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: 2023.05.13 at 06:58:41 PM BST
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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
264 * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
265 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
266 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
268 * </complexContent>
271 * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
273 * <complexContent>
274 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
276 * <element name="sequencePoint" maxOccurs="unbounded">
278 * <complexContent>
279 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
280 * <attGroup ref="{www.jalview.org}position"/>
281 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
283 * </complexContent>
286 * <element name="axis" maxOccurs="3" minOccurs="3">
288 * <complexContent>
289 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
290 * <attGroup ref="{www.jalview.org}position"/>
292 * </complexContent>
295 * <element name="seqPointMin">
297 * <complexContent>
298 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
299 * <attGroup ref="{www.jalview.org}position"/>
301 * </complexContent>
304 * <element name="seqPointMax">
306 * <complexContent>
307 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
308 * <attGroup ref="{www.jalview.org}position"/>
310 * </complexContent>
313 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
315 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
316 * <attGroup ref="{www.jalview.org}swingwindow"/>
317 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
318 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
319 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
320 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
321 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
322 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
323 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
324 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
325 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
327 * </complexContent>
330 * <element name="FeatureSettings" minOccurs="0">
332 * <complexContent>
333 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
335 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
337 * <complexContent>
338 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
340 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
341 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
343 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
344 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
345 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
346 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
347 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
348 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
349 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
350 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
351 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
352 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
353 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
354 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
356 * </complexContent>
359 * <element name="group" maxOccurs="unbounded" minOccurs="0">
361 * <complexContent>
362 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
363 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
364 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
366 * </complexContent>
371 * </complexContent>
377 * </complexContent>
383 @XmlAccessorType(XmlAccessType.FIELD)
384 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
396 public class JalviewModel {
398 @XmlElement(required = true)
399 @XmlSchemaType(name = "dateTime")
400 protected XMLGregorianCalendar creationDate;
401 @XmlElement(required = true)
402 protected String version;
403 @XmlElement(required = true)
404 protected VAMSAS vamsasModel;
405 @XmlElement(name = "JSeq")
406 protected List<JalviewModel.JSeq> jSeq;
407 @XmlElement(name = "JGroup")
408 protected List<JalviewModel.JGroup> jGroup;
409 @XmlElement(name = "Viewport")
410 protected List<JalviewModel.Viewport> viewport;
411 @XmlElement(name = "UserColours")
412 protected List<JalviewModel.UserColours> userColours;
413 protected List<JalviewModel.Tree> tree;
414 @XmlElement(name = "PcaViewer")
415 protected List<JalviewModel.PcaViewer> pcaViewer;
416 @XmlElement(name = "FeatureSettings")
417 protected JalviewModel.FeatureSettings featureSettings;
420 * Gets the value of the creationDate property.
424 * {@link XMLGregorianCalendar }
427 public XMLGregorianCalendar getCreationDate() {
432 * Sets the value of the creationDate property.
436 * {@link XMLGregorianCalendar }
439 public void setCreationDate(XMLGregorianCalendar value) {
440 this.creationDate = value;
444 * Gets the value of the version property.
451 public String getVersion() {
456 * Sets the value of the version property.
463 public void setVersion(String value) {
464 this.version = value;
468 * Gets the value of the vamsasModel property.
475 public VAMSAS getVamsasModel() {
480 * Sets the value of the vamsasModel property.
487 public void setVamsasModel(VAMSAS value) {
488 this.vamsasModel = value;
492 * Gets the value of the jSeq property.
495 * This accessor method returns a reference to the live list,
496 * not a snapshot. Therefore any modification you make to the
497 * returned list will be present inside the JAXB object.
498 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
501 * For example, to add a new item, do as follows:
503 * getJSeq().add(newItem);
508 * Objects of the following type(s) are allowed in the list
509 * {@link JalviewModel.JSeq }
513 public List<JalviewModel.JSeq> getJSeq() {
515 jSeq = new ArrayList<JalviewModel.JSeq>();
521 * Gets the value of the jGroup property.
524 * This accessor method returns a reference to the live list,
525 * not a snapshot. Therefore any modification you make to the
526 * returned list will be present inside the JAXB object.
527 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
530 * For example, to add a new item, do as follows:
532 * getJGroup().add(newItem);
537 * Objects of the following type(s) are allowed in the list
538 * {@link JalviewModel.JGroup }
542 public List<JalviewModel.JGroup> getJGroup() {
543 if (jGroup == null) {
544 jGroup = new ArrayList<JalviewModel.JGroup>();
550 * Gets the value of the viewport property.
553 * This accessor method returns a reference to the live list,
554 * not a snapshot. Therefore any modification you make to the
555 * returned list will be present inside the JAXB object.
556 * This is why there is not a <CODE>set</CODE> method for the viewport property.
559 * For example, to add a new item, do as follows:
561 * getViewport().add(newItem);
566 * Objects of the following type(s) are allowed in the list
567 * {@link JalviewModel.Viewport }
571 public List<JalviewModel.Viewport> getViewport() {
572 if (viewport == null) {
573 viewport = new ArrayList<JalviewModel.Viewport>();
575 return this.viewport;
579 * Gets the value of the userColours property.
582 * This accessor method returns a reference to the live list,
583 * not a snapshot. Therefore any modification you make to the
584 * returned list will be present inside the JAXB object.
585 * This is why there is not a <CODE>set</CODE> method for the userColours property.
588 * For example, to add a new item, do as follows:
590 * getUserColours().add(newItem);
595 * Objects of the following type(s) are allowed in the list
596 * {@link JalviewModel.UserColours }
600 public List<JalviewModel.UserColours> getUserColours() {
601 if (userColours == null) {
602 userColours = new ArrayList<JalviewModel.UserColours>();
604 return this.userColours;
608 * Gets the value of the tree property.
611 * This accessor method returns a reference to the live list,
612 * not a snapshot. Therefore any modification you make to the
613 * returned list will be present inside the JAXB object.
