2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
4 // Any modifications to this file will be lost upon recompilation of the source schema.
5 // Generated on: 2023.02.22 at 10:08:57 PM GMT
9 package jalview.xml.binding.jalview;
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
27 * <p>Java class for JalviewModel complex type.
29 * <p>The following schema fragment specifies the expected content contained within this class.
32 * <complexType name="JalviewModel">
34 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
36 * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
37 * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
38 * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
40 * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
43 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
45 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
46 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
49 * <extension base="{www.jalview.org}pdbentry">
51 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
54 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
55 * <attGroup ref="{www.jalview.org}swingwindow"/>
56 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
57 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
58 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
59 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
60 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
68 * </complexContent>
71 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
72 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
75 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
77 * <element name="secondaryStructure" maxOccurs="unbounded">
80 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
81 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
82 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
83 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
84 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
86 * </complexContent>
90 * <attGroup ref="{www.jalview.org}swingwindow"/>
91 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
92 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
93 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
94 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
96 * </complexContent>
100 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
101 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
102 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
104 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
105 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
107 * </complexContent>
110 * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
112 * <complexContent>
113 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
115 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
116 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
118 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
119 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
120 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
121 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
122 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
123 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
125 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
126 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
129 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
130 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
131 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
132 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
133 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
135 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
138 * </complexContent>
141 * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
143 * <complexContent>
144 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
146 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
149 * <complexContent>
150 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
151 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
154 * </complexContent>
157 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
159 * <complexContent>
160 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
161 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
162 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
163 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
165 * </complexContent>
168 * <element name="overview" minOccurs="0">
170 * <complexContent>
171 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
172 * <attGroup ref="{www.jalview.org}swingwindow"/>
173 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
174 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
175 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
176 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
177 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
179 * </complexContent>
183 * <attGroup ref="{www.jalview.org}swingwindow"/>
184 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
187 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
188 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
189 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
190 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
191 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
192 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
193 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
194 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
195 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
196 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
197 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
198 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
199 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
200 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
201 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
202 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
203 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
204 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
205 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
206 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
207 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
208 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
209 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
210 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
211 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
212 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
213 * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
214 * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
215 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
216 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
217 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
218 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
219 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
220 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
221 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
222 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
223 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
224 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
225 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
226 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
227 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
228 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
230 * </complexContent>
233 * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
235 * <complexContent>
236 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
238 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
240 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
242 * </complexContent>
245 * <element name="tree" maxOccurs="unbounded" minOccurs="0">
247 * <complexContent>
248 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
249 * <sequence minOccurs="0">
250 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
251 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
253 * <attGroup ref="{www.jalview.org}swingwindow"/>
254 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
255 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
256 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
257 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
258 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
259 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
260 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
261 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
262 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
263 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
264 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
266 * </complexContent>
269 * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
271 * <complexContent>
272 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
274 * <element name="sequencePoint" maxOccurs="unbounded">
276 * <complexContent>
277 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
278 * <attGroup ref="{www.jalview.org}position"/>
279 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
281 * </complexContent>
284 * <element name="axis" maxOccurs="3" minOccurs="3">
286 * <complexContent>
287 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
288 * <attGroup ref="{www.jalview.org}position"/>
290 * </complexContent>
293 * <element name="seqPointMin">
295 * <complexContent>
296 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
297 * <attGroup ref="{www.jalview.org}position"/>
299 * </complexContent>
302 * <element name="seqPointMax">
304 * <complexContent>
305 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
306 * <attGroup ref="{www.jalview.org}position"/>
308 * </complexContent>
311 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
313 * <attGroup ref="{www.jalview.org}swingwindow"/>
314 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
315 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
316 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
317 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
318 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
319 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
320 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
321 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
322 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
323 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
325 * </complexContent>
328 * <element name="FeatureSettings" minOccurs="0">
330 * <complexContent>
331 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
333 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
335 * <complexContent>
336 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
338 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
339 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
341 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
342 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
343 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
344 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
345 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
346 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
347 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
348 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
349 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
350 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
351 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
352 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
354 * </complexContent>
357 * <element name="group" maxOccurs="unbounded" minOccurs="0">
359 * <complexContent>
360 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
361 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
362 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
364 * </complexContent>
369 * </complexContent>
375 * </complexContent>
381 @XmlAccessorType(XmlAccessType.FIELD)
382 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
394 public class JalviewModel {
396 @XmlElement(required = true)
397 @XmlSchemaType(name = "dateTime")
398 protected XMLGregorianCalendar creationDate;
399 @XmlElement(required = true)
400 protected String version;
401 @XmlElement(required = true)
402 protected VAMSAS vamsasModel;
403 @XmlElement(name = "JSeq")
404 protected List<JalviewModel.JSeq> jSeq;
405 @XmlElement(name = "JGroup")
406 protected List<JalviewModel.JGroup> jGroup;
407 @XmlElement(name = "Viewport")
408 protected List<JalviewModel.Viewport> viewport;
409 @XmlElement(name = "UserColours")
410 protected List<JalviewModel.UserColours> userColours;
411 protected List<JalviewModel.Tree> tree;
412 @XmlElement(name = "PcaViewer")
413 protected List<JalviewModel.PcaViewer> pcaViewer;
414 @XmlElement(name = "FeatureSettings")
415 protected JalviewModel.FeatureSettings featureSettings;
418 * Gets the value of the creationDate property.
422 * {@link XMLGregorianCalendar }
425 public XMLGregorianCalendar getCreationDate() {
430 * Sets the value of the creationDate property.
434 * {@link XMLGregorianCalendar }
437 public void setCreationDate(XMLGregorianCalendar value) {
438 this.creationDate = value;
442 * Gets the value of the version property.
449 public String getVersion() {
454 * Sets the value of the version property.
461 public void setVersion(String value) {
462 this.version = value;
466 * Gets the value of the vamsasModel property.
473 public VAMSAS getVamsasModel() {
478 * Sets the value of the vamsasModel property.
485 public void setVamsasModel(VAMSAS value) {
486 this.vamsasModel = value;
490 * Gets the value of the jSeq property.
493 * This accessor method returns a reference to the live list,
494 * not a snapshot. Therefore any modification you make to the
495 * returned list will be present inside the JAXB object.
496 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
499 * For example, to add a new item, do as follows:
501 * getJSeq().add(newItem);
506 * Objects of the following type(s) are allowed in the list
507 * {@link JalviewModel.JSeq }
511 public List<JalviewModel.JSeq> getJSeq() {
513 jSeq = new ArrayList<JalviewModel.JSeq>();
519 * Gets the value of the jGroup property.
522 * This accessor method returns a reference to the live list,
523 * not a snapshot. Therefore any modification you make to the
524 * returned list will be present inside the JAXB object.
525 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
528 * For example, to add a new item, do as follows:
530 * getJGroup().add(newItem);
535 * Objects of the following type(s) are allowed in the list
536 * {@link JalviewModel.JGroup }
540 public List<JalviewModel.JGroup> getJGroup() {
541 if (jGroup == null) {
542 jGroup = new ArrayList<JalviewModel.JGroup>();
548 * Gets the value of the viewport property.
551 * This accessor method returns a reference to the live list,
552 * not a snapshot. Therefore any modification you make to the
553 * returned list will be present inside the JAXB object.
554 * This is why there is not a <CODE>set</CODE> method for the viewport property.
557 * For example, to add a new item, do as follows:
559 * getViewport().add(newItem);
564 * Objects of the following type(s) are allowed in the list
565 * {@link JalviewModel.Viewport }
569 public List<JalviewModel.Viewport> getViewport() {
570 if (viewport == null) {
571 viewport = new ArrayList<JalviewModel.Viewport>();
573 return this.viewport;
577 * Gets the value of the userColours property.
580 * This accessor method returns a reference to the live list,
581 * not a snapshot. Therefore any modification you make to the
582 * returned list will be present inside the JAXB object.
583 * This is why there is not a <CODE>set</CODE> method for the userColours property.
586 * For example, to add a new item, do as follows:
588 * getUserColours().add(newItem);
593 * Objects of the following type(s) are allowed in the list
594 * {@link JalviewModel.UserColours }
598 public List<JalviewModel.UserColours> getUserColours() {
599 if (userColours == null) {
600 userColours = new ArrayList<JalviewModel.UserColours>();
602 return this.userColours;
606 * Gets the value of the tree property.
609 * This accessor method returns a reference to the live list,
610 * not a snapshot. Therefore any modification you make to the
611 * returned list will be present inside the JAXB object.
612 * This is why there is not a <CODE>set</CODE> method for the tree property.
615 * For example, to add a new item, do as follows:
617 * getTree().add(newItem);
622 * Objects of the following type(s) are allowed in the list
623 * {@link JalviewModel.Tree }
627 public List<JalviewModel.Tree> getTree() {
629 tree = new ArrayList<JalviewModel.Tree>();
635 * Gets the value of the pcaViewer property.
638 * This accessor method returns a reference to the live list,
639 * not a snapshot. Therefore any modification you make to the
640 * returned list will be present inside the JAXB object.
641 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
644 * For example, to add a new item, do as follows:
646 * getPcaViewer().add(newItem);
651 * Objects of the following type(s) are allowed in the list
652 * {@link JalviewModel.PcaViewer }
656 public List<JalviewModel.PcaViewer> getPcaViewer() {
657 if (pcaViewer == null) {
658 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
660 return this.pcaViewer;
664 * Gets the value of the featureSettings property.
668 * {@link JalviewModel.FeatureSettings }
671 public JalviewModel.FeatureSettings getFeatureSettings() {
672 return featureSettings;
676 * Sets the value of the featureSettings property.
680 * {@link JalviewModel.FeatureSettings }
683 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
684 this.featureSettings = value;
689 * <p>Java class for anonymous complex type.
691 * <p>The following schema fragment specifies the expected content contained within this class.
695 * <complexContent>
696 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
698 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
700 * <complexContent>
701 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
703 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
704 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
706 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
707 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
708 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
709 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
710 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
711 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
712 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
713 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
714 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
715 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
716 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
717 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
719 * </complexContent>
722 * <element name="group" maxOccurs="unbounded" minOccurs="0">
724 * <complexContent>
725 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
726 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
727 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
729 * </complexContent>
734 * </complexContent>
740 @XmlAccessorType(XmlAccessType.FIELD)
741 @XmlType(name = "", propOrder = {
745 public static class FeatureSettings {
747 @XmlElement(namespace = "www.jalview.org")
748 protected List<JalviewModel.FeatureSettings.Setting> setting;
749 @XmlElement(namespace = "www.jalview.org")
750 protected List<JalviewModel.FeatureSettings.Group> group;
753 * Gets the value of the setting property.
756 * This accessor method returns a reference to the live list,
757 * not a snapshot. Therefore any modification you make to the
758 * returned list will be present inside the JAXB object.
759 * This is why there is not a <CODE>set</CODE> method for the setting property.
762 * For example, to add a new item, do as follows:
764 * getSetting().add(newItem);
769 * Objects of the following type(s) are allowed in the list
770 * {@link JalviewModel.FeatureSettings.Setting }
774 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
775 if (setting == null) {
776 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
782 * Gets the value of the group property.
