getXPos() {
4113 * Sets the value of the xPos property.
4120 public void setXPos(Float value) {
4125 * Gets the value of the yPos property.
4128 * possible object is
4132 public Float getYPos() {
4137 * Sets the value of the yPos property.
4144 public void setYPos(Float value) {
4149 * Gets the value of the zPos property.
4152 * possible object is
4156 public Float getZPos() {
4161 * Sets the value of the zPos property.
4168 public void setZPos(Float value) {
4178 * <p>Java class for anonymous complex type.
4180 * <p>The following schema fragment specifies the expected content contained within this class.
4184 * <complexContent>
4185 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4186 * <sequence minOccurs="0">
4187 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4188 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4190 * <attGroup ref="{www.jalview.org}swingwindow"/>
4191 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4192 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4193 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4194 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4195 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4196 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4197 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4198 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4199 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4200 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4201 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4203 * </complexContent>
4209 @XmlAccessorType(XmlAccessType.FIELD)
4210 @XmlType(name = "", propOrder = {
4214 public static class Tree {
4216 @XmlElement(namespace = "www.jalview.org")
4217 protected String title;
4218 @XmlElement(namespace = "www.jalview.org")
4219 protected String newick;
4220 @XmlAttribute(name = "fontName")
4221 protected String fontName;
4222 @XmlAttribute(name = "fontSize")
4223 protected Integer fontSize;
4224 @XmlAttribute(name = "fontStyle")
4225 protected Integer fontStyle;
4226 @XmlAttribute(name = "threshold")
4227 protected Float threshold;
4228 @XmlAttribute(name = "showBootstrap")
4229 protected Boolean showBootstrap;
4230 @XmlAttribute(name = "showDistances")
4231 protected Boolean showDistances;
4232 @XmlAttribute(name = "markUnlinked")
4233 protected Boolean markUnlinked;
4234 @XmlAttribute(name = "fitToWindow")
4235 protected Boolean fitToWindow;
4236 @XmlAttribute(name = "currentTree")
4237 protected Boolean currentTree;
4238 @XmlAttribute(name = "id")
4239 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4241 @XmlSchemaType(name = "ID")
4242 protected String id;
4243 @XmlAttribute(name = "linkToAllViews")
4244 protected Boolean linkToAllViews;
4245 @XmlAttribute(name = "width")
4246 protected Integer width;
4247 @XmlAttribute(name = "height")
4248 protected Integer height;
4249 @XmlAttribute(name = "xpos")
4250 protected Integer xpos;
4251 @XmlAttribute(name = "ypos")
4252 protected Integer ypos;
4255 * Gets the value of the title property.
4258 * possible object is
4262 public String getTitle() {
4267 * Sets the value of the title property.
4274 public void setTitle(String value) {
4279 * Gets the value of the newick property.
4282 * possible object is
4286 public String getNewick() {
4291 * Sets the value of the newick property.
4298 public void setNewick(String value) {
4299 this.newick = value;
4303 * Gets the value of the fontName property.
4306 * possible object is
4310 public String getFontName() {
4315 * Sets the value of the fontName property.
4322 public void setFontName(String value) {
4323 this.fontName = value;
4327 * Gets the value of the fontSize property.
4330 * possible object is
4334 public Integer getFontSize() {
4339 * Sets the value of the fontSize property.
4346 public void setFontSize(Integer value) {
4347 this.fontSize = value;
4351 * Gets the value of the fontStyle property.
4354 * possible object is
4358 public Integer getFontStyle() {
4363 * Sets the value of the fontStyle property.
4370 public void setFontStyle(Integer value) {
4371 this.fontStyle = value;
4375 * Gets the value of the threshold property.
4378 * possible object is
4382 public Float getThreshold() {
4387 * Sets the value of the threshold property.
4394 public void setThreshold(Float value) {
4395 this.threshold = value;
4399 * Gets the value of the showBootstrap property.
4402 * possible object is
4406 public Boolean isShowBootstrap() {
4407 return showBootstrap;
4411 * Sets the value of the showBootstrap property.
4418 public void setShowBootstrap(Boolean value) {
4419 this.showBootstrap = value;
4423 * Gets the value of the showDistances property.
4426 * possible object is
4430 public Boolean isShowDistances() {
4431 return showDistances;
4435 * Sets the value of the showDistances property.