614 * This is why there is not a <CODE>set</CODE> method for the tree property.
617 * For example, to add a new item, do as follows:
619 * getTree().add(newItem);
624 * Objects of the following type(s) are allowed in the list
625 * {@link JalviewModel.Tree }
629 public List<JalviewModel.Tree> getTree() {
631 tree = new ArrayList<JalviewModel.Tree>();
637 * Gets the value of the pcaViewer property.
640 * This accessor method returns a reference to the live list,
641 * not a snapshot. Therefore any modification you make to the
642 * returned list will be present inside the JAXB object.
643 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
646 * For example, to add a new item, do as follows:
648 * getPcaViewer().add(newItem);
653 * Objects of the following type(s) are allowed in the list
654 * {@link JalviewModel.PcaViewer }
658 public List<JalviewModel.PcaViewer> getPcaViewer() {
659 if (pcaViewer == null) {
660 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
662 return this.pcaViewer;
666 * Gets the value of the featureSettings property.
670 * {@link JalviewModel.FeatureSettings }
673 public JalviewModel.FeatureSettings getFeatureSettings() {
674 return featureSettings;
678 * Sets the value of the featureSettings property.
682 * {@link JalviewModel.FeatureSettings }
685 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
686 this.featureSettings = value;
691 * <p>Java class for anonymous complex type.
693 * <p>The following schema fragment specifies the expected content contained within this class.
697 * <complexContent>
698 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
700 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
702 * <complexContent>
703 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
705 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
706 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
708 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
709 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
710 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
711 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
712 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
713 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
714 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
715 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
716 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
717 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
718 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
719 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
721 * </complexContent>
724 * <element name="group" maxOccurs="unbounded" minOccurs="0">
726 * <complexContent>
727 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
728 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
729 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
731 * </complexContent>
736 * </complexContent>
742 @XmlAccessorType(XmlAccessType.FIELD)
743 @XmlType(name = "", propOrder = {
747 public static class FeatureSettings {
749 @XmlElement(namespace = "www.jalview.org")
750 protected List<JalviewModel.FeatureSettings.Setting> setting;
751 @XmlElement(namespace = "www.jalview.org")
752 protected List<JalviewModel.FeatureSettings.Group> group;
755 * Gets the value of the setting property.
758 * This accessor method returns a reference to the live list,
759 * not a snapshot. Therefore any modification you make to the
760 * returned list will be present inside the JAXB object.
761 * This is why there is not a <CODE>set</CODE> method for the setting property.
764 * For example, to add a new item, do as follows:
766 * getSetting().add(newItem);
771 * Objects of the following type(s) are allowed in the list
772 * {@link JalviewModel.FeatureSettings.Setting }
776 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
777 if (setting == null) {
778 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
784 * Gets the value of the group property.
787 * This accessor method returns a reference to the live list,
788 * not a snapshot. Therefore any modification you make to the
789 * returned list will be present inside the JAXB object.
790 * This is why there is not a <CODE>set</CODE> method for the group property.
793 * For example, to add a new item, do as follows:
795 * getGroup().add(newItem);
800 * Objects of the following type(s) are allowed in the list
801 * {@link JalviewModel.FeatureSettings.Group }
805 public List<JalviewModel.FeatureSettings.Group> getGroup() {
807 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
814 * <p>Java class for anonymous complex type.
816 * <p>The following schema fragment specifies the expected content contained within this class.
820 * <complexContent>
821 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
822 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
823 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
825 * </complexContent>
831 @XmlAccessorType(XmlAccessType.FIELD)
833 public static class Group {
835 @XmlAttribute(name = "name", required = true)
836 protected String name;
837 @XmlAttribute(name = "display", required = true)
838 protected boolean display;
841 * Gets the value of the name property.
848 public String getName() {
853 * Sets the value of the name property.
860 public void setName(String value) {
865 * Gets the value of the display property.
868 public boolean isDisplay() {
873 * Sets the value of the display property.
876 public void setDisplay(boolean value) {
877 this.display = value;
884 * <p>Java class for anonymous complex type.
886 * <p>The following schema fragment specifies the expected content contained within this class.
890 * <complexContent>
891 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
893 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
894 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
896 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
897 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
898 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
899 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
900 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
901 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
902 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
903 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
904 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
905 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
906 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
907 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
909 * </complexContent>
915 @XmlAccessorType(XmlAccessType.FIELD)
916 @XmlType(name = "", propOrder = {
920 public static class Setting {
922 @XmlElement(namespace = "www.jalview.org")
923 protected List<String> attributeName;
924 @XmlElement(namespace = "www.jalview.org")
925 protected FeatureMatcherSet matcherSet;
926 @XmlAttribute(name = "type", required = true)
927 protected String type;
928 @XmlAttribute(name = "colour", required = true)
929 protected int colour;
930 @XmlAttribute(name = "display", required = true)
931 protected boolean display;
932 @XmlAttribute(name = "order")
933 protected Float order;
934 @XmlAttribute(name = "mincolour")
935 protected Integer mincolour;
936 @XmlAttribute(name = "noValueColour")
937 protected NoValueColour noValueColour;
938 @XmlAttribute(name = "threshold")
939 protected Float threshold;
940 @XmlAttribute(name = "threshstate")
941 protected Integer threshstate;
942 @XmlAttribute(name = "max")
944 @XmlAttribute(name = "min")
946 @XmlAttribute(name = "colourByLabel")
947 protected Boolean colourByLabel;
948 @XmlAttribute(name = "autoScale")
949 protected Boolean autoScale;
952 * Gets the value of the attributeName property.
955 * This accessor method returns a reference to the live list,
956 * not a snapshot. Therefore any modification you make to the
957 * returned list will be present inside the JAXB object.