785 * This accessor method returns a reference to the live list,
786 * not a snapshot. Therefore any modification you make to the
787 * returned list will be present inside the JAXB object.
788 * This is why there is not a <CODE>set</CODE> method for the group property.
791 * For example, to add a new item, do as follows:
793 * getGroup().add(newItem);
798 * Objects of the following type(s) are allowed in the list
799 * {@link JalviewModel.FeatureSettings.Group }
803 public List<JalviewModel.FeatureSettings.Group> getGroup() {
805 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
812 * <p>Java class for anonymous complex type.
814 * <p>The following schema fragment specifies the expected content contained within this class.
818 * <complexContent>
819 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
820 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
821 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
823 * </complexContent>
829 @XmlAccessorType(XmlAccessType.FIELD)
831 public static class Group {
833 @XmlAttribute(name = "name", required = true)
834 protected String name;
835 @XmlAttribute(name = "display", required = true)
836 protected boolean display;
839 * Gets the value of the name property.
846 public String getName() {
851 * Sets the value of the name property.
858 public void setName(String value) {
863 * Gets the value of the display property.
866 public boolean isDisplay() {
871 * Sets the value of the display property.
874 public void setDisplay(boolean value) {
875 this.display = value;
882 * <p>Java class for anonymous complex type.
884 * <p>The following schema fragment specifies the expected content contained within this class.
888 * <complexContent>
889 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
891 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
892 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
894 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
895 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
896 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
897 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
898 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
899 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
900 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
901 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
902 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
903 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
904 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
905 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
907 * </complexContent>
913 @XmlAccessorType(XmlAccessType.FIELD)
914 @XmlType(name = "", propOrder = {
918 public static class Setting {
920 @XmlElement(namespace = "www.jalview.org")
921 protected List<String> attributeName;
922 @XmlElement(namespace = "www.jalview.org")
923 protected FeatureMatcherSet matcherSet;
924 @XmlAttribute(name = "type", required = true)
925 protected String type;
926 @XmlAttribute(name = "colour", required = true)
927 protected int colour;
928 @XmlAttribute(name = "display", required = true)
929 protected boolean display;
930 @XmlAttribute(name = "order")
931 protected Float order;
932 @XmlAttribute(name = "mincolour")
933 protected Integer mincolour;
934 @XmlAttribute(name = "noValueColour")
935 protected NoValueColour noValueColour;
936 @XmlAttribute(name = "threshold")
937 protected Float threshold;
938 @XmlAttribute(name = "threshstate")
939 protected Integer threshstate;
940 @XmlAttribute(name = "max")
942 @XmlAttribute(name = "min")
944 @XmlAttribute(name = "colourByLabel")
945 protected Boolean colourByLabel;
946 @XmlAttribute(name = "autoScale")
947 protected Boolean autoScale;
950 * Gets the value of the attributeName property.
953 * This accessor method returns a reference to the live list,
954 * not a snapshot. Therefore any modification you make to the
955 * returned list will be present inside the JAXB object.
956 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
959 * For example, to add a new item, do as follows:
961 * getAttributeName().add(newItem);
966 * Objects of the following type(s) are allowed in the list
971 public List<String> getAttributeName() {
972 if (attributeName == null) {
973 attributeName = new ArrayList<String>();
975 return this.attributeName;
979 * Gets the value of the matcherSet property.
983 * {@link FeatureMatcherSet }
986 public FeatureMatcherSet getMatcherSet() {
991 * Sets the value of the matcherSet property.
995 * {@link FeatureMatcherSet }
998 public void setMatcherSet(FeatureMatcherSet value) {
999 this.matcherSet = value;
1003 * Gets the value of the type property.
1006 * possible object is
1010 public String getType() {
1015 * Sets the value of the type property.
1022 public void setType(String value) {
1027 * Gets the value of the colour property.
1030 public int getColour() {
1035 * Sets the value of the colour property.
1038 public void setColour(int value) {
1039 this.colour = value;
1043 * Gets the value of the display property.
1046 public boolean isDisplay() {
1051 * Sets the value of the display property.
1054 public void setDisplay(boolean value) {
1055 this.display = value;
1059 * Gets the value of the order property.
1062 * possible object is
1066 public Float getOrder() {
1071 * Sets the value of the order property.
1078 public void setOrder(Float value) {
1083 * Gets the value of the mincolour property.
1086 * possible object is
1090 public Integer getMincolour() {
1095 * Sets the value of the mincolour property.
1102 public void setMincolour(Integer value) {
1103 this.mincolour = value;
1107 * Gets the value of the noValueColour property.
1110 * possible object is
1111 * {@link NoValueColour }
1114 public NoValueColour getNoValueColour() {
1115 if (noValueColour == null) {
1116 return NoValueColour.MIN;
1118 return noValueColour;
1123 * Sets the value of the noValueColour property.
1127 * {@link NoValueColour }
1130 public void setNoValueColour(NoValueColour value) {
1131 this.noValueColour = value;
1135 * Gets the value of the threshold property.
1138 * possible object is
1142 public Float getThreshold() {
1147 * Sets the value of the threshold property.
1154 public void setThreshold(Float value) {
1155 this.threshold = value;
1159 * Gets the value of the threshstate property.
1162 * possible object is
1166 public Integer getThreshstate() {
1171 * Sets the value of the threshstate property.
1178 public void setThreshstate(Integer value) {
1179 this.threshstate = value;
1183 * Gets the value of the max property.
1186 * possible object is
1190 public Float getMax() {
1195 * Sets the value of the max property.
1202 public void setMax(Float value) {
1207 * Gets the value of the min property.
1210 * possible object is
1214 public Float getMin() {
1219 * Sets the value of the min property.
1226 public void setMin(Float value) {
1231 * Gets the value of the colourByLabel property.
1234 * possible object is
1238 public Boolean isColourByLabel() {
1239 return colourByLabel;
1243 * Sets the value of the colourByLabel property.
1250 public void setColourByLabel(Boolean value) {
1251 this.colourByLabel = value;
1255 * Gets the value of the autoScale property.
1258 * possible object is
1262 public Boolean isAutoScale() {
1267 * Sets the value of the autoScale property.
1274 public void setAutoScale(Boolean value) {
1275 this.autoScale = value;
1284 * <p>Java class for anonymous complex type.
1286 * <p>The following schema fragment specifies the expected content contained within this class.
1290 * <complexContent>
1291 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1293 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1294 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1296 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1297 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1298 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1299 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1300 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1301 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1302 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1303 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1304 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1305 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1306 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1307 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1308 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1309 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1310 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1311 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1312 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1313 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1314 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1316 * </complexContent>
1322 @XmlAccessorType(XmlAccessType.FIELD)
1323 @XmlType(name = "", propOrder = {
1327 public static class JGroup {
1329 @XmlElement(namespace = "www.jalview.org", required = true)
1330 protected List<String> seq;
1331 @XmlElement(namespace = "www.jalview.org")
1332 protected AnnotationColourScheme annotationColours;
1333 @XmlAttribute(name = "start")
1334 protected Integer start;
1335 @XmlAttribute(name = "end")
1336 protected Integer end;
1337 @XmlAttribute(name = "name")
1338 protected String name;
1339 @XmlAttribute(name = "colour")
1340 protected String colour;
1341 @XmlAttribute(name = "consThreshold")
1342 protected Integer consThreshold;
1343 @XmlAttribute(name = "pidThreshold")
1344 protected Integer pidThreshold;
1345 @XmlAttribute(name = "outlineColour")
1346 protected Integer outlineColour;
1347 @XmlAttribute(name = "displayBoxes")
1348 protected Boolean displayBoxes;
1349 @XmlAttribute(name = "displayText")
1350 protected Boolean displayText;
1351 @XmlAttribute(name = "colourText")
1352 protected Boolean colourText;
1353 @XmlAttribute(name = "textCol1")
1354 protected Integer textCol1;
1355 @XmlAttribute(name = "textCol2")
1356 protected Integer textCol2;
1357 @XmlAttribute(name = "textColThreshold")
1358 protected Integer textColThreshold;
1359 @XmlAttribute(name = "showUnconserved")
1360 protected Boolean showUnconserved;
1361 @XmlAttribute(name = "ignoreGapsinConsensus")
1362 protected Boolean ignoreGapsinConsensus;
1363 @XmlAttribute(name = "showConsensusHistogram")
1364 protected Boolean showConsensusHistogram;
1365 @XmlAttribute(name = "showSequenceLogo")
1366 protected Boolean showSequenceLogo;
1367 @XmlAttribute(name = "normaliseSequenceLogo")
1368 protected Boolean normaliseSequenceLogo;
1369 @XmlAttribute(name = "id")
1370 protected String id;
1373 * Gets the value of the seq property.
1376 * This accessor method returns a reference to the live list,
1377 * not a snapshot. Therefore any modification you make to the
1378 * returned list will be present inside the JAXB object.
1379 * This is why there is not a <CODE>set</CODE> method for the seq property.
1382 * For example, to add a new item, do as follows:
1384 * getSeq().add(newItem);
1389 * Objects of the following type(s) are allowed in the list
1394 public List<String> getSeq() {
1396 seq = new ArrayList<String>();
1402 * Gets the value of the annotationColours property.
1405 * possible object is
1406 * {@link AnnotationColourScheme }
1409 public AnnotationColourScheme getAnnotationColours() {
1410 return annotationColours;
1414 * Sets the value of the annotationColours property.
1418 * {@link AnnotationColourScheme }
1421 public void setAnnotationColours(AnnotationColourScheme value) {
1422 this.annotationColours = value;
1426 * Gets the value of the start property.
1429 * possible object is
1433 public Integer getStart() {
1438 * Sets the value of the start property.
1445 public void setStart(Integer value) {
1450 * Gets the value of the end property.
1453 * possible object is
1457 public Integer getEnd() {
1462 * Sets the value of the end property.
1469 public void setEnd(Integer value) {
1474 * Gets the value of the name property.
1477 * possible object is
1481 public String getName() {
1486 * Sets the value of the name property.
1493 public void setName(String value) {
1498 * Gets the value of the colour property.
1501 * possible object is
1505 public String getColour() {
1510 * Sets the value of the colour property.
1517 public void setColour(String value) {
1518 this.colour = value;
1522 * Gets the value of the consThreshold property.
1525 * possible object is
1529 public Integer getConsThreshold() {
1530 return consThreshold;
1534 * Sets the value of the consThreshold property.
1541 public void setConsThreshold(Integer value) {
1542 this.consThreshold = value;
1546 * Gets the value of the pidThreshold property.
1549 * possible object is
1553 public Integer getPidThreshold() {
1554 return pidThreshold;
1558 * Sets the value of the pidThreshold property.
1565 public void setPidThreshold(Integer value) {
1566 this.pidThreshold = value;
1570 * Gets the value of the outlineColour property.
1573 * possible object is
1577 public Integer getOutlineColour() {
1578 return outlineColour;
1582 * Sets the value of the outlineColour property.