4442 public void setShowDistances(Boolean value) {
4443 this.showDistances = value;
4447 * Gets the value of the markUnlinked property.
4450 * possible object is
4454 public Boolean isMarkUnlinked() {
4455 return markUnlinked;
4459 * Sets the value of the markUnlinked property.
4466 public void setMarkUnlinked(Boolean value) {
4467 this.markUnlinked = value;
4471 * Gets the value of the fitToWindow property.
4474 * possible object is
4478 public Boolean isFitToWindow() {
4483 * Sets the value of the fitToWindow property.
4490 public void setFitToWindow(Boolean value) {
4491 this.fitToWindow = value;
4495 * Gets the value of the currentTree property.
4498 * possible object is
4502 public Boolean isCurrentTree() {
4507 * Sets the value of the currentTree property.
4514 public void setCurrentTree(Boolean value) {
4515 this.currentTree = value;
4519 * Gets the value of the id property.
4522 * possible object is
4526 public String getId() {
4531 * Sets the value of the id property.
4538 public void setId(String value) {
4543 * Gets the value of the linkToAllViews property.
4546 * possible object is
4550 public boolean isLinkToAllViews() {
4551 if (linkToAllViews == null) {
4554 return linkToAllViews;
4559 * Sets the value of the linkToAllViews property.
4566 public void setLinkToAllViews(Boolean value) {
4567 this.linkToAllViews = value;
4571 * Gets the value of the width property.
4574 * possible object is
4578 public Integer getWidth() {
4583 * Sets the value of the width property.
4590 public void setWidth(Integer value) {
4595 * Gets the value of the height property.
4598 * possible object is
4602 public Integer getHeight() {
4607 * Sets the value of the height property.
4614 public void setHeight(Integer value) {
4615 this.height = value;
4619 * Gets the value of the xpos property.
4622 * possible object is
4626 public Integer getXpos() {
4631 * Sets the value of the xpos property.
4638 public void setXpos(Integer value) {
4643 * Gets the value of the ypos property.
4646 * possible object is
4650 public Integer getYpos() {
4655 * Sets the value of the ypos property.
4662 public void setYpos(Integer value) {
4670 * <p>Java class for anonymous complex type.
4672 * <p>The following schema fragment specifies the expected content contained within this class.
4676 * <complexContent>
4677 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4679 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4681 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4683 * </complexContent>
4689 @XmlAccessorType(XmlAccessType.FIELD)
4690 @XmlType(name = "", propOrder = {
4693 public static class UserColours {
4695 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4696 protected JalviewUserColours userColourScheme;
4697 @XmlAttribute(name = "id")
4698 protected String id;
4701 * Gets the value of the userColourScheme property.
4704 * possible object is
4705 * {@link JalviewUserColours }
4708 public JalviewUserColours getUserColourScheme() {
4709 return userColourScheme;
4713 * Sets the value of the userColourScheme property.
4717 * {@link JalviewUserColours }
4720 public void setUserColourScheme(JalviewUserColours value) {
4721 this.userColourScheme = value;
4725 * Gets the value of the id property.
4728 * possible object is
4732 public String getId() {
4737 * Sets the value of the id property.
4744 public void setId(String value) {
4752 * <p>Java class for anonymous complex type.
4754 * <p>The following schema fragment specifies the expected content contained within this class.