958 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
961 * For example, to add a new item, do as follows:
963 * getAttributeName().add(newItem);
968 * Objects of the following type(s) are allowed in the list
973 public List<String> getAttributeName() {
974 if (attributeName == null) {
975 attributeName = new ArrayList<String>();
977 return this.attributeName;
981 * Gets the value of the matcherSet property.
985 * {@link FeatureMatcherSet }
988 public FeatureMatcherSet getMatcherSet() {
993 * Sets the value of the matcherSet property.
997 * {@link FeatureMatcherSet }
1000 public void setMatcherSet(FeatureMatcherSet value) {
1001 this.matcherSet = value;
1005 * Gets the value of the type property.
1008 * possible object is
1012 public String getType() {
1017 * Sets the value of the type property.
1024 public void setType(String value) {
1029 * Gets the value of the colour property.
1032 public int getColour() {
1037 * Sets the value of the colour property.
1040 public void setColour(int value) {
1041 this.colour = value;
1045 * Gets the value of the display property.
1048 public boolean isDisplay() {
1053 * Sets the value of the display property.
1056 public void setDisplay(boolean value) {
1057 this.display = value;
1061 * Gets the value of the order property.
1064 * possible object is
1068 public Float getOrder() {
1073 * Sets the value of the order property.
1080 public void setOrder(Float value) {
1085 * Gets the value of the mincolour property.
1088 * possible object is
1092 public Integer getMincolour() {
1097 * Sets the value of the mincolour property.
1104 public void setMincolour(Integer value) {
1105 this.mincolour = value;
1109 * Gets the value of the noValueColour property.
1112 * possible object is
1113 * {@link NoValueColour }
1116 public NoValueColour getNoValueColour() {
1117 if (noValueColour == null) {
1118 return NoValueColour.MIN;
1120 return noValueColour;
1125 * Sets the value of the noValueColour property.
1129 * {@link NoValueColour }
1132 public void setNoValueColour(NoValueColour value) {
1133 this.noValueColour = value;
1137 * Gets the value of the threshold property.
1140 * possible object is
1144 public Float getThreshold() {
1149 * Sets the value of the threshold property.
1156 public void setThreshold(Float value) {
1157 this.threshold = value;
1161 * Gets the value of the threshstate property.
1164 * possible object is
1168 public Integer getThreshstate() {
1173 * Sets the value of the threshstate property.
1180 public void setThreshstate(Integer value) {
1181 this.threshstate = value;
1185 * Gets the value of the max property.
1188 * possible object is
1192 public Float getMax() {
1197 * Sets the value of the max property.
1204 public void setMax(Float value) {
1209 * Gets the value of the min property.
1212 * possible object is
1216 public Float getMin() {
1221 * Sets the value of the min property.
1228 public void setMin(Float value) {
1233 * Gets the value of the colourByLabel property.
1236 * possible object is
1240 public Boolean isColourByLabel() {
1241 return colourByLabel;
1245 * Sets the value of the colourByLabel property.
1252 public void setColourByLabel(Boolean value) {
1253 this.colourByLabel = value;
1257 * Gets the value of the autoScale property.
1260 * possible object is
1264 public Boolean isAutoScale() {
1269 * Sets the value of the autoScale property.
1276 public void setAutoScale(Boolean value) {
1277 this.autoScale = value;
1286 * <p>Java class for anonymous complex type.
1288 * <p>The following schema fragment specifies the expected content contained within this class.
1292 * <complexContent>
1293 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1295 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1296 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1298 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1299 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1300 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1301 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1302 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1303 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1304 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1305 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1306 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1307 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1308 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1309 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1310 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1311 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1312 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1313 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1314 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1315 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1316 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1318 * </complexContent>
1324 @XmlAccessorType(XmlAccessType.FIELD)
1325 @XmlType(name = "", propOrder = {
1329 public static class JGroup {
1331 @XmlElement(namespace = "www.jalview.org", required = true)
1332 protected List<String> seq;
1333 @XmlElement(namespace = "www.jalview.org")
1334 protected AnnotationColourScheme annotationColours;
1335 @XmlAttribute(name = "start")
1336 protected Integer start;
1337 @XmlAttribute(name = "end")
1338 protected Integer end;
1339 @XmlAttribute(name = "name")
1340 protected String name;
1341 @XmlAttribute(name = "colour")
1342 protected String colour;
1343 @XmlAttribute(name = "consThreshold")
1344 protected Integer consThreshold;
1345 @XmlAttribute(name = "pidThreshold")
1346 protected Integer pidThreshold;
1347 @XmlAttribute(name = "outlineColour")
1348 protected Integer outlineColour;
1349 @XmlAttribute(name = "displayBoxes")
1350 protected Boolean displayBoxes;
1351 @XmlAttribute(name = "displayText")
1352 protected Boolean displayText;
1353 @XmlAttribute(name = "colourText")
1354 protected Boolean colourText;
1355 @XmlAttribute(name = "textCol1")
1356 protected Integer textCol1;
1357 @XmlAttribute(name = "textCol2")
1358 protected Integer textCol2;
1359 @XmlAttribute(name = "textColThreshold")
1360 protected Integer textColThreshold;
1361 @XmlAttribute(name = "showUnconserved")
1362 protected Boolean showUnconserved;
1363 @XmlAttribute(name = "ignoreGapsinConsensus")
1364 protected Boolean ignoreGapsinConsensus;
1365 @XmlAttribute(name = "showConsensusHistogram")
1366 protected Boolean showConsensusHistogram;
1367 @XmlAttribute(name = "showSequenceLogo")
1368 protected Boolean showSequenceLogo;
1369 @XmlAttribute(name = "normaliseSequenceLogo")
1370 protected Boolean normaliseSequenceLogo;
1371 @XmlAttribute(name = "id")
1372 protected String id;
1375 * Gets the value of the seq property.
1378 * This accessor method returns a reference to the live list,
1379 * not a snapshot. Therefore any modification you make to the
1380 * returned list will be present inside the JAXB object.