1589 public void setOutlineColour(Integer value) {
1590 this.outlineColour = value;
1594 * Gets the value of the displayBoxes property.
1597 * possible object is
1601 public Boolean isDisplayBoxes() {
1602 return displayBoxes;
1606 * Sets the value of the displayBoxes property.
1613 public void setDisplayBoxes(Boolean value) {
1614 this.displayBoxes = value;
1618 * Gets the value of the displayText property.
1621 * possible object is
1625 public Boolean isDisplayText() {
1630 * Sets the value of the displayText property.
1637 public void setDisplayText(Boolean value) {
1638 this.displayText = value;
1642 * Gets the value of the colourText property.
1645 * possible object is
1649 public Boolean isColourText() {
1654 * Sets the value of the colourText property.
1661 public void setColourText(Boolean value) {
1662 this.colourText = value;
1666 * Gets the value of the textCol1 property.
1669 * possible object is
1673 public Integer getTextCol1() {
1678 * Sets the value of the textCol1 property.
1685 public void setTextCol1(Integer value) {
1686 this.textCol1 = value;
1690 * Gets the value of the textCol2 property.
1693 * possible object is
1697 public Integer getTextCol2() {
1702 * Sets the value of the textCol2 property.
1709 public void setTextCol2(Integer value) {
1710 this.textCol2 = value;
1714 * Gets the value of the textColThreshold property.
1717 * possible object is
1721 public Integer getTextColThreshold() {
1722 return textColThreshold;
1726 * Sets the value of the textColThreshold property.
1733 public void setTextColThreshold(Integer value) {
1734 this.textColThreshold = value;
1738 * Gets the value of the showUnconserved property.
1741 * possible object is
1745 public Boolean isShowUnconserved() {
1746 return showUnconserved;
1750 * Sets the value of the showUnconserved property.
1757 public void setShowUnconserved(Boolean value) {
1758 this.showUnconserved = value;
1762 * Gets the value of the ignoreGapsinConsensus property.
1765 * possible object is
1769 public boolean isIgnoreGapsinConsensus() {
1770 if (ignoreGapsinConsensus == null) {
1773 return ignoreGapsinConsensus;
1778 * Sets the value of the ignoreGapsinConsensus property.
1785 public void setIgnoreGapsinConsensus(Boolean value) {
1786 this.ignoreGapsinConsensus = value;
1790 * Gets the value of the showConsensusHistogram property.
1793 * possible object is
1797 public boolean isShowConsensusHistogram() {
1798 if (showConsensusHistogram == null) {
1801 return showConsensusHistogram;
1806 * Sets the value of the showConsensusHistogram property.
1813 public void setShowConsensusHistogram(Boolean value) {
1814 this.showConsensusHistogram = value;
1818 * Gets the value of the showSequenceLogo property.
1821 * possible object is
1825 public boolean isShowSequenceLogo() {
1826 if (showSequenceLogo == null) {
1829 return showSequenceLogo;
1834 * Sets the value of the showSequenceLogo property.
1841 public void setShowSequenceLogo(Boolean value) {
1842 this.showSequenceLogo = value;
1846 * Gets the value of the normaliseSequenceLogo property.
1849 * possible object is
1853 public boolean isNormaliseSequenceLogo() {
1854 if (normaliseSequenceLogo == null) {
1857 return normaliseSequenceLogo;
1862 * Sets the value of the normaliseSequenceLogo property.
1869 public void setNormaliseSequenceLogo(Boolean value) {
1870 this.normaliseSequenceLogo = value;
1874 * Gets the value of the id property.
1877 * possible object is
1881 public String getId() {
1886 * Sets the value of the id property.
1893 public void setId(String value) {
1901 * <p>Java class for anonymous complex type.
1903 * <p>The following schema fragment specifies the expected content contained within this class.
1907 * <complexContent>
1908 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1910 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1911 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1913 * <complexContent>
1914 * <extension base="{www.jalview.org}pdbentry">
1916 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1918 * <simpleContent>
1919 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1920 * <attGroup ref="{www.jalview.org}swingwindow"/>
1921 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1922 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1923 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1924 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1925 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1926 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1928 * </simpleContent>
1933 * </complexContent>
1936 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1937 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1939 * <complexContent>
1940 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1942 * <element name="secondaryStructure" maxOccurs="unbounded">
1944 * <complexContent>
1945 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1946 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1947 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1948 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1949 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1951 * </complexContent>
1955 * <attGroup ref="{www.jalview.org}swingwindow"/>
1956 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1957 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1958 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1959 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1961 * </complexContent>
1965 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1966 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1967 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1968 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1969 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1970 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1972 * </complexContent>
1978 @XmlAccessorType(XmlAccessType.FIELD)
1979 @XmlType(name = "", propOrder = {
1985 public static class JSeq {
1987 @XmlElement(namespace = "www.jalview.org")
1988 protected List<Feature> features;
1989 @XmlElement(namespace = "www.jalview.org")
1990 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1991 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1992 protected List<Integer> hiddenSequences;
1993 @XmlElement(namespace = "www.jalview.org")
1994 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1995 @XmlAttribute(name = "colour")
1996 protected Integer colour;
1997 @XmlAttribute(name = "start", required = true)
1998 protected int start;
1999 @XmlAttribute(name = "end", required = true)
2001 @XmlAttribute(name = "id", required = true)
2002 protected String id;
2003 @XmlAttribute(name = "hidden")
2004 protected Boolean hidden;
2005 @XmlAttribute(name = "viewreference")
2006 protected Boolean viewreference;
2009 * Gets the value of the features property.
2012 * This accessor method returns a reference to the live list,
2013 * not a snapshot. Therefore any modification you make to the
2014 * returned list will be present inside the JAXB object.
2015 * This is why there is not a <CODE>set</CODE> method for the features property.
2018 * For example, to add a new item, do as follows:
2020 * getFeatures().add(newItem);
2025 * Objects of the following type(s) are allowed in the list
2030 public List<Feature> getFeatures() {
2031 if (features == null) {
2032 features = new ArrayList<Feature>();
2034 return this.features;
2038 * Gets the value of the pdbids property.
2041 * This accessor method returns a reference to the live list,
2042 * not a snapshot. Therefore any modification you make to the
2043 * returned list will be present inside the JAXB object.
2044 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2047 * For example, to add a new item, do as follows:
2049 * getPdbids().add(newItem);
2054 * Objects of the following type(s) are allowed in the list
2055 * {@link JalviewModel.JSeq.Pdbids }
2059 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2060 if (pdbids == null) {
2061 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2067 * Gets the value of the hiddenSequences property.
2070 * This accessor method returns a reference to the live list,
2071 * not a snapshot. Therefore any modification you make to the
2072 * returned list will be present inside the JAXB object.
2073 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2076 * For example, to add a new item, do as follows:
2078 * getHiddenSequences().add(newItem);
2083 * Objects of the following type(s) are allowed in the list
2088 public List<Integer> getHiddenSequences() {
2089 if (hiddenSequences == null) {
2090 hiddenSequences = new ArrayList<Integer>();
2092 return this.hiddenSequences;
2096 * Gets the value of the rnaViewer property.
2099 * This accessor method returns a reference to the live list,
2100 * not a snapshot. Therefore any modification you make to the
2101 * returned list will be present inside the JAXB object.
2102 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2105 * For example, to add a new item, do as follows:
2107 * getRnaViewer().add(newItem);
2112 * Objects of the following type(s) are allowed in the list
2113 * {@link JalviewModel.JSeq.RnaViewer }
2117 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2118 if (rnaViewer == null) {
2119 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2121 return this.rnaViewer;
2125 * Gets the value of the colour property.
2128 * possible object is
2132 public Integer getColour() {
2137 * Sets the value of the colour property.
2144 public void setColour(Integer value) {
2145 this.colour = value;
2149 * Gets the value of the start property.
2152 public int getStart() {
2157 * Sets the value of the start property.
2160 public void setStart(int value) {
2165 * Gets the value of the end property.
2168 public int getEnd() {
2173 * Sets the value of the end property.
2176 public void setEnd(int value) {
2181 * Gets the value of the id property.
2184 * possible object is
2188 public String getId() {
2193 * Sets the value of the id property.
2200 public void setId(String value) {
2205 * Gets the value of the hidden property.
2208 * possible object is
2212 public Boolean isHidden() {
2217 * Sets the value of the hidden property.
2224 public void setHidden(Boolean value) {
2225 this.hidden = value;
2229 * Gets the value of the viewreference property.
2232 * possible object is
2236 public Boolean isViewreference() {
2237 return viewreference;
2241 * Sets the value of the viewreference property.
2248 public void setViewreference(Boolean value) {
2249 this.viewreference = value;
2254 * <p>Java class for anonymous complex type.
2256 * <p>The following schema fragment specifies the expected content contained within this class.
2260 * <complexContent>
2261 * <extension base="{www.jalview.org}pdbentry">
2263 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2265 * <simpleContent>
2266 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2267 * <attGroup ref="{www.jalview.org}swingwindow"/>
2268 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2269 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2270 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2271 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2272 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2273 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2275 * </simpleContent>
2280 * </complexContent>
2286 @XmlAccessorType(XmlAccessType.FIELD)
2287 @XmlType(name = "", propOrder = {
2290 public static class Pdbids
2294 @XmlElement(namespace = "www.jalview.org")
2295 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2298 * Gets the value of the structureState property.
2301 * This accessor method returns a reference to the live list,
2302 * not a snapshot. Therefore any modification you make to the
2303 * returned list will be present inside the JAXB object.
2304 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2307 * For example, to add a new item, do as follows:
2309 * getStructureState().add(newItem);
2314 * Objects of the following type(s) are allowed in the list
2315 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2319 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2320 if (structureState == null) {
2321 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2323 return this.structureState;
2328 * <p>Java class for anonymous complex type.
2330 * <p>The following schema fragment specifies the expected content contained within this class.
2334 * <simpleContent>
2335 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2336 * <attGroup ref="{www.jalview.org}swingwindow"/>
2337 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2338 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2339 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2340 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2341 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2342 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2344 * </simpleContent>
2350 @XmlAccessorType(XmlAccessType.FIELD)
2351 @XmlType(name = "", propOrder = {
2354 public static class StructureState {
2357 protected String value;
2358 @XmlAttribute(name = "visible")
2359 protected Boolean visible;
2360 @XmlAttribute(name = "viewId")
2361 protected String viewId;
2362 @XmlAttribute(name = "alignwithAlignPanel")
2363 protected Boolean alignwithAlignPanel;
2364 @XmlAttribute(name = "colourwithAlignPanel")
2365 protected Boolean colourwithAlignPanel;
2366 @XmlAttribute(name = "colourByJmol")
2367 protected Boolean colourByJmol;
2368 @XmlAttribute(name = "type")
2369 protected String type;
2370 @XmlAttribute(name = "width")
2371 protected Integer width;
2372 @XmlAttribute(name = "height")
2373 protected Integer height;
2374 @XmlAttribute(name = "xpos")
2375 protected Integer xpos;
2376 @XmlAttribute(name = "ypos")
2377 protected Integer ypos;
2380 * Gets the value of the value property.