4758 * <complexContent>
4759 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4761 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4762 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4764 * <complexContent>
4765 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4766 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4767 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4769 * </complexContent>
4772 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4774 * <complexContent>
4775 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4776 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4777 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4778 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4780 * </complexContent>
4783 * <element name="overview" minOccurs="0">
4785 * <complexContent>
4786 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4787 * <attGroup ref="{www.jalview.org}swingwindow"/>
4788 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4789 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4790 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4791 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4793 * </complexContent>
4797 * <attGroup ref="{www.jalview.org}swingwindow"/>
4798 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4799 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4800 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4801 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4802 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4803 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4804 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4805 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4806 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4807 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4809 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4811 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4812 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4813 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4816 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4817 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4818 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4819 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4820 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4821 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4822 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4824 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4825 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4826 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4827 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4828 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4829 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4830 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4831 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4832 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4833 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4834 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4835 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4836 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4837 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4838 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4839 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4840 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4842 * </complexContent>
4848 @XmlAccessorType(XmlAccessType.FIELD)
4849 @XmlType(name = "", propOrder = {
4850 "annotationColours",
4855 public static class Viewport {
4857 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4858 protected AnnotationColourScheme annotationColours;
4859 @XmlElement(namespace = "www.jalview.org")
4860 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4861 @XmlElement(namespace = "www.jalview.org")
4862 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4863 @XmlElement(namespace = "www.jalview.org")
4864 protected JalviewModel.Viewport.Overview overview;
4865 @XmlAttribute(name = "conservationSelected")
4866 protected Boolean conservationSelected;
4867 @XmlAttribute(name = "pidSelected")
4868 protected Boolean pidSelected;
4869 @XmlAttribute(name = "bgColour")
4870 protected String bgColour;
4871 @XmlAttribute(name = "consThreshold")
4872 protected Integer consThreshold;
4873 @XmlAttribute(name = "pidThreshold")
4874 protected Integer pidThreshold;
4875 @XmlAttribute(name = "title")
4876 protected String title;
4877 @XmlAttribute(name = "showFullId")
4878 protected Boolean showFullId;
4879 @XmlAttribute(name = "rightAlignIds")
4880 protected Boolean rightAlignIds;
4881 @XmlAttribute(name = "showText")
4882 protected Boolean showText;
4883 @XmlAttribute(name = "showColourText")
4884 protected Boolean showColourText;
4885 @XmlAttribute(name = "showUnconserved")
4886 protected Boolean showUnconserved;
4887 @XmlAttribute(name = "showBoxes")
4888 protected Boolean showBoxes;
4889 @XmlAttribute(name = "wrapAlignment")
4890 protected Boolean wrapAlignment;
4891 @XmlAttribute(name = "renderGaps")
4892 protected Boolean renderGaps;
4893 @XmlAttribute(name = "showSequenceFeatures")
4894 protected Boolean showSequenceFeatures;
4895 @XmlAttribute(name = "showNPfeatureTooltip")
4896 protected Boolean showNPfeatureTooltip;
4897 @XmlAttribute(name = "showDbRefTooltip")
4898 protected Boolean showDbRefTooltip;
4899 @XmlAttribute(name = "followHighlight")
4900 protected Boolean followHighlight;
4901 @XmlAttribute(name = "followSelection")
4902 protected Boolean followSelection;
4903 @XmlAttribute(name = "showAnnotation")
4904 protected Boolean showAnnotation;
4905 @XmlAttribute(name = "centreColumnLabels")
4906 protected Boolean centreColumnLabels;
4907 @XmlAttribute(name = "showGroupConservation")
4908 protected Boolean showGroupConservation;
4909 @XmlAttribute(name = "showGroupConsensus")
4910 protected Boolean showGroupConsensus;
4911 @XmlAttribute(name = "showConsensusHistogram")
4912 protected Boolean showConsensusHistogram;
4913 @XmlAttribute(name = "showSequenceLogo")
4914 protected Boolean showSequenceLogo;
4915 @XmlAttribute(name = "normaliseSequenceLogo")
4916 protected Boolean normaliseSequenceLogo;
4917 @XmlAttribute(name = "ignoreGapsinConsensus")
4918 protected Boolean ignoreGapsinConsensus;
4919 @XmlAttribute(name = "startRes")
4920 protected Integer startRes;
4921 @XmlAttribute(name = "startSeq")
4922 protected Integer startSeq;
4923 @XmlAttribute(name = "fontName")
4924 protected String fontName;
4925 @XmlAttribute(name = "fontSize")
4926 protected Integer fontSize;
4927 @XmlAttribute(name = "fontStyle")
4928 protected Integer fontStyle;
4929 @XmlAttribute(name = "scaleProteinAsCdna")
4930 protected Boolean scaleProteinAsCdna;
4931 @XmlAttribute(name = "viewName")
4932 protected String viewName;
4933 @XmlAttribute(name = "sequenceSetId")
4934 protected String sequenceSetId;
4935 @XmlAttribute(name = "gatheredViews")
4936 protected Boolean gatheredViews;
4937 @XmlAttribute(name = "textCol1")
4938 protected Integer textCol1;
4939 @XmlAttribute(name = "textCol2")
4940 protected Integer textCol2;
4941 @XmlAttribute(name = "textColThreshold")
4942 protected Integer textColThreshold;
4943 @XmlAttribute(name = "id")
4944 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4946 @XmlSchemaType(name = "ID")
4947 protected String id;
4948 @XmlAttribute(name = "complementId")
4949 protected String complementId;
4950 @XmlAttribute(name = "showComplementFeatures")
4951 protected Boolean showComplementFeatures;
4952 @XmlAttribute(name = "showComplementFeaturesOnTop")
4953 protected Boolean showComplementFeaturesOnTop;
4954 @XmlAttribute(name = "width")
4955 protected Integer width;
4956 @XmlAttribute(name = "height")
4957 protected Integer height;
4958 @XmlAttribute(name = "xpos")
4959 protected Integer xpos;
4960 @XmlAttribute(name = "ypos")
4961 protected Integer ypos;
4964 * Gets the value of the annotationColours property.