1381 * This is why there is not a <CODE>set</CODE> method for the seq property.
1384 * For example, to add a new item, do as follows:
1386 * getSeq().add(newItem);
1391 * Objects of the following type(s) are allowed in the list
1396 public List<String> getSeq() {
1398 seq = new ArrayList<String>();
1404 * Gets the value of the annotationColours property.
1407 * possible object is
1408 * {@link AnnotationColourScheme }
1411 public AnnotationColourScheme getAnnotationColours() {
1412 return annotationColours;
1416 * Sets the value of the annotationColours property.
1420 * {@link AnnotationColourScheme }
1423 public void setAnnotationColours(AnnotationColourScheme value) {
1424 this.annotationColours = value;
1428 * Gets the value of the start property.
1431 * possible object is
1435 public Integer getStart() {
1440 * Sets the value of the start property.
1447 public void setStart(Integer value) {
1452 * Gets the value of the end property.
1455 * possible object is
1459 public Integer getEnd() {
1464 * Sets the value of the end property.
1471 public void setEnd(Integer value) {
1476 * Gets the value of the name property.
1479 * possible object is
1483 public String getName() {
1488 * Sets the value of the name property.
1495 public void setName(String value) {
1500 * Gets the value of the colour property.
1503 * possible object is
1507 public String getColour() {
1512 * Sets the value of the colour property.
1519 public void setColour(String value) {
1520 this.colour = value;
1524 * Gets the value of the consThreshold property.
1527 * possible object is
1531 public Integer getConsThreshold() {
1532 return consThreshold;
1536 * Sets the value of the consThreshold property.
1543 public void setConsThreshold(Integer value) {
1544 this.consThreshold = value;
1548 * Gets the value of the pidThreshold property.
1551 * possible object is
1555 public Integer getPidThreshold() {
1556 return pidThreshold;
1560 * Sets the value of the pidThreshold property.
1567 public void setPidThreshold(Integer value) {
1568 this.pidThreshold = value;
1572 * Gets the value of the outlineColour property.
1575 * possible object is
1579 public Integer getOutlineColour() {
1580 return outlineColour;
1584 * Sets the value of the outlineColour property.
1591 public void setOutlineColour(Integer value) {
1592 this.outlineColour = value;
1596 * Gets the value of the displayBoxes property.
1599 * possible object is
1603 public Boolean isDisplayBoxes() {
1604 return displayBoxes;
1608 * Sets the value of the displayBoxes property.
1615 public void setDisplayBoxes(Boolean value) {
1616 this.displayBoxes = value;
1620 * Gets the value of the displayText property.
1623 * possible object is
1627 public Boolean isDisplayText() {
1632 * Sets the value of the displayText property.
1639 public void setDisplayText(Boolean value) {
1640 this.displayText = value;
1644 * Gets the value of the colourText property.
1647 * possible object is
1651 public Boolean isColourText() {
1656 * Sets the value of the colourText property.
1663 public void setColourText(Boolean value) {
1664 this.colourText = value;
1668 * Gets the value of the textCol1 property.
1671 * possible object is
1675 public Integer getTextCol1() {
1680 * Sets the value of the textCol1 property.
1687 public void setTextCol1(Integer value) {
1688 this.textCol1 = value;
1692 * Gets the value of the textCol2 property.
1695 * possible object is
1699 public Integer getTextCol2() {
1704 * Sets the value of the textCol2 property.
1711 public void setTextCol2(Integer value) {
1712 this.textCol2 = value;
1716 * Gets the value of the textColThreshold property.
1719 * possible object is
1723 public Integer getTextColThreshold() {
1724 return textColThreshold;
1728 * Sets the value of the textColThreshold property.
1735 public void setTextColThreshold(Integer value) {
1736 this.textColThreshold = value;
1740 * Gets the value of the showUnconserved property.
1743 * possible object is
1747 public Boolean isShowUnconserved() {
1748 return showUnconserved;
1752 * Sets the value of the showUnconserved property.
1759 public void setShowUnconserved(Boolean value) {
1760 this.showUnconserved = value;
1764 * Gets the value of the ignoreGapsinConsensus property.
1767 * possible object is
1771 public boolean isIgnoreGapsinConsensus() {
1772 if (ignoreGapsinConsensus == null) {
1775 return ignoreGapsinConsensus;
1780 * Sets the value of the ignoreGapsinConsensus property.
1787 public void setIgnoreGapsinConsensus(Boolean value) {
1788 this.ignoreGapsinConsensus = value;
1792 * Gets the value of the showConsensusHistogram property.
1795 * possible object is
1799 public boolean isShowConsensusHistogram() {
1800 if (showConsensusHistogram == null) {
1803 return showConsensusHistogram;
1808 * Sets the value of the showConsensusHistogram property.
1815 public void setShowConsensusHistogram(Boolean value) {
1816 this.showConsensusHistogram = value;
1820 * Gets the value of the showSequenceLogo property.
1823 * possible object is
1827 public boolean isShowSequenceLogo() {
1828 if (showSequenceLogo == null) {
1831 return showSequenceLogo;
1836 * Sets the value of the showSequenceLogo property.
1843 public void setShowSequenceLogo(Boolean value) {
1844 this.showSequenceLogo = value;
1848 * Gets the value of the normaliseSequenceLogo property.
1851 * possible object is
1855 public boolean isNormaliseSequenceLogo() {
1856 if (normaliseSequenceLogo == null) {
1859 return normaliseSequenceLogo;
1864 * Sets the value of the normaliseSequenceLogo property.
1871 public void setNormaliseSequenceLogo(Boolean value) {
1872 this.normaliseSequenceLogo = value;
1876 * Gets the value of the id property.
1879 * possible object is
1883 public String getId() {
1888 * Sets the value of the id property.
1895 public void setId(String value) {
1903 * <p>Java class for anonymous complex type.