2383 * possible object is
2387 public String getValue() {
2392 * Sets the value of the value property.
2399 public void setValue(String value) {
2404 * Gets the value of the visible property.
2407 * possible object is
2411 public Boolean isVisible() {
2416 * Sets the value of the visible property.
2423 public void setVisible(Boolean value) {
2424 this.visible = value;
2428 * Gets the value of the viewId property.
2431 * possible object is
2435 public String getViewId() {
2440 * Sets the value of the viewId property.
2447 public void setViewId(String value) {
2448 this.viewId = value;
2452 * Gets the value of the alignwithAlignPanel property.
2455 * possible object is
2459 public boolean isAlignwithAlignPanel() {
2460 if (alignwithAlignPanel == null) {
2463 return alignwithAlignPanel;
2468 * Sets the value of the alignwithAlignPanel property.
2475 public void setAlignwithAlignPanel(Boolean value) {
2476 this.alignwithAlignPanel = value;
2480 * Gets the value of the colourwithAlignPanel property.
2483 * possible object is
2487 public boolean isColourwithAlignPanel() {
2488 if (colourwithAlignPanel == null) {
2491 return colourwithAlignPanel;
2496 * Sets the value of the colourwithAlignPanel property.
2503 public void setColourwithAlignPanel(Boolean value) {
2504 this.colourwithAlignPanel = value;
2508 * Gets the value of the colourByJmol property.
2511 * possible object is
2515 public boolean isColourByJmol() {
2516 if (colourByJmol == null) {
2519 return colourByJmol;
2524 * Sets the value of the colourByJmol property.
2531 public void setColourByJmol(Boolean value) {
2532 this.colourByJmol = value;
2536 * Gets the value of the type property.
2539 * possible object is
2543 public String getType() {
2548 * Sets the value of the type property.
2555 public void setType(String value) {
2560 * Gets the value of the width property.
2563 * possible object is
2567 public Integer getWidth() {
2572 * Sets the value of the width property.
2579 public void setWidth(Integer value) {
2584 * Gets the value of the height property.
2587 * possible object is
2591 public Integer getHeight() {
2596 * Sets the value of the height property.
2603 public void setHeight(Integer value) {
2604 this.height = value;
2608 * Gets the value of the xpos property.
2611 * possible object is
2615 public Integer getXpos() {
2620 * Sets the value of the xpos property.
2627 public void setXpos(Integer value) {
2632 * Gets the value of the ypos property.
2635 * possible object is
2639 public Integer getYpos() {
2644 * Sets the value of the ypos property.
2651 public void setYpos(Integer value) {
2661 * <p>Java class for anonymous complex type.
2663 * <p>The following schema fragment specifies the expected content contained within this class.
2667 * <complexContent>
2668 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2670 * <element name="secondaryStructure" maxOccurs="unbounded">
2672 * <complexContent>
2673 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2674 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2675 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2676 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2677 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2679 * </complexContent>
2683 * <attGroup ref="{www.jalview.org}swingwindow"/>
2684 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2685 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2686 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2687 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2689 * </complexContent>
2695 @XmlAccessorType(XmlAccessType.FIELD)
2696 @XmlType(name = "", propOrder = {
2697 "secondaryStructure"
2699 public static class RnaViewer {
2701 @XmlElement(namespace = "www.jalview.org", required = true)
2702 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2703 @XmlAttribute(name = "title")
2704 protected String title;
2705 @XmlAttribute(name = "viewId")
2706 protected String viewId;
2707 @XmlAttribute(name = "dividerLocation")
2708 protected Integer dividerLocation;
2709 @XmlAttribute(name = "selectedRna")
2710 protected Integer selectedRna;
2711 @XmlAttribute(name = "width")
2712 protected Integer width;
2713 @XmlAttribute(name = "height")
2714 protected Integer height;
2715 @XmlAttribute(name = "xpos")
2716 protected Integer xpos;
2717 @XmlAttribute(name = "ypos")
2718 protected Integer ypos;
2721 * Gets the value of the secondaryStructure property.
2724 * This accessor method returns a reference to the live list,
2725 * not a snapshot. Therefore any modification you make to the
2726 * returned list will be present inside the JAXB object.
2727 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2730 * For example, to add a new item, do as follows:
2732 * getSecondaryStructure().add(newItem);
2737 * Objects of the following type(s) are allowed in the list
2738 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2742 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2743 if (secondaryStructure == null) {
2744 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2746 return this.secondaryStructure;
2750 * Gets the value of the title property.
2753 * possible object is
2757 public String getTitle() {
2762 * Sets the value of the title property.
2769 public void setTitle(String value) {
2774 * Gets the value of the viewId property.
2777 * possible object is
2781 public String getViewId() {
2786 * Sets the value of the viewId property.
2793 public void setViewId(String value) {
2794 this.viewId = value;
2798 * Gets the value of the dividerLocation property.
2801 * possible object is
2805 public Integer getDividerLocation() {
2806 return dividerLocation;
2810 * Sets the value of the dividerLocation property.
2817 public void setDividerLocation(Integer value) {
2818 this.dividerLocation = value;
2822 * Gets the value of the selectedRna property.
2825 * possible object is
2829 public Integer getSelectedRna() {
2834 * Sets the value of the selectedRna property.
2841 public void setSelectedRna(Integer value) {
2842 this.selectedRna = value;
2846 * Gets the value of the width property.
2849 * possible object is
2853 public Integer getWidth() {
2858 * Sets the value of the width property.
2865 public void setWidth(Integer value) {
2870 * Gets the value of the height property.
2873 * possible object is
2877 public Integer getHeight() {
2882 * Sets the value of the height property.
2889 public void setHeight(Integer value) {
2890 this.height = value;
2894 * Gets the value of the xpos property.
2897 * possible object is
2901 public Integer getXpos() {
2906 * Sets the value of the xpos property.
2913 public void setXpos(Integer value) {
2918 * Gets the value of the ypos property.
2921 * possible object is
2925 public Integer getYpos() {
2930 * Sets the value of the ypos property.
2937 public void setYpos(Integer value) {
2943 * <p>Java class for anonymous complex type.
2945 * <p>The following schema fragment specifies the expected content contained within this class.
2949 * <complexContent>
2950 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2951 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2952 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2953 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2954 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2956 * </complexContent>
2962 @XmlAccessorType(XmlAccessType.FIELD)
2964 public static class SecondaryStructure {
2966 @XmlAttribute(name = "title")
2967 protected String title;
2968 @XmlAttribute(name = "annotationId", required = true)
2969 protected String annotationId;
2970 @XmlAttribute(name = "gapped")
2971 protected Boolean gapped;
2972 @XmlAttribute(name = "viewerState")
2973 protected String viewerState;
2976 * Gets the value of the title property.
2979 * possible object is
2983 public String getTitle() {
2988 * Sets the value of the title property.
2995 public void setTitle(String value) {
3000 * Gets the value of the annotationId property.
3003 * possible object is
3007 public String getAnnotationId() {
3008 return annotationId;
3012 * Sets the value of the annotationId property.
3019 public void setAnnotationId(String value) {
3020 this.annotationId = value;
3024 * Gets the value of the gapped property.
3027 * possible object is
3031 public Boolean isGapped() {
3036 * Sets the value of the gapped property.
3043 public void setGapped(Boolean value) {
3044 this.gapped = value;
3048 * Gets the value of the viewerState property.
3051 * possible object is
3055 public String getViewerState() {
3060 * Sets the value of the viewerState property.
3067 public void setViewerState(String value) {
3068 this.viewerState = value;
3079 * <p>Java class for anonymous complex type.
3081 * <p>The following schema fragment specifies the expected content contained within this class.
3085 * <complexContent>
3086 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3088 * <element name="sequencePoint" maxOccurs="unbounded">
3090 * <complexContent>
3091 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3092 * <attGroup ref="{www.jalview.org}position"/>
3093 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3095 * </complexContent>
3098 * <element name="axis" maxOccurs="3" minOccurs="3">
3100 * <complexContent>
3101 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3102 * <attGroup ref="{www.jalview.org}position"/>
3104 * </complexContent>
3107 * <element name="seqPointMin">
3109 * <complexContent>
3110 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3111 * <attGroup ref="{www.jalview.org}position"/>
3113 * </complexContent>
3116 * <element name="seqPointMax">
3118 * <complexContent>
3119 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3120 * <attGroup ref="{www.jalview.org}position"/>
3122 * </complexContent>
3125 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3127 * <attGroup ref="{www.jalview.org}swingwindow"/>
3128 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
3129 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3130 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3131 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3132 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3133 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3134 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3135 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3136 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3137 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3139 * </complexContent>
3145 @XmlAccessorType(XmlAccessType.FIELD)
3146 @XmlType(name = "", propOrder = {
3153 public static class PcaViewer {
3155 @XmlElement(namespace = "www.jalview.org", required = true)
3156 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3157 @XmlElement(namespace = "www.jalview.org", required = true)
3158 protected List<JalviewModel.PcaViewer.Axis> axis;
3159 @XmlElement(namespace = "www.jalview.org", required = true)
3160 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3161 @XmlElement(namespace = "www.jalview.org", required = true)
3162 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3163 @XmlElement(namespace = "www.jalview.org", required = true)
3164 protected PcaDataType pcaData;
3165 @XmlAttribute(name = "title")
3166 protected String title;
3167 @XmlAttribute(name = "scoreModelName")
3168 protected String scoreModelName;
3169 @XmlAttribute(name = "xDim")
3170 protected Integer xDim;
3171 @XmlAttribute(name = "yDim")
3172 protected Integer yDim;
3173 @XmlAttribute(name = "zDim")
3174 protected Integer zDim;
3175 @XmlAttribute(name = "bgColour")
3176 protected Integer bgColour;
3177 @XmlAttribute(name = "scaleFactor")
3178 protected Float scaleFactor;
3179 @XmlAttribute(name = "showLabels")
3180 protected Boolean showLabels;
3181 @XmlAttribute(name = "linkToAllViews")
3182 protected Boolean linkToAllViews;
3183 @XmlAttribute(name = "width")
3184 protected Integer width;
3185 @XmlAttribute(name = "height")
3186 protected Integer height;
3187 @XmlAttribute(name = "xpos")
3188 protected Integer xpos;
3189 @XmlAttribute(name = "ypos")
3190 protected Integer ypos;
3191 @XmlAttribute(name = "includeGaps")
3192 protected Boolean includeGaps;
3193 @XmlAttribute(name = "matchGaps")
3194 protected Boolean matchGaps;
3195 @XmlAttribute(name = "includeGappedColumns")
3196 protected Boolean includeGappedColumns;
3197 @XmlAttribute(name = "denominateByShortestLength")
3198 protected Boolean denominateByShortestLength;
3201 * Gets the value of the sequencePoint property.
3204 * This accessor method returns a reference to the live list,
3205 * not a snapshot. Therefore any modification you make to the
3206 * returned list will be present inside the JAXB object.