4967 * possible object is
4968 * {@link AnnotationColourScheme }
4971 public AnnotationColourScheme getAnnotationColours() {
4972 return annotationColours;
4976 * Sets the value of the annotationColours property.
4980 * {@link AnnotationColourScheme }
4983 public void setAnnotationColours(AnnotationColourScheme value) {
4984 this.annotationColours = value;
4988 * Gets the value of the hiddenColumns property.
4991 * This accessor method returns a reference to the live list,
4992 * not a snapshot. Therefore any modification you make to the
4993 * returned list will be present inside the JAXB object.
4994 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4997 * For example, to add a new item, do as follows:
4999 * getHiddenColumns().add(newItem);
5004 * Objects of the following type(s) are allowed in the list
5005 * {@link JalviewModel.Viewport.HiddenColumns }
5009 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5010 if (hiddenColumns == null) {
5011 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5013 return this.hiddenColumns;
5017 * Gets the value of the calcIdParam property.
5020 * This accessor method returns a reference to the live list,
5021 * not a snapshot. Therefore any modification you make to the
5022 * returned list will be present inside the JAXB object.
5023 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5026 * For example, to add a new item, do as follows:
5028 * getCalcIdParam().add(newItem);
5033 * Objects of the following type(s) are allowed in the list
5034 * {@link JalviewModel.Viewport.CalcIdParam }
5038 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5039 if (calcIdParam == null) {
5040 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5042 return this.calcIdParam;
5046 * Gets the value of the overview property.
5049 * possible object is
5050 * {@link JalviewModel.Viewport.Overview }
5053 public JalviewModel.Viewport.Overview getOverview() {
5058 * Sets the value of the overview property.
5062 * {@link JalviewModel.Viewport.Overview }
5065 public void setOverview(JalviewModel.Viewport.Overview value) {
5066 this.overview = value;
5070 * Gets the value of the conservationSelected property.
5073 * possible object is
5077 public Boolean isConservationSelected() {
5078 return conservationSelected;
5082 * Sets the value of the conservationSelected property.
5089 public void setConservationSelected(Boolean value) {
5090 this.conservationSelected = value;
5094 * Gets the value of the pidSelected property.
5097 * possible object is
5101 public Boolean isPidSelected() {
5106 * Sets the value of the pidSelected property.
5113 public void setPidSelected(Boolean value) {
5114 this.pidSelected = value;
5118 * Gets the value of the bgColour property.
5121 * possible object is
5125 public String getBgColour() {
5130 * Sets the value of the bgColour property.
5137 public void setBgColour(String value) {
5138 this.bgColour = value;
5142 * Gets the value of the consThreshold property.
5145 * possible object is
5149 public Integer getConsThreshold() {
5150 return consThreshold;
5154 * Sets the value of the consThreshold property.
5161 public void setConsThreshold(Integer value) {
5162 this.consThreshold = value;
5166 * Gets the value of the pidThreshold property.
5169 * possible object is
5173 public Integer getPidThreshold() {
5174 return pidThreshold;
5178 * Sets the value of the pidThreshold property.
5185 public void setPidThreshold(Integer value) {
5186 this.pidThreshold = value;
5190 * Gets the value of the title property.
5193 * possible object is
5197 public String getTitle() {
5202 * Sets the value of the title property.