1905 * <p>The following schema fragment specifies the expected content contained within this class.
1909 * <complexContent>
1910 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1912 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1913 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1915 * <complexContent>
1916 * <extension base="{www.jalview.org}pdbentry">
1918 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1920 * <simpleContent>
1921 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1922 * <attGroup ref="{www.jalview.org}swingwindow"/>
1923 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1924 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1925 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1926 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1927 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1928 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1930 * </simpleContent>
1935 * </complexContent>
1938 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1939 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1941 * <complexContent>
1942 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1944 * <element name="secondaryStructure" maxOccurs="unbounded">
1946 * <complexContent>
1947 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1948 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1949 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1950 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1951 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1953 * </complexContent>
1957 * <attGroup ref="{www.jalview.org}swingwindow"/>
1958 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1959 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1960 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1961 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1963 * </complexContent>
1967 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1968 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1969 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1970 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1971 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1972 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1974 * </complexContent>
1980 @XmlAccessorType(XmlAccessType.FIELD)
1981 @XmlType(name = "", propOrder = {
1987 public static class JSeq {
1989 @XmlElement(namespace = "www.jalview.org")
1990 protected List<Feature> features;
1991 @XmlElement(namespace = "www.jalview.org")
1992 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1993 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1994 protected List<Integer> hiddenSequences;
1995 @XmlElement(namespace = "www.jalview.org")
1996 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1997 @XmlAttribute(name = "colour")
1998 protected Integer colour;
1999 @XmlAttribute(name = "start", required = true)
2000 protected int start;
2001 @XmlAttribute(name = "end", required = true)
2003 @XmlAttribute(name = "id", required = true)
2004 protected String id;
2005 @XmlAttribute(name = "hidden")
2006 protected Boolean hidden;
2007 @XmlAttribute(name = "viewreference")
2008 protected Boolean viewreference;
2011 * Gets the value of the features property.
2014 * This accessor method returns a reference to the live list,
2015 * not a snapshot. Therefore any modification you make to the
2016 * returned list will be present inside the JAXB object.
2017 * This is why there is not a <CODE>set</CODE> method for the features property.
2020 * For example, to add a new item, do as follows:
2022 * getFeatures().add(newItem);
2027 * Objects of the following type(s) are allowed in the list
2032 public List<Feature> getFeatures() {
2033 if (features == null) {
2034 features = new ArrayList<Feature>();
2036 return this.features;
2040 * Gets the value of the pdbids property.
2043 * This accessor method returns a reference to the live list,
2044 * not a snapshot. Therefore any modification you make to the
2045 * returned list will be present inside the JAXB object.
2046 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2049 * For example, to add a new item, do as follows:
2051 * getPdbids().add(newItem);
2056 * Objects of the following type(s) are allowed in the list
2057 * {@link JalviewModel.JSeq.Pdbids }
2061 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2062 if (pdbids == null) {
2063 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2069 * Gets the value of the hiddenSequences property.
2072 * This accessor method returns a reference to the live list,
2073 * not a snapshot. Therefore any modification you make to the
2074 * returned list will be present inside the JAXB object.
2075 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2078 * For example, to add a new item, do as follows:
2080 * getHiddenSequences().add(newItem);
2085 * Objects of the following type(s) are allowed in the list
2090 public List<Integer> getHiddenSequences() {
2091 if (hiddenSequences == null) {
2092 hiddenSequences = new ArrayList<Integer>();
2094 return this.hiddenSequences;
2098 * Gets the value of the rnaViewer property.
2101 * This accessor method returns a reference to the live list,
2102 * not a snapshot. Therefore any modification you make to the
2103 * returned list will be present inside the JAXB object.
2104 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2107 * For example, to add a new item, do as follows:
2109 * getRnaViewer().add(newItem);
2114 * Objects of the following type(s) are allowed in the list
2115 * {@link JalviewModel.JSeq.RnaViewer }
2119 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2120 if (rnaViewer == null) {
2121 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2123 return this.rnaViewer;
2127 * Gets the value of the colour property.
2130 * possible object is
2134 public Integer getColour() {
2139 * Sets the value of the colour property.
2146 public void setColour(Integer value) {
2147 this.colour = value;
2151 * Gets the value of the start property.
2154 public int getStart() {
2159 * Sets the value of the start property.
2162 public void setStart(int value) {
2167 * Gets the value of the end property.
2170 public int getEnd() {
2175 * Sets the value of the end property.
2178 public void setEnd(int value) {
2183 * Gets the value of the id property.
2186 * possible object is
2190 public String getId() {
2195 * Sets the value of the id property.
2202 public void setId(String value) {
2207 * Gets the value of the hidden property.
2210 * possible object is
2214 public Boolean isHidden() {
2219 * Sets the value of the hidden property.
2226 public void setHidden(Boolean value) {
2227 this.hidden = value;
2231 * Gets the value of the viewreference property.
2234 * possible object is
2238 public Boolean isViewreference() {
2239 return viewreference;
2243 * Sets the value of the viewreference property.
2250 public void setViewreference(Boolean value) {
2251 this.viewreference = value;
2256 * <p>Java class for anonymous complex type.
2258 * <p>The following schema fragment specifies the expected content contained within this class.
2262 * <complexContent>
2263 * <extension base="{www.jalview.org}pdbentry">
2265 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2267 * <simpleContent>
2268 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2269 * <attGroup ref="{www.jalview.org}swingwindow"/>
2270 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2271 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2272 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2273 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2274 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2275 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2277 * </simpleContent>
2282 * </complexContent>
2288 @XmlAccessorType(XmlAccessType.FIELD)
2289 @XmlType(name = "", propOrder = {
2292 public static class Pdbids
2296 @XmlElement(namespace = "www.jalview.org")
2297 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2300 * Gets the value of the structureState property.