3207 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3210 * For example, to add a new item, do as follows:
3212 * getSequencePoint().add(newItem);
3217 * Objects of the following type(s) are allowed in the list
3218 * {@link JalviewModel.PcaViewer.SequencePoint }
3222 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3223 if (sequencePoint == null) {
3224 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3226 return this.sequencePoint;
3230 * Gets the value of the axis property.
3233 * This accessor method returns a reference to the live list,
3234 * not a snapshot. Therefore any modification you make to the
3235 * returned list will be present inside the JAXB object.
3236 * This is why there is not a <CODE>set</CODE> method for the axis property.
3239 * For example, to add a new item, do as follows:
3241 * getAxis().add(newItem);
3246 * Objects of the following type(s) are allowed in the list
3247 * {@link JalviewModel.PcaViewer.Axis }
3251 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3253 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3259 * Gets the value of the seqPointMin property.
3262 * possible object is
3263 * {@link JalviewModel.PcaViewer.SeqPointMin }
3266 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3271 * Sets the value of the seqPointMin property.
3275 * {@link JalviewModel.PcaViewer.SeqPointMin }
3278 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3279 this.seqPointMin = value;
3283 * Gets the value of the seqPointMax property.
3286 * possible object is
3287 * {@link JalviewModel.PcaViewer.SeqPointMax }
3290 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3295 * Sets the value of the seqPointMax property.
3299 * {@link JalviewModel.PcaViewer.SeqPointMax }
3302 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3303 this.seqPointMax = value;
3307 * Gets the value of the pcaData property.
3310 * possible object is
3311 * {@link PcaDataType }
3314 public PcaDataType getPcaData() {
3319 * Sets the value of the pcaData property.
3323 * {@link PcaDataType }
3326 public void setPcaData(PcaDataType value) {
3327 this.pcaData = value;
3331 * Gets the value of the title property.
3334 * possible object is
3338 public String getTitle() {
3343 * Sets the value of the title property.
3350 public void setTitle(String value) {
3355 * Gets the value of the scoreModelName property.
3358 * possible object is
3362 public String getScoreModelName() {
3363 return scoreModelName;
3367 * Sets the value of the scoreModelName property.
3374 public void setScoreModelName(String value) {
3375 this.scoreModelName = value;
3379 * Gets the value of the xDim property.
3382 * possible object is
3386 public Integer getXDim() {
3391 * Sets the value of the xDim property.
3398 public void setXDim(Integer value) {
3403 * Gets the value of the yDim property.
3406 * possible object is
3410 public Integer getYDim() {
3415 * Sets the value of the yDim property.
3422 public void setYDim(Integer value) {
3427 * Gets the value of the zDim property.
3430 * possible object is
3434 public Integer getZDim() {
3439 * Sets the value of the zDim property.
3446 public void setZDim(Integer value) {
3451 * Gets the value of the bgColour property.
3454 * possible object is
3458 public Integer getBgColour() {
3463 * Sets the value of the bgColour property.
3470 public void setBgColour(Integer value) {
3471 this.bgColour = value;
3475 * Gets the value of the scaleFactor property.
3478 * possible object is
3482 public Float getScaleFactor() {
3487 * Sets the value of the scaleFactor property.
3494 public void setScaleFactor(Float value) {
3495 this.scaleFactor = value;
3499 * Gets the value of the showLabels property.
3502 * possible object is
3506 public Boolean isShowLabels() {
3511 * Sets the value of the showLabels property.
3518 public void setShowLabels(Boolean value) {
3519 this.showLabels = value;
3523 * Gets the value of the linkToAllViews property.
3526 * possible object is
3530 public Boolean isLinkToAllViews() {
3531 return linkToAllViews;
3535 * Sets the value of the linkToAllViews property.
3542 public void setLinkToAllViews(Boolean value) {
3543 this.linkToAllViews = value;
3547 * Gets the value of the width property.
3550 * possible object is
3554 public Integer getWidth() {
3559 * Sets the value of the width property.
3566 public void setWidth(Integer value) {
3571 * Gets the value of the height property.
3574 * possible object is
3578 public Integer getHeight() {
3583 * Sets the value of the height property.
3590 public void setHeight(Integer value) {
3591 this.height = value;
3595 * Gets the value of the xpos property.
3598 * possible object is
3602 public Integer getXpos() {
3607 * Sets the value of the xpos property.
3614 public void setXpos(Integer value) {
3619 * Gets the value of the ypos property.
3622 * possible object is
3626 public Integer getYpos() {
3631 * Sets the value of the ypos property.
3638 public void setYpos(Integer value) {
3643 * Gets the value of the includeGaps property.
3646 * possible object is
3650 public Boolean isIncludeGaps() {
3655 * Sets the value of the includeGaps property.
3662 public void setIncludeGaps(Boolean value) {
3663 this.includeGaps = value;
3667 * Gets the value of the matchGaps property.
3670 * possible object is
3674 public Boolean isMatchGaps() {
3679 * Sets the value of the matchGaps property.
3686 public void setMatchGaps(Boolean value) {
3687 this.matchGaps = value;
3691 * Gets the value of the includeGappedColumns property.
3694 * possible object is
3698 public Boolean isIncludeGappedColumns() {
3699 return includeGappedColumns;
3703 * Sets the value of the includeGappedColumns property.
3710 public void setIncludeGappedColumns(Boolean value) {
3711 this.includeGappedColumns = value;
3715 * Gets the value of the denominateByShortestLength property.
3718 * possible object is
3722 public Boolean isDenominateByShortestLength() {
3723 return denominateByShortestLength;
3727 * Sets the value of the denominateByShortestLength property.
3734 public void setDenominateByShortestLength(Boolean value) {
3735 this.denominateByShortestLength = value;
3740 * <p>Java class for anonymous complex type.
3742 * <p>The following schema fragment specifies the expected content contained within this class.
3746 * <complexContent>
3747 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3748 * <attGroup ref="{www.jalview.org}position"/>
3750 * </complexContent>
3756 @XmlAccessorType(XmlAccessType.FIELD)
3758 public static class Axis {
3760 @XmlAttribute(name = "xPos")
3761 protected Float xPos;
3762 @XmlAttribute(name = "yPos")
3763 protected Float yPos;
3764 @XmlAttribute(name = "zPos")
3765 protected Float zPos;
3768 * Gets the value of the xPos property.
3771 * possible object is
3775 public Float getXPos() {
3780 * Sets the value of the xPos property.
3787 public void setXPos(Float value) {
3792 * Gets the value of the yPos property.
3795 * possible object is
3799 public Float getYPos() {
3804 * Sets the value of the yPos property.
3811 public void setYPos(Float value) {
3816 * Gets the value of the zPos property.
3819 * possible object is
3823 public Float getZPos() {
3828 * Sets the value of the zPos property.
3835 public void setZPos(Float value) {
3843 * <p>Java class for anonymous complex type.
3845 * <p>The following schema fragment specifies the expected content contained within this class.
3849 * <complexContent>
3850 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3851 * <attGroup ref="{www.jalview.org}position"/>
3853 * </complexContent>
3859 @XmlAccessorType(XmlAccessType.FIELD)
3861 public static class SeqPointMax {
3863 @XmlAttribute(name = "xPos")
3864 protected Float xPos;
3865 @XmlAttribute(name = "yPos")
3866 protected Float yPos;
3867 @XmlAttribute(name = "zPos")
3868 protected Float zPos;
3871 * Gets the value of the xPos property.
3874 * possible object is
3878 public Float getXPos() {
3883 * Sets the value of the xPos property.
3890 public void setXPos(Float value) {
3895 * Gets the value of the yPos property.
3898 * possible object is
3902 public Float getYPos() {
3907 * Sets the value of the yPos property.
3914 public void setYPos(Float value) {
3919 * Gets the value of the zPos property.
3922 * possible object is
3926 public Float getZPos() {
3931 * Sets the value of the zPos property.
3938 public void setZPos(Float value) {
3946 * <p>Java class for anonymous complex type.
3948 * <p>The following schema fragment specifies the expected content contained within this class.
3952 * <complexContent>
3953 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3954 * <attGroup ref="{www.jalview.org}position"/>
3956 * </complexContent>
3962 @XmlAccessorType(XmlAccessType.FIELD)
3964 public static class SeqPointMin {
3966 @XmlAttribute(name = "xPos")
3967 protected Float xPos;
3968 @XmlAttribute(name = "yPos")
3969 protected Float yPos;
3970 @XmlAttribute(name = "zPos")
3971 protected Float zPos;
3974 * Gets the value of the xPos property.
3977 * possible object is
3981 public Float getXPos() {
3986 * Sets the value of the xPos property.
3993 public void setXPos(Float value) {
3998 * Gets the value of the yPos property.
4001 * possible object is
4005 public Float getYPos() {
4010 * Sets the value of the yPos property.
4017 public void setYPos(Float value) {
4022 * Gets the value of the zPos property.
4025 * possible object is
4029 public Float getZPos() {
4034 * Sets the value of the zPos property.
4041 public void setZPos(Float value) {
4049 * <p>Java class for anonymous complex type.
4051 * <p>The following schema fragment specifies the expected content contained within this class.
4055 * <complexContent>
4056 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4057 * <attGroup ref="{www.jalview.org}position"/>
4058 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4060 * </complexContent>
4066 @XmlAccessorType(XmlAccessType.FIELD)
4068 public static class SequencePoint {
4070 @XmlAttribute(name = "sequenceRef")
4071 protected String sequenceRef;
4072 @XmlAttribute(name = "xPos")
4073 protected Float xPos;
4074 @XmlAttribute(name = "yPos")
4075 protected Float yPos;
4076 @XmlAttribute(name = "zPos")
4077 protected Float zPos;
4080 * Gets the value of the sequenceRef property.
4083 * possible object is
4087 public String getSequenceRef() {
4092 * Sets the value of the sequenceRef property.
4099 public void setSequenceRef(String value) {
4100 this.sequenceRef = value;
4104 * Gets the value of the xPos property.
4107 * possible object is
4111 public Float getXPos() {
4116 * Sets the value of the xPos property.
4123 public void setXPos(Float value) {
4128 * Gets the value of the yPos property.
4131 * possible object is
4135 public Float getYPos() {
4140 * Sets the value of the yPos property.
4147 public void setYPos(Float value) {
4152 * Gets the value of the zPos property.
4155 * possible object is
4159 public Float getZPos() {
4164 * Sets the value of the zPos property.
4171 public void setZPos(Float value) {
4181 * <p>Java class for anonymous complex type.
4183 * <p>The following schema fragment specifies the expected content contained within this class.