5209 public void setTitle(String value) {
5214 * Gets the value of the showFullId property.
5217 * possible object is
5221 public Boolean isShowFullId() {
5226 * Sets the value of the showFullId property.
5233 public void setShowFullId(Boolean value) {
5234 this.showFullId = value;
5238 * Gets the value of the rightAlignIds property.
5241 * possible object is
5245 public Boolean isRightAlignIds() {
5246 return rightAlignIds;
5250 * Sets the value of the rightAlignIds property.
5257 public void setRightAlignIds(Boolean value) {
5258 this.rightAlignIds = value;
5262 * Gets the value of the showText property.
5265 * possible object is
5269 public Boolean isShowText() {
5274 * Sets the value of the showText property.
5281 public void setShowText(Boolean value) {
5282 this.showText = value;
5286 * Gets the value of the showColourText property.
5289 * possible object is
5293 public Boolean isShowColourText() {
5294 return showColourText;
5298 * Sets the value of the showColourText property.
5305 public void setShowColourText(Boolean value) {
5306 this.showColourText = value;
5310 * Gets the value of the showUnconserved property.
5313 * possible object is
5317 public boolean isShowUnconserved() {
5318 if (showUnconserved == null) {
5321 return showUnconserved;
5326 * Sets the value of the showUnconserved property.
5333 public void setShowUnconserved(Boolean value) {
5334 this.showUnconserved = value;
5338 * Gets the value of the showBoxes property.
5341 * possible object is
5345 public Boolean isShowBoxes() {
5350 * Sets the value of the showBoxes property.
5357 public void setShowBoxes(Boolean value) {
5358 this.showBoxes = value;
5362 * Gets the value of the wrapAlignment property.
5365 * possible object is
5369 public Boolean isWrapAlignment() {
5370 return wrapAlignment;
5374 * Sets the value of the wrapAlignment property.
5381 public void setWrapAlignment(Boolean value) {
5382 this.wrapAlignment = value;
5386 * Gets the value of the renderGaps property.
5389 * possible object is
5393 public Boolean isRenderGaps() {
5398 * Sets the value of the renderGaps property.
5405 public void setRenderGaps(Boolean value) {
5406 this.renderGaps = value;
5410 * Gets the value of the showSequenceFeatures property.
5413 * possible object is
5417 public Boolean isShowSequenceFeatures() {
5418 return showSequenceFeatures;
5422 * Sets the value of the showSequenceFeatures property.
5429 public void setShowSequenceFeatures(Boolean value) {
5430 this.showSequenceFeatures = value;
5434 * Gets the value of the showNPfeatureTooltip property.
5437 * possible object is
5441 public Boolean isShowNPfeatureTooltip() {
5442 return showNPfeatureTooltip;
5446 * Sets the value of the showNPfeatureTooltip property.
5453 public void setShowNPfeatureTooltip(Boolean value) {
5454 this.showNPfeatureTooltip = value;
5458 * Gets the value of the showDbRefTooltip property.
5461 * possible object is
5465 public Boolean isShowDbRefTooltip() {
5466 return showDbRefTooltip;
5470 * Sets the value of the showDbRefTooltip property.
5477 public void setShowDbRefTooltip(Boolean value) {
5478 this.showDbRefTooltip = value;
5482 * Gets the value of the followHighlight property.
5485 * possible object is
5489 public boolean isFollowHighlight() {
5490 if (followHighlight == null) {
5493 return followHighlight;
5498 * Sets the value of the followHighlight property.
5505 public void setFollowHighlight(Boolean value) {
5506 this.followHighlight = value;
5510 * Gets the value of the followSelection property.
5513 * possible object is
5517 public boolean isFollowSelection() {
5518 if (followSelection == null) {
5521 return followSelection;
5526 * Sets the value of the followSelection property.
5533 public void setFollowSelection(Boolean value) {
5534 this.followSelection = value;
5538 * Gets the value of the showAnnotation property.
5541 * possible object is
5545 public Boolean isShowAnnotation() {
5546 return showAnnotation;
5550 * Sets the value of the showAnnotation property.
5557 public void setShowAnnotation(Boolean value) {
5558 this.showAnnotation = value;
5562 * Gets the value of the centreColumnLabels property.