2303 * This accessor method returns a reference to the live list,
2304 * not a snapshot. Therefore any modification you make to the
2305 * returned list will be present inside the JAXB object.
2306 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2309 * For example, to add a new item, do as follows:
2311 * getStructureState().add(newItem);
2316 * Objects of the following type(s) are allowed in the list
2317 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2321 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2322 if (structureState == null) {
2323 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2325 return this.structureState;
2330 * <p>Java class for anonymous complex type.
2332 * <p>The following schema fragment specifies the expected content contained within this class.
2336 * <simpleContent>
2337 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2338 * <attGroup ref="{www.jalview.org}swingwindow"/>
2339 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2340 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2341 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2342 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2343 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2344 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2346 * </simpleContent>
2352 @XmlAccessorType(XmlAccessType.FIELD)
2353 @XmlType(name = "", propOrder = {
2356 public static class StructureState {
2359 protected String value;
2360 @XmlAttribute(name = "visible")
2361 protected Boolean visible;
2362 @XmlAttribute(name = "viewId")
2363 protected String viewId;
2364 @XmlAttribute(name = "alignwithAlignPanel")
2365 protected Boolean alignwithAlignPanel;
2366 @XmlAttribute(name = "colourwithAlignPanel")
2367 protected Boolean colourwithAlignPanel;
2368 @XmlAttribute(name = "colourByJmol")
2369 protected Boolean colourByJmol;
2370 @XmlAttribute(name = "type")
2371 protected String type;
2372 @XmlAttribute(name = "width")
2373 protected Integer width;
2374 @XmlAttribute(name = "height")
2375 protected Integer height;
2376 @XmlAttribute(name = "xpos")
2377 protected Integer xpos;
2378 @XmlAttribute(name = "ypos")
2379 protected Integer ypos;
2382 * Gets the value of the value property.
2385 * possible object is
2389 public String getValue() {
2394 * Sets the value of the value property.
2401 public void setValue(String value) {
2406 * Gets the value of the visible property.
2409 * possible object is
2413 public Boolean isVisible() {
2418 * Sets the value of the visible property.
2425 public void setVisible(Boolean value) {
2426 this.visible = value;
2430 * Gets the value of the viewId property.
2433 * possible object is
2437 public String getViewId() {
2442 * Sets the value of the viewId property.
2449 public void setViewId(String value) {
2450 this.viewId = value;
2454 * Gets the value of the alignwithAlignPanel property.
2457 * possible object is
2461 public boolean isAlignwithAlignPanel() {
2462 if (alignwithAlignPanel == null) {
2465 return alignwithAlignPanel;
2470 * Sets the value of the alignwithAlignPanel property.
2477 public void setAlignwithAlignPanel(Boolean value) {
2478 this.alignwithAlignPanel = value;
2482 * Gets the value of the colourwithAlignPanel property.
2485 * possible object is
2489 public boolean isColourwithAlignPanel() {
2490 if (colourwithAlignPanel == null) {
2493 return colourwithAlignPanel;
2498 * Sets the value of the colourwithAlignPanel property.
2505 public void setColourwithAlignPanel(Boolean value) {
2506 this.colourwithAlignPanel = value;
2510 * Gets the value of the colourByJmol property.
2513 * possible object is
2517 public boolean isColourByJmol() {
2518 if (colourByJmol == null) {
2521 return colourByJmol;
2526 * Sets the value of the colourByJmol property.
2533 public void setColourByJmol(Boolean value) {
2534 this.colourByJmol = value;
2538 * Gets the value of the type property.
2541 * possible object is
2545 public String getType() {
2550 * Sets the value of the type property.
2557 public void setType(String value) {
2562 * Gets the value of the width property.
2565 * possible object is
2569 public Integer getWidth() {
2574 * Sets the value of the width property.
2581 public void setWidth(Integer value) {
2586 * Gets the value of the height property.
2589 * possible object is
2593 public Integer getHeight() {
2598 * Sets the value of the height property.
2605 public void setHeight(Integer value) {
2606 this.height = value;
2610 * Gets the value of the xpos property.
2613 * possible object is
2617 public Integer getXpos() {
2622 * Sets the value of the xpos property.
2629 public void setXpos(Integer value) {
2634 * Gets the value of the ypos property.
2637 * possible object is
2641 public Integer getYpos() {
2646 * Sets the value of the ypos property.
2653 public void setYpos(Integer value) {
2663 * <p>Java class for anonymous complex type.
2665 * <p>The following schema fragment specifies the expected content contained within this class.
2669 * <complexContent>
2670 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2672 * <element name="secondaryStructure" maxOccurs="unbounded">
2674 * <complexContent>
2675 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2676 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2677 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2678 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2679 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2681 * </complexContent>
2685 * <attGroup ref="{www.jalview.org}swingwindow"/>
2686 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2687 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2688 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2689 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2691 * </complexContent>
2697 @XmlAccessorType(XmlAccessType.FIELD)
2698 @XmlType(name = "", propOrder = {
2699 "secondaryStructure"
2701 public static class RnaViewer {
2703 @XmlElement(namespace = "www.jalview.org", required = true)
2704 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2705 @XmlAttribute(name = "title")
2706 protected String title;
2707 @XmlAttribute(name = "viewId")
2708 protected String viewId;
2709 @XmlAttribute(name = "dividerLocation")
2710 protected Integer dividerLocation;
2711 @XmlAttribute(name = "selectedRna")
2712 protected Integer selectedRna;
2713 @XmlAttribute(name = "width")
2714 protected Integer width;
2715 @XmlAttribute(name = "height")
2716 protected Integer height;
2717 @XmlAttribute(name = "xpos")
2718 protected Integer xpos;
2719 @XmlAttribute(name = "ypos")
2720 protected Integer ypos;
2723 * Gets the value of the secondaryStructure property.
2726 * This accessor method returns a reference to the live list,
2727 * not a snapshot. Therefore any modification you make to the
2728 * returned list will be present inside the JAXB object.