4187 * <complexContent>
4188 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4189 * <sequence minOccurs="0">
4190 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4191 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4193 * <attGroup ref="{www.jalview.org}swingwindow"/>
4194 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4195 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4196 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4197 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4198 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4199 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4200 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4201 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4202 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4203 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4204 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4206 * </complexContent>
4212 @XmlAccessorType(XmlAccessType.FIELD)
4213 @XmlType(name = "", propOrder = {
4217 public static class Tree {
4219 @XmlElement(namespace = "www.jalview.org")
4220 protected String title;
4221 @XmlElement(namespace = "www.jalview.org")
4222 protected String newick;
4223 @XmlAttribute(name = "fontName")
4224 protected String fontName;
4225 @XmlAttribute(name = "fontSize")
4226 protected Integer fontSize;
4227 @XmlAttribute(name = "fontStyle")
4228 protected Integer fontStyle;
4229 @XmlAttribute(name = "threshold")
4230 protected Float threshold;
4231 @XmlAttribute(name = "showBootstrap")
4232 protected Boolean showBootstrap;
4233 @XmlAttribute(name = "showDistances")
4234 protected Boolean showDistances;
4235 @XmlAttribute(name = "markUnlinked")
4236 protected Boolean markUnlinked;
4237 @XmlAttribute(name = "fitToWindow")
4238 protected Boolean fitToWindow;
4239 @XmlAttribute(name = "currentTree")
4240 protected Boolean currentTree;
4241 @XmlAttribute(name = "id")
4242 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4244 @XmlSchemaType(name = "ID")
4245 protected String id;
4246 @XmlAttribute(name = "linkToAllViews")
4247 protected Boolean linkToAllViews;
4248 @XmlAttribute(name = "width")
4249 protected Integer width;
4250 @XmlAttribute(name = "height")
4251 protected Integer height;
4252 @XmlAttribute(name = "xpos")
4253 protected Integer xpos;
4254 @XmlAttribute(name = "ypos")
4255 protected Integer ypos;
4258 * Gets the value of the title property.
4261 * possible object is
4265 public String getTitle() {
4270 * Sets the value of the title property.
4277 public void setTitle(String value) {
4282 * Gets the value of the newick property.
4285 * possible object is
4289 public String getNewick() {
4294 * Sets the value of the newick property.
4301 public void setNewick(String value) {
4302 this.newick = value;
4306 * Gets the value of the fontName property.
4309 * possible object is
4313 public String getFontName() {
4318 * Sets the value of the fontName property.
4325 public void setFontName(String value) {
4326 this.fontName = value;
4330 * Gets the value of the fontSize property.
4333 * possible object is
4337 public Integer getFontSize() {
4342 * Sets the value of the fontSize property.
4349 public void setFontSize(Integer value) {
4350 this.fontSize = value;
4354 * Gets the value of the fontStyle property.
4357 * possible object is
4361 public Integer getFontStyle() {
4366 * Sets the value of the fontStyle property.
4373 public void setFontStyle(Integer value) {
4374 this.fontStyle = value;
4378 * Gets the value of the threshold property.
4381 * possible object is
4385 public Float getThreshold() {
4390 * Sets the value of the threshold property.
4397 public void setThreshold(Float value) {
4398 this.threshold = value;
4402 * Gets the value of the showBootstrap property.
4405 * possible object is
4409 public Boolean isShowBootstrap() {
4410 return showBootstrap;
4414 * Sets the value of the showBootstrap property.
4421 public void setShowBootstrap(Boolean value) {
4422 this.showBootstrap = value;
4426 * Gets the value of the showDistances property.
4429 * possible object is
4433 public Boolean isShowDistances() {
4434 return showDistances;
4438 * Sets the value of the showDistances property.
4445 public void setShowDistances(Boolean value) {
4446 this.showDistances = value;
4450 * Gets the value of the markUnlinked property.
4453 * possible object is
4457 public Boolean isMarkUnlinked() {
4458 return markUnlinked;
4462 * Sets the value of the markUnlinked property.
4469 public void setMarkUnlinked(Boolean value) {
4470 this.markUnlinked = value;
4474 * Gets the value of the fitToWindow property.
4477 * possible object is
4481 public Boolean isFitToWindow() {
4486 * Sets the value of the fitToWindow property.
4493 public void setFitToWindow(Boolean value) {
4494 this.fitToWindow = value;
4498 * Gets the value of the currentTree property.
4501 * possible object is
4505 public Boolean isCurrentTree() {
4510 * Sets the value of the currentTree property.
4517 public void setCurrentTree(Boolean value) {
4518 this.currentTree = value;
4522 * Gets the value of the id property.
4525 * possible object is
4529 public String getId() {
4534 * Sets the value of the id property.
4541 public void setId(String value) {
4546 * Gets the value of the linkToAllViews property.
4549 * possible object is
4553 public boolean isLinkToAllViews() {
4554 if (linkToAllViews == null) {
4557 return linkToAllViews;
4562 * Sets the value of the linkToAllViews property.
4569 public void setLinkToAllViews(Boolean value) {
4570 this.linkToAllViews = value;
4574 * Gets the value of the width property.
4577 * possible object is
4581 public Integer getWidth() {
4586 * Sets the value of the width property.
4593 public void setWidth(Integer value) {
4598 * Gets the value of the height property.
4601 * possible object is
4605 public Integer getHeight() {
4610 * Sets the value of the height property.
4617 public void setHeight(Integer value) {
4618 this.height = value;
4622 * Gets the value of the xpos property.
4625 * possible object is
4629 public Integer getXpos() {
4634 * Sets the value of the xpos property.
4641 public void setXpos(Integer value) {
4646 * Gets the value of the ypos property.
4649 * possible object is
4653 public Integer getYpos() {
4658 * Sets the value of the ypos property.
4665 public void setYpos(Integer value) {
4673 * <p>Java class for anonymous complex type.
4675 * <p>The following schema fragment specifies the expected content contained within this class.
4679 * <complexContent>
4680 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4682 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4684 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4686 * </complexContent>
4692 @XmlAccessorType(XmlAccessType.FIELD)
4693 @XmlType(name = "", propOrder = {
4696 public static class UserColours {
4698 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4699 protected JalviewUserColours userColourScheme;
4700 @XmlAttribute(name = "id")
4701 protected String id;
4704 * Gets the value of the userColourScheme property.
4707 * possible object is
4708 * {@link JalviewUserColours }
4711 public JalviewUserColours getUserColourScheme() {
4712 return userColourScheme;
4716 * Sets the value of the userColourScheme property.
4720 * {@link JalviewUserColours }
4723 public void setUserColourScheme(JalviewUserColours value) {
4724 this.userColourScheme = value;
4728 * Gets the value of the id property.
4731 * possible object is
4735 public String getId() {
4740 * Sets the value of the id property.
4747 public void setId(String value) {
4755 * <p>Java class for anonymous complex type.
4757 * <p>The following schema fragment specifies the expected content contained within this class.
4761 * <complexContent>
4762 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4764 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4765 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4767 * <complexContent>
4768 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4769 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4770 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4772 * </complexContent>
4775 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4777 * <complexContent>
4778 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4779 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4780 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4781 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4783 * </complexContent>
4786 * <element name="overview" minOccurs="0">
4788 * <complexContent>
4789 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4790 * <attGroup ref="{www.jalview.org}swingwindow"/>
4791 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4792 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4793 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4794 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4795 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4797 * </complexContent>
4801 * <attGroup ref="{www.jalview.org}swingwindow"/>
4802 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4803 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4804 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4805 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4806 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4807 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4808 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4809 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4811 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4812 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4813 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4816 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4817 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4818 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4819 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4820 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4821 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4822 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4824 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4825 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4826 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4827 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4828 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4829 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4830 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4831 * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
4832 * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
4833 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4834 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4835 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4836 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4837 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4838 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4839 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4840 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4841 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4842 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4843 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4844 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4845 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4846 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4848 * </complexContent>
4854 @XmlAccessorType(XmlAccessType.FIELD)
4855 @XmlType(name = "", propOrder = {
4856 "annotationColours",
4861 public static class Viewport {
4863 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4864 protected AnnotationColourScheme annotationColours;
4865 @XmlElement(namespace = "www.jalview.org")
4866 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4867 @XmlElement(namespace = "www.jalview.org")
4868 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4869 @XmlElement(namespace = "www.jalview.org")
4870 protected JalviewModel.Viewport.Overview overview;
4871 @XmlAttribute(name = "conservationSelected")
4872 protected Boolean conservationSelected;
4873 @XmlAttribute(name = "pidSelected")
4874 protected Boolean pidSelected;
4875 @XmlAttribute(name = "bgColour")
4876 protected String bgColour;
4877 @XmlAttribute(name = "consThreshold")
4878 protected Integer consThreshold;
4879 @XmlAttribute(name = "pidThreshold")
4880 protected Integer pidThreshold;
4881 @XmlAttribute(name = "title")
4882 protected String title;
4883 @XmlAttribute(name = "showFullId")
4884 protected Boolean showFullId;
4885 @XmlAttribute(name = "rightAlignIds")
4886 protected Boolean rightAlignIds;
4887 @XmlAttribute(name = "showText")
4888 protected Boolean showText;
4889 @XmlAttribute(name = "showColourText")
4890 protected Boolean showColourText;
4891 @XmlAttribute(name = "showUnconserved")
4892 protected Boolean showUnconserved;
4893 @XmlAttribute(name = "showBoxes")
4894 protected Boolean showBoxes;
4895 @XmlAttribute(name = "wrapAlignment")
4896 protected Boolean wrapAlignment;
4897 @XmlAttribute(name = "renderGaps")
4898 protected Boolean renderGaps;
4899 @XmlAttribute(name = "showSequenceFeatures")
4900 protected Boolean showSequenceFeatures;
4901 @XmlAttribute(name = "showNPfeatureTooltip")
4902 protected Boolean showNPfeatureTooltip;
4903 @XmlAttribute(name = "showDbRefTooltip")
4904 protected Boolean showDbRefTooltip;
4905 @XmlAttribute(name = "followHighlight")
4906 protected Boolean followHighlight;
4907 @XmlAttribute(name = "followSelection")
4908 protected Boolean followSelection;
4909 @XmlAttribute(name = "showAnnotation")
4910 protected Boolean showAnnotation;
4911 @XmlAttribute(name = "centreColumnLabels")
4912 protected Boolean centreColumnLabels;
4913 @XmlAttribute(name = "showGroupConservation")
4914 protected Boolean showGroupConservation;
4915 @XmlAttribute(name = "showGroupConsensus")
4916 protected Boolean showGroupConsensus;
4917 @XmlAttribute(name = "showConsensusHistogram")
4918 protected Boolean showConsensusHistogram;
4919 @XmlAttribute(name = "showSequenceLogo")
4920 protected Boolean showSequenceLogo;
4921 @XmlAttribute(name = "normaliseSequenceLogo")
4922 protected Boolean normaliseSequenceLogo;
4923 @XmlAttribute(name = "ignoreGapsinConsensus")
4924 protected Boolean ignoreGapsinConsensus;
4925 @XmlAttribute(name = "startRes")
4926 protected Integer startRes;
4927 @XmlAttribute(name = "startSeq")
4928 protected Integer startSeq;
4929 @XmlAttribute(name = "charWidth")
4930 protected Integer charWidth;
4931 @XmlAttribute(name = "charHeight")
4932 protected Integer charHeight;
4933 @XmlAttribute(name = "fontName")
4934 protected String fontName;
4935 @XmlAttribute(name = "fontSize")
4936 protected Integer fontSize;
4937 @XmlAttribute(name = "fontStyle")
4938 protected Integer fontStyle;
4939 @XmlAttribute(name = "scaleProteinAsCdna")
4940 protected Boolean scaleProteinAsCdna;
4941 @XmlAttribute(name = "viewName")
4942 protected String viewName;
4943 @XmlAttribute(name = "sequenceSetId")
4944 protected String sequenceSetId;
4945 @XmlAttribute(name = "gatheredViews")
4946 protected Boolean gatheredViews;
4947 @XmlAttribute(name = "textCol1")
4948 protected Integer textCol1;
4949 @XmlAttribute(name = "textCol2")
4950 protected Integer textCol2;
4951 @XmlAttribute(name = "textColThreshold")
4952 protected Integer textColThreshold;
4953 @XmlAttribute(name = "id")
4954 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4956 @XmlSchemaType(name = "ID")
4957 protected String id;
4958 @XmlAttribute(name = "complementId")
4959 protected String complementId;
4960 @XmlAttribute(name = "showComplementFeatures")
4961 protected Boolean showComplementFeatures;
4962 @XmlAttribute(name = "showComplementFeaturesOnTop")
4963 protected Boolean showComplementFeaturesOnTop;
4964 @XmlAttribute(name = "width")
4965 protected Integer width;
4966 @XmlAttribute(name = "height")
4967 protected Integer height;
4968 @XmlAttribute(name = "xpos")
4969 protected Integer xpos;
4970 @XmlAttribute(name = "ypos")
4971 protected Integer ypos;
4974 * Gets the value of the annotationColours property.