5565 * possible object is
5569 public boolean isCentreColumnLabels() {
5570 if (centreColumnLabels == null) {
5573 return centreColumnLabels;
5578 * Sets the value of the centreColumnLabels property.
5585 public void setCentreColumnLabels(Boolean value) {
5586 this.centreColumnLabels = value;
5590 * Gets the value of the showGroupConservation property.
5593 * possible object is
5597 public boolean isShowGroupConservation() {
5598 if (showGroupConservation == null) {
5601 return showGroupConservation;
5606 * Sets the value of the showGroupConservation property.
5613 public void setShowGroupConservation(Boolean value) {
5614 this.showGroupConservation = value;
5618 * Gets the value of the showGroupConsensus property.
5621 * possible object is
5625 public boolean isShowGroupConsensus() {
5626 if (showGroupConsensus == null) {
5629 return showGroupConsensus;
5634 * Sets the value of the showGroupConsensus property.
5641 public void setShowGroupConsensus(Boolean value) {
5642 this.showGroupConsensus = value;
5646 * Gets the value of the showConsensusHistogram property.
5649 * possible object is
5653 public boolean isShowConsensusHistogram() {
5654 if (showConsensusHistogram == null) {
5657 return showConsensusHistogram;
5662 * Sets the value of the showConsensusHistogram property.
5669 public void setShowConsensusHistogram(Boolean value) {
5670 this.showConsensusHistogram = value;
5674 * Gets the value of the showSequenceLogo property.
5677 * possible object is
5681 public boolean isShowSequenceLogo() {
5682 if (showSequenceLogo == null) {
5685 return showSequenceLogo;
5690 * Sets the value of the showSequenceLogo property.
5697 public void setShowSequenceLogo(Boolean value) {
5698 this.showSequenceLogo = value;
5702 * Gets the value of the normaliseSequenceLogo property.
5705 * possible object is
5709 public boolean isNormaliseSequenceLogo() {
5710 if (normaliseSequenceLogo == null) {
5713 return normaliseSequenceLogo;
5718 * Sets the value of the normaliseSequenceLogo property.
5725 public void setNormaliseSequenceLogo(Boolean value) {
5726 this.normaliseSequenceLogo = value;
5730 * Gets the value of the ignoreGapsinConsensus property.
5733 * possible object is
5737 public boolean isIgnoreGapsinConsensus() {
5738 if (ignoreGapsinConsensus == null) {
5741 return ignoreGapsinConsensus;
5746 * Sets the value of the ignoreGapsinConsensus property.
5753 public void setIgnoreGapsinConsensus(Boolean value) {
5754 this.ignoreGapsinConsensus = value;
5758 * Gets the value of the startRes property.
5761 * possible object is
5765 public Integer getStartRes() {
5770 * Sets the value of the startRes property.
5777 public void setStartRes(Integer value) {
5778 this.startRes = value;
5782 * Gets the value of the startSeq property.
5785 * possible object is
5789 public Integer getStartSeq() {
5794 * Sets the value of the startSeq property.
5801 public void setStartSeq(Integer value) {
5802 this.startSeq = value;
5806 * Gets the value of the fontName property.
5809 * possible object is
5813 public String getFontName() {
5818 * Sets the value of the fontName property.
5825 public void setFontName(String value) {
5826 this.fontName = value;
5830 * Gets the value of the fontSize property.
5833 * possible object is
5837 public Integer getFontSize() {
5842 * Sets the value of the fontSize property.
5849 public void setFontSize(Integer value) {
5850 this.fontSize = value;
5854 * Gets the value of the fontStyle property.
5857 * possible object is
5861 public Integer getFontStyle() {
5866 * Sets the value of the fontStyle property.
5873 public void setFontStyle(Integer value) {
5874 this.fontStyle = value;
5878 * Gets the value of the scaleProteinAsCdna property.
5881 * possible object is
5885 public boolean isScaleProteinAsCdna() {
5886 if (scaleProteinAsCdna == null) {
5889 return scaleProteinAsCdna;
5894 * Sets the value of the scaleProteinAsCdna property.
5901 public void setScaleProteinAsCdna(Boolean value) {
5902 this.scaleProteinAsCdna = value;
5906 * Gets the value of the viewName property.