2729 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2732 * For example, to add a new item, do as follows:
2734 * getSecondaryStructure().add(newItem);
2739 * Objects of the following type(s) are allowed in the list
2740 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2744 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2745 if (secondaryStructure == null) {
2746 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2748 return this.secondaryStructure;
2752 * Gets the value of the title property.
2755 * possible object is
2759 public String getTitle() {
2764 * Sets the value of the title property.
2771 public void setTitle(String value) {
2776 * Gets the value of the viewId property.
2779 * possible object is
2783 public String getViewId() {
2788 * Sets the value of the viewId property.
2795 public void setViewId(String value) {
2796 this.viewId = value;
2800 * Gets the value of the dividerLocation property.
2803 * possible object is
2807 public Integer getDividerLocation() {
2808 return dividerLocation;
2812 * Sets the value of the dividerLocation property.
2819 public void setDividerLocation(Integer value) {
2820 this.dividerLocation = value;
2824 * Gets the value of the selectedRna property.
2827 * possible object is
2831 public Integer getSelectedRna() {
2836 * Sets the value of the selectedRna property.
2843 public void setSelectedRna(Integer value) {
2844 this.selectedRna = value;
2848 * Gets the value of the width property.
2851 * possible object is
2855 public Integer getWidth() {
2860 * Sets the value of the width property.
2867 public void setWidth(Integer value) {
2872 * Gets the value of the height property.
2875 * possible object is
2879 public Integer getHeight() {
2884 * Sets the value of the height property.
2891 public void setHeight(Integer value) {
2892 this.height = value;
2896 * Gets the value of the xpos property.
2899 * possible object is
2903 public Integer getXpos() {
2908 * Sets the value of the xpos property.
2915 public void setXpos(Integer value) {
2920 * Gets the value of the ypos property.
2923 * possible object is
2927 public Integer getYpos() {
2932 * Sets the value of the ypos property.
2939 public void setYpos(Integer value) {
2945 * <p>Java class for anonymous complex type.
2947 * <p>The following schema fragment specifies the expected content contained within this class.
2951 * <complexContent>
2952 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2953 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2954 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2955 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2956 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2958 * </complexContent>
2964 @XmlAccessorType(XmlAccessType.FIELD)
2966 public static class SecondaryStructure {
2968 @XmlAttribute(name = "title")
2969 protected String title;
2970 @XmlAttribute(name = "annotationId", required = true)
2971 protected String annotationId;
2972 @XmlAttribute(name = "gapped")
2973 protected Boolean gapped;
2974 @XmlAttribute(name = "viewerState")
2975 protected String viewerState;
2978 * Gets the value of the title property.
2981 * possible object is
2985 public String getTitle() {
2990 * Sets the value of the title property.
2997 public void setTitle(String value) {
3002 * Gets the value of the annotationId property.
3005 * possible object is
3009 public String getAnnotationId() {
3010 return annotationId;
3014 * Sets the value of the annotationId property.
3021 public void setAnnotationId(String value) {
3022 this.annotationId = value;
3026 * Gets the value of the gapped property.
3029 * possible object is
3033 public Boolean isGapped() {
3038 * Sets the value of the gapped property.
3045 public void setGapped(Boolean value) {
3046 this.gapped = value;
3050 * Gets the value of the viewerState property.
3053 * possible object is
3057 public String getViewerState() {
3062 * Sets the value of the viewerState property.
3069 public void setViewerState(String value) {
3070 this.viewerState = value;
3081 * <p>Java class for anonymous complex type.
3083 * <p>The following schema fragment specifies the expected content contained within this class.
3087 * <complexContent>
3088 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3090 * <element name="sequencePoint" maxOccurs="unbounded">
3092 * <complexContent>
3093 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3094 * <attGroup ref="{www.jalview.org}position"/>
3095 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3097 * </complexContent>
3100 * <element name="axis" maxOccurs="3" minOccurs="3">
3102 * <complexContent>
3103 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3104 * <attGroup ref="{www.jalview.org}position"/>
3106 * </complexContent>
3109 * <element name="seqPointMin">
3111 * <complexContent>
3112 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3113 * <attGroup ref="{www.jalview.org}position"/>
3115 * </complexContent>
3118 * <element name="seqPointMax">
3120 * <complexContent>
3121 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3122 * <attGroup ref="{www.jalview.org}position"/>
3124 * </complexContent>
3127 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3129 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
3130 * <attGroup ref="{www.jalview.org}swingwindow"/>
3131 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3132 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3133 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3134 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3135 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3136 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3137 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3138 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3139 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3141 * </complexContent>
3147 @XmlAccessorType(XmlAccessType.FIELD)
3148 @XmlType(name = "", propOrder = {
3155 public static class PcaViewer {
3157 @XmlElement(namespace = "www.jalview.org", required = true)
3158 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3159 @XmlElement(namespace = "www.jalview.org", required = true)
3160 protected List<JalviewModel.PcaViewer.Axis> axis;
3161 @XmlElement(namespace = "www.jalview.org", required = true)
3162 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3163 @XmlElement(namespace = "www.jalview.org", required = true)
3164 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3165 @XmlElement(namespace = "www.jalview.org", required = true)
3166 protected PcaDataType pcaData;
3167 @XmlAttribute(name = "title")
3168 protected String title;
3169 @XmlAttribute(name = "scoreModelName")
3170 protected String scoreModelName;
3171 @XmlAttribute(name = "xDim")
3172 protected Integer xDim;
3173 @XmlAttribute(name = "yDim")
3174 protected Integer yDim;
3175 @XmlAttribute(name = "zDim")
3176 protected Integer zDim;
3177 @XmlAttribute(name = "bgColour")
3178 protected Integer bgColour;
3179 @XmlAttribute(name = "scaleFactor")
3180 protected Float scaleFactor;
3181 @XmlAttribute(name = "showLabels")
3182 protected Boolean showLabels;
3183 @XmlAttribute(name = "linkToAllViews")
3184 protected Boolean linkToAllViews;
3185 @XmlAttribute(name = "includeGaps")
3186 protected Boolean includeGaps;
3187 @XmlAttribute(name = "matchGaps")
3188 protected Boolean matchGaps;
3189 @XmlAttribute(name = "includeGappedColumns")
3190 protected Boolean includeGappedColumns;
3191 @XmlAttribute(name = "denominateByShortestLength")
3192 protected Boolean denominateByShortestLength;
3193 @XmlAttribute(name = "width")
3194 protected Integer width;
3195 @XmlAttribute(name = "height")
3196 protected Integer height;
3197 @XmlAttribute(name = "xpos")
3198 protected Integer xpos;
3199 @XmlAttribute(name = "ypos")
3200 protected Integer ypos;
3203 * Gets the value of the sequencePoint property.