4977 * possible object is
4978 * {@link AnnotationColourScheme }
4981 public AnnotationColourScheme getAnnotationColours() {
4982 return annotationColours;
4986 * Sets the value of the annotationColours property.
4990 * {@link AnnotationColourScheme }
4993 public void setAnnotationColours(AnnotationColourScheme value) {
4994 this.annotationColours = value;
4998 * Gets the value of the hiddenColumns property.
5001 * This accessor method returns a reference to the live list,
5002 * not a snapshot. Therefore any modification you make to the
5003 * returned list will be present inside the JAXB object.
5004 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
5007 * For example, to add a new item, do as follows:
5009 * getHiddenColumns().add(newItem);
5014 * Objects of the following type(s) are allowed in the list
5015 * {@link JalviewModel.Viewport.HiddenColumns }
5019 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5020 if (hiddenColumns == null) {
5021 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5023 return this.hiddenColumns;
5027 * Gets the value of the calcIdParam property.
5030 * This accessor method returns a reference to the live list,
5031 * not a snapshot. Therefore any modification you make to the
5032 * returned list will be present inside the JAXB object.
5033 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5036 * For example, to add a new item, do as follows:
5038 * getCalcIdParam().add(newItem);
5043 * Objects of the following type(s) are allowed in the list
5044 * {@link JalviewModel.Viewport.CalcIdParam }
5048 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5049 if (calcIdParam == null) {
5050 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5052 return this.calcIdParam;
5056 * Gets the value of the overview property.
5059 * possible object is
5060 * {@link JalviewModel.Viewport.Overview }
5063 public JalviewModel.Viewport.Overview getOverview() {
5068 * Sets the value of the overview property.
5072 * {@link JalviewModel.Viewport.Overview }
5075 public void setOverview(JalviewModel.Viewport.Overview value) {
5076 this.overview = value;
5080 * Gets the value of the conservationSelected property.
5083 * possible object is
5087 public Boolean isConservationSelected() {
5088 return conservationSelected;
5092 * Sets the value of the conservationSelected property.
5099 public void setConservationSelected(Boolean value) {
5100 this.conservationSelected = value;
5104 * Gets the value of the pidSelected property.
5107 * possible object is
5111 public Boolean isPidSelected() {
5116 * Sets the value of the pidSelected property.
5123 public void setPidSelected(Boolean value) {
5124 this.pidSelected = value;
5128 * Gets the value of the bgColour property.
5131 * possible object is
5135 public String getBgColour() {
5140 * Sets the value of the bgColour property.
5147 public void setBgColour(String value) {
5148 this.bgColour = value;
5152 * Gets the value of the consThreshold property.
5155 * possible object is
5159 public Integer getConsThreshold() {
5160 return consThreshold;
5164 * Sets the value of the consThreshold property.
5171 public void setConsThreshold(Integer value) {
5172 this.consThreshold = value;
5176 * Gets the value of the pidThreshold property.
5179 * possible object is
5183 public Integer getPidThreshold() {
5184 return pidThreshold;
5188 * Sets the value of the pidThreshold property.
5195 public void setPidThreshold(Integer value) {
5196 this.pidThreshold = value;
5200 * Gets the value of the title property.
5203 * possible object is
5207 public String getTitle() {
5212 * Sets the value of the title property.
5219 public void setTitle(String value) {
5224 * Gets the value of the showFullId property.
5227 * possible object is
5231 public Boolean isShowFullId() {
5236 * Sets the value of the showFullId property.
5243 public void setShowFullId(Boolean value) {
5244 this.showFullId = value;
5248 * Gets the value of the rightAlignIds property.
5251 * possible object is
5255 public Boolean isRightAlignIds() {
5256 return rightAlignIds;
5260 * Sets the value of the rightAlignIds property.
5267 public void setRightAlignIds(Boolean value) {
5268 this.rightAlignIds = value;
5272 * Gets the value of the showText property.
5275 * possible object is
5279 public Boolean isShowText() {
5284 * Sets the value of the showText property.
5291 public void setShowText(Boolean value) {
5292 this.showText = value;
5296 * Gets the value of the showColourText property.
5299 * possible object is
5303 public Boolean isShowColourText() {
5304 return showColourText;
5308 * Sets the value of the showColourText property.
5315 public void setShowColourText(Boolean value) {
5316 this.showColourText = value;
5320 * Gets the value of the showUnconserved property.
5323 * possible object is
5327 public boolean isShowUnconserved() {
5328 if (showUnconserved == null) {
5331 return showUnconserved;
5336 * Sets the value of the showUnconserved property.
5343 public void setShowUnconserved(Boolean value) {
5344 this.showUnconserved = value;
5348 * Gets the value of the showBoxes property.
5351 * possible object is
5355 public Boolean isShowBoxes() {
5360 * Sets the value of the showBoxes property.
5367 public void setShowBoxes(Boolean value) {
5368 this.showBoxes = value;
5372 * Gets the value of the wrapAlignment property.
5375 * possible object is
5379 public Boolean isWrapAlignment() {
5380 return wrapAlignment;
5384 * Sets the value of the wrapAlignment property.
5391 public void setWrapAlignment(Boolean value) {
5392 this.wrapAlignment = value;
5396 * Gets the value of the renderGaps property.
5399 * possible object is
5403 public Boolean isRenderGaps() {
5408 * Sets the value of the renderGaps property.
5415 public void setRenderGaps(Boolean value) {
5416 this.renderGaps = value;
5420 * Gets the value of the showSequenceFeatures property.
5423 * possible object is
5427 public Boolean isShowSequenceFeatures() {
5428 return showSequenceFeatures;
5432 * Sets the value of the showSequenceFeatures property.
5439 public void setShowSequenceFeatures(Boolean value) {
5440 this.showSequenceFeatures = value;
5444 * Gets the value of the showNPfeatureTooltip property.
5447 * possible object is
5451 public Boolean isShowNPfeatureTooltip() {
5452 return showNPfeatureTooltip;
5456 * Sets the value of the showNPfeatureTooltip property.
5463 public void setShowNPfeatureTooltip(Boolean value) {
5464 this.showNPfeatureTooltip = value;
5468 * Gets the value of the showDbRefTooltip property.
5471 * possible object is
5475 public Boolean isShowDbRefTooltip() {
5476 return showDbRefTooltip;
5480 * Sets the value of the showDbRefTooltip property.
5487 public void setShowDbRefTooltip(Boolean value) {
5488 this.showDbRefTooltip = value;
5492 * Gets the value of the followHighlight property.
5495 * possible object is
5499 public boolean isFollowHighlight() {
5500 if (followHighlight == null) {
5503 return followHighlight;
5508 * Sets the value of the followHighlight property.
5515 public void setFollowHighlight(Boolean value) {
5516 this.followHighlight = value;
5520 * Gets the value of the followSelection property.
5523 * possible object is
5527 public boolean isFollowSelection() {
5528 if (followSelection == null) {
5531 return followSelection;
5536 * Sets the value of the followSelection property.
5543 public void setFollowSelection(Boolean value) {
5544 this.followSelection = value;
5548 * Gets the value of the showAnnotation property.
5551 * possible object is
5555 public Boolean isShowAnnotation() {
5556 return showAnnotation;
5560 * Sets the value of the showAnnotation property.
5567 public void setShowAnnotation(Boolean value) {
5568 this.showAnnotation = value;
5572 * Gets the value of the centreColumnLabels property.
5575 * possible object is
5579 public boolean isCentreColumnLabels() {
5580 if (centreColumnLabels == null) {
5583 return centreColumnLabels;
5588 * Sets the value of the centreColumnLabels property.
5595 public void setCentreColumnLabels(Boolean value) {
5596 this.centreColumnLabels = value;
5600 * Gets the value of the showGroupConservation property.
5603 * possible object is
5607 public boolean isShowGroupConservation() {
5608 if (showGroupConservation == null) {
5611 return showGroupConservation;
5616 * Sets the value of the showGroupConservation property.
5623 public void setShowGroupConservation(Boolean value) {
5624 this.showGroupConservation = value;
5628 * Gets the value of the showGroupConsensus property.
5631 * possible object is
5635 public boolean isShowGroupConsensus() {
5636 if (showGroupConsensus == null) {
5639 return showGroupConsensus;
5644 * Sets the value of the showGroupConsensus property.
5651 public void setShowGroupConsensus(Boolean value) {
5652 this.showGroupConsensus = value;
5656 * Gets the value of the showConsensusHistogram property.
5659 * possible object is
5663 public boolean isShowConsensusHistogram() {
5664 if (showConsensusHistogram == null) {
5667 return showConsensusHistogram;
5672 * Sets the value of the showConsensusHistogram property.
5679 public void setShowConsensusHistogram(Boolean value) {
5680 this.showConsensusHistogram = value;
5684 * Gets the value of the showSequenceLogo property.
5687 * possible object is
5691 public boolean isShowSequenceLogo() {
5692 if (showSequenceLogo == null) {
5695 return showSequenceLogo;
5700 * Sets the value of the showSequenceLogo property.
5707 public void setShowSequenceLogo(Boolean value) {
5708 this.showSequenceLogo = value;
5712 * Gets the value of the normaliseSequenceLogo property.
5715 * possible object is
5719 public boolean isNormaliseSequenceLogo() {
5720 if (normaliseSequenceLogo == null) {
5723 return normaliseSequenceLogo;
5728 * Sets the value of the normaliseSequenceLogo property.
5735 public void setNormaliseSequenceLogo(Boolean value) {
5736 this.normaliseSequenceLogo = value;
5740 * Gets the value of the ignoreGapsinConsensus property.