5909 * possible object is
5913 public String getViewName() {
5918 * Sets the value of the viewName property.
5925 public void setViewName(String value) {
5926 this.viewName = value;
5930 * Gets the value of the sequenceSetId property.
5933 * possible object is
5937 public String getSequenceSetId() {
5938 return sequenceSetId;
5942 * Sets the value of the sequenceSetId property.
5949 public void setSequenceSetId(String value) {
5950 this.sequenceSetId = value;
5954 * Gets the value of the gatheredViews property.
5957 * possible object is
5961 public Boolean isGatheredViews() {
5962 return gatheredViews;
5966 * Sets the value of the gatheredViews property.
5973 public void setGatheredViews(Boolean value) {
5974 this.gatheredViews = value;
5978 * Gets the value of the textCol1 property.
5981 * possible object is
5985 public Integer getTextCol1() {
5990 * Sets the value of the textCol1 property.
5997 public void setTextCol1(Integer value) {
5998 this.textCol1 = value;
6002 * Gets the value of the textCol2 property.
6005 * possible object is
6009 public Integer getTextCol2() {
6014 * Sets the value of the textCol2 property.
6021 public void setTextCol2(Integer value) {
6022 this.textCol2 = value;
6026 * Gets the value of the textColThreshold property.
6029 * possible object is
6033 public Integer getTextColThreshold() {
6034 return textColThreshold;
6038 * Sets the value of the textColThreshold property.
6045 public void setTextColThreshold(Integer value) {
6046 this.textColThreshold = value;
6050 * Gets the value of the id property.
6053 * possible object is
6057 public String getId() {
6062 * Sets the value of the id property.
6069 public void setId(String value) {
6074 * Gets the value of the complementId property.
6077 * possible object is
6081 public String getComplementId() {
6082 return complementId;
6086 * Sets the value of the complementId property.
6093 public void setComplementId(String value) {
6094 this.complementId = value;
6098 * Gets the value of the showComplementFeatures property.
6101 * possible object is
6105 public boolean isShowComplementFeatures() {
6106 if (showComplementFeatures == null) {
6109 return showComplementFeatures;
6114 * Sets the value of the showComplementFeatures property.
6121 public void setShowComplementFeatures(Boolean value) {
6122 this.showComplementFeatures = value;
6126 * Gets the value of the showComplementFeaturesOnTop property.
6129 * possible object is
6133 public boolean isShowComplementFeaturesOnTop() {
6134 if (showComplementFeaturesOnTop == null) {
6137 return showComplementFeaturesOnTop;
6142 * Sets the value of the showComplementFeaturesOnTop property.
6149 public void setShowComplementFeaturesOnTop(Boolean value) {
6150 this.showComplementFeaturesOnTop = value;
6154 * Gets the value of the width property.
6157 * possible object is
6161 public Integer getWidth() {
6166 * Sets the value of the width property.
6173 public void setWidth(Integer value) {
6178 * Gets the value of the height property.
6181 * possible object is
6185 public Integer getHeight() {
6190 * Sets the value of the height property.
6197 public void setHeight(Integer value) {
6198 this.height = value;
6202 * Gets the value of the xpos property.
6205 * possible object is
6209 public Integer getXpos() {
6214 * Sets the value of the xpos property.
6221 public void setXpos(Integer value) {
6226 * Gets the value of the ypos property.
6229 * possible object is
6233 public Integer getYpos() {
6238 * Sets the value of the ypos property.
6245 public void setYpos(Integer value) {
6251 * <p>Java class for anonymous complex type.
6253 * <p>The following schema fragment specifies the expected content contained within this class.
6257 * <complexContent>
6258 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6259 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6260 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6261 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6263 * </complexContent>
6269 @XmlAccessorType(XmlAccessType.FIELD)
6271 public static class CalcIdParam
6272 extends WebServiceParameterSet
6275 @XmlAttribute(name = "calcId", required = true)
6276 protected String calcId;
6277 @XmlAttribute(name = "needsUpdate")
6278 protected Boolean needsUpdate;
6279 @XmlAttribute(name = "autoUpdate", required = true)
6280 protected boolean autoUpdate;
6283 * Gets the value of the calcId property.
6286 * possible object is
6290 public String getCalcId() {
6295 * Sets the value of the calcId property.