5743 * possible object is
5747 public boolean isIgnoreGapsinConsensus() {
5748 if (ignoreGapsinConsensus == null) {
5751 return ignoreGapsinConsensus;
5756 * Sets the value of the ignoreGapsinConsensus property.
5763 public void setIgnoreGapsinConsensus(Boolean value) {
5764 this.ignoreGapsinConsensus = value;
5768 * Gets the value of the startRes property.
5771 * possible object is
5775 public Integer getStartRes() {
5780 * Sets the value of the startRes property.
5787 public void setStartRes(Integer value) {
5788 this.startRes = value;
5792 * Gets the value of the startSeq property.
5795 * possible object is
5799 public Integer getStartSeq() {
5804 * Sets the value of the startSeq property.
5811 public void setStartSeq(Integer value) {
5812 this.startSeq = value;
5816 * Gets the value of the charWidth property.
5819 * possible object is
5823 public Integer getCharWidth() {
5828 * Sets the value of the charWidth property.
5835 public void setCharWidth(Integer value) {
5836 this.charWidth = value;
5840 * Gets the value of the charHeight property.
5843 * possible object is
5847 public Integer getCharHeight() {
5852 * Sets the value of the charHeight property.
5859 public void setCharHeight(Integer value) {
5860 this.charHeight = value;
5864 * Gets the value of the fontName property.
5867 * possible object is
5871 public String getFontName() {
5876 * Sets the value of the fontName property.
5883 public void setFontName(String value) {
5884 this.fontName = value;
5888 * Gets the value of the fontSize property.
5891 * possible object is
5895 public Integer getFontSize() {
5900 * Sets the value of the fontSize property.
5907 public void setFontSize(Integer value) {
5908 this.fontSize = value;
5912 * Gets the value of the fontStyle property.
5915 * possible object is
5919 public Integer getFontStyle() {
5924 * Sets the value of the fontStyle property.
5931 public void setFontStyle(Integer value) {
5932 this.fontStyle = value;
5936 * Gets the value of the scaleProteinAsCdna property.
5939 * possible object is
5943 public boolean isScaleProteinAsCdna() {
5944 if (scaleProteinAsCdna == null) {
5947 return scaleProteinAsCdna;
5952 * Sets the value of the scaleProteinAsCdna property.
5959 public void setScaleProteinAsCdna(Boolean value) {
5960 this.scaleProteinAsCdna = value;
5964 * Gets the value of the viewName property.
5967 * possible object is
5971 public String getViewName() {
5976 * Sets the value of the viewName property.
5983 public void setViewName(String value) {
5984 this.viewName = value;
5988 * Gets the value of the sequenceSetId property.
5991 * possible object is
5995 public String getSequenceSetId() {
5996 return sequenceSetId;
6000 * Sets the value of the sequenceSetId property.
6007 public void setSequenceSetId(String value) {
6008 this.sequenceSetId = value;
6012 * Gets the value of the gatheredViews property.
6015 * possible object is
6019 public Boolean isGatheredViews() {
6020 return gatheredViews;
6024 * Sets the value of the gatheredViews property.
6031 public void setGatheredViews(Boolean value) {
6032 this.gatheredViews = value;
6036 * Gets the value of the textCol1 property.
6039 * possible object is
6043 public Integer getTextCol1() {
6048 * Sets the value of the textCol1 property.
6055 public void setTextCol1(Integer value) {
6056 this.textCol1 = value;
6060 * Gets the value of the textCol2 property.
6063 * possible object is
6067 public Integer getTextCol2() {
6072 * Sets the value of the textCol2 property.
6079 public void setTextCol2(Integer value) {
6080 this.textCol2 = value;
6084 * Gets the value of the textColThreshold property.
6087 * possible object is
6091 public Integer getTextColThreshold() {
6092 return textColThreshold;
6096 * Sets the value of the textColThreshold property.
6103 public void setTextColThreshold(Integer value) {
6104 this.textColThreshold = value;
6108 * Gets the value of the id property.
6111 * possible object is
6115 public String getId() {
6120 * Sets the value of the id property.
6127 public void setId(String value) {
6132 * Gets the value of the complementId property.
6135 * possible object is
6139 public String getComplementId() {
6140 return complementId;
6144 * Sets the value of the complementId property.
6151 public void setComplementId(String value) {
6152 this.complementId = value;
6156 * Gets the value of the showComplementFeatures property.
6159 * possible object is
6163 public boolean isShowComplementFeatures() {
6164 if (showComplementFeatures == null) {
6167 return showComplementFeatures;
6172 * Sets the value of the showComplementFeatures property.
6179 public void setShowComplementFeatures(Boolean value) {
6180 this.showComplementFeatures = value;
6184 * Gets the value of the showComplementFeaturesOnTop property.
6187 * possible object is
6191 public boolean isShowComplementFeaturesOnTop() {
6192 if (showComplementFeaturesOnTop == null) {
6195 return showComplementFeaturesOnTop;
6200 * Sets the value of the showComplementFeaturesOnTop property.
6207 public void setShowComplementFeaturesOnTop(Boolean value) {
6208 this.showComplementFeaturesOnTop = value;
6212 * Gets the value of the width property.
6215 * possible object is
6219 public Integer getWidth() {
6224 * Sets the value of the width property.
6231 public void setWidth(Integer value) {
6236 * Gets the value of the height property.
6239 * possible object is
6243 public Integer getHeight() {
6248 * Sets the value of the height property.
6255 public void setHeight(Integer value) {
6256 this.height = value;
6260 * Gets the value of the xpos property.
6263 * possible object is
6267 public Integer getXpos() {
6272 * Sets the value of the xpos property.
6279 public void setXpos(Integer value) {
6284 * Gets the value of the ypos property.
6287 * possible object is
6291 public Integer getYpos() {
6296 * Sets the value of the ypos property.
6303 public void setYpos(Integer value) {
6309 * <p>Java class for anonymous complex type.
6311 * <p>The following schema fragment specifies the expected content contained within this class.
6315 * <complexContent>
6316 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6317 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6318 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6319 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6321 * </complexContent>
6327 @XmlAccessorType(XmlAccessType.FIELD)
6329 public static class CalcIdParam
6330 extends WebServiceParameterSet
6333 @XmlAttribute(name = "calcId", required = true)
6334 protected String calcId;
6335 @XmlAttribute(name = "needsUpdate")
6336 protected Boolean needsUpdate;
6337 @XmlAttribute(name = "autoUpdate", required = true)
6338 protected boolean autoUpdate;
6341 * Gets the value of the calcId property.
6344 * possible object is
6348 public String getCalcId() {
6353 * Sets the value of the calcId property.
6360 public void setCalcId(String value) {
6361 this.calcId = value;
6365 * Gets the value of the needsUpdate property.
6368 * possible object is
6372 public boolean isNeedsUpdate() {
6373 if (needsUpdate == null) {
6381 * Sets the value of the needsUpdate property.
6388 public void setNeedsUpdate(Boolean value) {
6389 this.needsUpdate = value;
6393 * Gets the value of the autoUpdate property.
6396 public boolean isAutoUpdate() {
6401 * Sets the value of the autoUpdate property.
6404 public void setAutoUpdate(boolean value) {
6405 this.autoUpdate = value;
6412 * <p>Java class for anonymous complex type.
6414 * <p>The following schema fragment specifies the expected content contained within this class.
6418 * <complexContent>
6419 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6420 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6421 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6423 * </complexContent>
6429 @XmlAccessorType(XmlAccessType.FIELD)
6431 public static class HiddenColumns {
6433 @XmlAttribute(name = "start")
6434 protected Integer start;
6435 @XmlAttribute(name = "end")
6436 protected Integer end;
6439 * Gets the value of the start property.
6442 * possible object is
6446 public Integer getStart() {
6451 * Sets the value of the start property.
6458 public void setStart(Integer value) {
6463 * Gets the value of the end property.
6466 * possible object is
6470 public Integer getEnd() {
6475 * Sets the value of the end property.
6482 public void setEnd(Integer value) {
6490 * <p>Java class for anonymous complex type.
6492 * <p>The following schema fragment specifies the expected content contained within this class.
6496 * <complexContent>
6497 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6498 * <attGroup ref="{www.jalview.org}swingwindow"/>
6499 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6500 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6501 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6502 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6503 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
6505 * </complexContent>
6511 @XmlAccessorType(XmlAccessType.FIELD)
6513 public static class Overview {
6515 @XmlAttribute(name = "showHidden")
6516 protected Boolean showHidden;
6517 @XmlAttribute(name = "residueColour")
6518 protected Integer residueColour;
6519 @XmlAttribute(name = "gapColour")
6520 protected Integer gapColour;
6521 @XmlAttribute(name = "hiddenColour")
6522 protected Integer hiddenColour;
6523 @XmlAttribute(name = "title")
6524 protected String title;
6525 @XmlAttribute(name = "width")
6526 protected Integer width;
6527 @XmlAttribute(name = "height")
6528 protected Integer height;
6529 @XmlAttribute(name = "xpos")
6530 protected Integer xpos;
6531 @XmlAttribute(name = "ypos")
6532 protected Integer ypos;
6535 * Gets the value of the showHidden property.
6538 * possible object is
6542 public Boolean isShowHidden() {
6547 * Sets the value of the showHidden property.
6554 public void setShowHidden(Boolean value) {
6555 this.showHidden = value;
6559 * Gets the value of the residueColour property.
6562 * possible object is
6566 public Integer getResidueColour() {
6567 return residueColour;
6571 * Sets the value of the residueColour property.
6578 public void setResidueColour(Integer value) {
6579 this.residueColour = value;
6583 * Gets the value of the gapColour property.
6586 * possible object is
6590 public Integer getGapColour() {
6595 * Sets the value of the gapColour property.
6602 public void setGapColour(Integer value) {
6603 this.gapColour = value;
6607 * Gets the value of the hiddenColour property.
6610 * possible object is
6614 public Integer getHiddenColour() {
6615 return hiddenColour;
6619 * Sets the value of the hiddenColour property.
6626 public void setHiddenColour(Integer value) {
6627 this.hiddenColour = value;
6631 * Gets the value of the title property.
6634 * possible object is
6638 public String getTitle() {
6643 * Sets the value of the title property.
6650 public void setTitle(String value) {
6655 * Gets the value of the width property.
6658 * possible object is
6662 public Integer getWidth() {
6667 * Sets the value of the width property.
6674 public void setWidth(Integer value) {
6679 * Gets the value of the height property.
6682 * possible object is
6686 public Integer getHeight() {
6691 * Sets the value of the height property.
6698 public void setHeight(Integer value) {
6699 this.height = value;
6703 * Gets the value of the xpos property.
6706 * possible object is
6710 public Integer getXpos() {
6715 * Sets the value of the xpos property.
6722 public void setXpos(Integer value) {
6727 * Gets the value of the ypos property.
6730 * possible object is
6734 public Integer getYpos() {
6739 * Sets the value of the ypos property.
6746 public void setYpos(Integer value) {