6302 public void setCalcId(String value) {
6303 this.calcId = value;
6307 * Gets the value of the needsUpdate property.
6310 * possible object is
6314 public boolean isNeedsUpdate() {
6315 if (needsUpdate == null) {
6323 * Sets the value of the needsUpdate property.
6330 public void setNeedsUpdate(Boolean value) {
6331 this.needsUpdate = value;
6335 * Gets the value of the autoUpdate property.
6338 public boolean isAutoUpdate() {
6343 * Sets the value of the autoUpdate property.
6346 public void setAutoUpdate(boolean value) {
6347 this.autoUpdate = value;
6354 * <p>Java class for anonymous complex type.
6356 * <p>The following schema fragment specifies the expected content contained within this class.
6360 * <complexContent>
6361 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6362 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6363 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6365 * </complexContent>
6371 @XmlAccessorType(XmlAccessType.FIELD)
6373 public static class HiddenColumns {
6375 @XmlAttribute(name = "start")
6376 protected Integer start;
6377 @XmlAttribute(name = "end")
6378 protected Integer end;
6381 * Gets the value of the start property.
6384 * possible object is
6388 public Integer getStart() {
6393 * Sets the value of the start property.
6400 public void setStart(Integer value) {
6405 * Gets the value of the end property.
6408 * possible object is
6412 public Integer getEnd() {
6417 * Sets the value of the end property.
6424 public void setEnd(Integer value) {
6432 * <p>Java class for anonymous complex type.
6434 * <p>The following schema fragment specifies the expected content contained within this class.
6438 * <complexContent>
6439 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6440 * <attGroup ref="{www.jalview.org}swingwindow"/>
6441 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6442 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6443 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6444 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6446 * </complexContent>
6452 @XmlAccessorType(XmlAccessType.FIELD)
6454 public static class Overview {
6456 @XmlAttribute(name = "showHidden")
6457 protected Boolean showHidden;
6458 @XmlAttribute(name = "residueColour")
6459 protected Integer residueColour;
6460 @XmlAttribute(name = "gapColour")
6461 protected Integer gapColour;
6462 @XmlAttribute(name = "hiddenColour")
6463 protected Integer hiddenColour;
6464 @XmlAttribute(name = "width")
6465 protected Integer width;
6466 @XmlAttribute(name = "height")
6467 protected Integer height;
6468 @XmlAttribute(name = "xpos")
6469 protected Integer xpos;
6470 @XmlAttribute(name = "ypos")
6471 protected Integer ypos;
6474 * Gets the value of the showHidden property.
6477 * possible object is
6481 public Boolean isShowHidden() {
6486 * Sets the value of the showHidden property.
6493 public void setShowHidden(Boolean value) {
6494 this.showHidden = value;
6498 * Gets the value of the residueColour property.
6501 * possible object is
6505 public Integer getResidueColour() {
6506 return residueColour;
6510 * Sets the value of the residueColour property.
6517 public void setResidueColour(Integer value) {
6518 this.residueColour = value;
6522 * Gets the value of the gapColour property.
6525 * possible object is
6529 public Integer getGapColour() {
6534 * Sets the value of the gapColour property.
6541 public void setGapColour(Integer value) {
6542 this.gapColour = value;
6546 * Gets the value of the hiddenColour property.
6549 * possible object is
6553 public Integer getHiddenColour() {
6554 return hiddenColour;
6558 * Sets the value of the hiddenColour property.
6565 public void setHiddenColour(Integer value) {
6566 this.hiddenColour = value;
6570 * Gets the value of the width property.
6573 * possible object is
6577 public Integer getWidth() {
6582 * Sets the value of the width property.
6589 public void setWidth(Integer value) {
6594 * Gets the value of the height property.
6597 * possible object is
6601 public Integer getHeight() {
6606 * Sets the value of the height property.
6613 public void setHeight(Integer value) {
6614 this.height = value;
6618 * Gets the value of the xpos property.
6621 * possible object is
6625 public Integer getXpos() {
6630 * Sets the value of the xpos property.
6637 public void setXpos(Integer value) {
6642 * Gets the value of the ypos property.
6645 * possible object is
6649 public Integer getYpos() {
6654 * Sets the value of the ypos property.
6661 public void setYpos(Integer value) {