3206 * This accessor method returns a reference to the live list,
3207 * not a snapshot. Therefore any modification you make to the
3208 * returned list will be present inside the JAXB object.
3209 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3212 * For example, to add a new item, do as follows:
3214 * getSequencePoint().add(newItem);
3219 * Objects of the following type(s) are allowed in the list
3220 * {@link JalviewModel.PcaViewer.SequencePoint }
3224 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3225 if (sequencePoint == null) {
3226 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3228 return this.sequencePoint;
3232 * Gets the value of the axis property.
3235 * This accessor method returns a reference to the live list,
3236 * not a snapshot. Therefore any modification you make to the
3237 * returned list will be present inside the JAXB object.
3238 * This is why there is not a <CODE>set</CODE> method for the axis property.
3241 * For example, to add a new item, do as follows:
3243 * getAxis().add(newItem);
3248 * Objects of the following type(s) are allowed in the list
3249 * {@link JalviewModel.PcaViewer.Axis }
3253 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3255 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3261 * Gets the value of the seqPointMin property.
3264 * possible object is
3265 * {@link JalviewModel.PcaViewer.SeqPointMin }
3268 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3273 * Sets the value of the seqPointMin property.
3277 * {@link JalviewModel.PcaViewer.SeqPointMin }
3280 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3281 this.seqPointMin = value;
3285 * Gets the value of the seqPointMax property.
3288 * possible object is
3289 * {@link JalviewModel.PcaViewer.SeqPointMax }
3292 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3297 * Sets the value of the seqPointMax property.
3301 * {@link JalviewModel.PcaViewer.SeqPointMax }
3304 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3305 this.seqPointMax = value;
3309 * Gets the value of the pcaData property.
3312 * possible object is
3313 * {@link PcaDataType }
3316 public PcaDataType getPcaData() {
3321 * Sets the value of the pcaData property.
3325 * {@link PcaDataType }
3328 public void setPcaData(PcaDataType value) {
3329 this.pcaData = value;
3333 * Gets the value of the title property.
3336 * possible object is
3340 public String getTitle() {
3345 * Sets the value of the title property.
3352 public void setTitle(String value) {
3357 * Gets the value of the scoreModelName property.
3360 * possible object is
3364 public String getScoreModelName() {
3365 return scoreModelName;
3369 * Sets the value of the scoreModelName property.
3376 public void setScoreModelName(String value) {
3377 this.scoreModelName = value;
3381 * Gets the value of the xDim property.
3384 * possible object is
3388 public Integer getXDim() {
3393 * Sets the value of the xDim property.
3400 public void setXDim(Integer value) {
3405 * Gets the value of the yDim property.
3408 * possible object is
3412 public Integer getYDim() {
3417 * Sets the value of the yDim property.
3424 public void setYDim(Integer value) {
3429 * Gets the value of the zDim property.
3432 * possible object is
3436 public Integer getZDim() {
3441 * Sets the value of the zDim property.
3448 public void setZDim(Integer value) {
3453 * Gets the value of the bgColour property.
3456 * possible object is
3460 public Integer getBgColour() {
3465 * Sets the value of the bgColour property.
3472 public void setBgColour(Integer value) {
3473 this.bgColour = value;
3477 * Gets the value of the scaleFactor property.
3480 * possible object is
3484 public Float getScaleFactor() {
3489 * Sets the value of the scaleFactor property.
3496 public void setScaleFactor(Float value) {
3497 this.scaleFactor = value;
3501 * Gets the value of the showLabels property.
3504 * possible object is
3508 public Boolean isShowLabels() {
3513 * Sets the value of the showLabels property.
3520 public void setShowLabels(Boolean value) {
3521 this.showLabels = value;
3525 * Gets the value of the linkToAllViews property.
3528 * possible object is
3532 public Boolean isLinkToAllViews() {
3533 return linkToAllViews;
3537 * Sets the value of the linkToAllViews property.
3544 public void setLinkToAllViews(Boolean value) {
3545 this.linkToAllViews = value;
3549 * Gets the value of the includeGaps property.
3552 * possible object is
3556 public Boolean isIncludeGaps() {
3561 * Sets the value of the includeGaps property.
3568 public void setIncludeGaps(Boolean value) {
3569 this.includeGaps = value;
3573 * Gets the value of the matchGaps property.
3576 * possible object is
3580 public Boolean isMatchGaps() {
3585 * Sets the value of the matchGaps property.
3592 public void setMatchGaps(Boolean value) {
3593 this.matchGaps = value;
3597 * Gets the value of the includeGappedColumns property.
3600 * possible object is
3604 public Boolean isIncludeGappedColumns() {
3605 return includeGappedColumns;
3609 * Sets the value of the includeGappedColumns property.
3616 public void setIncludeGappedColumns(Boolean value) {
3617 this.includeGappedColumns = value;
3621 * Gets the value of the denominateByShortestLength property.
3624 * possible object is
3628 public Boolean isDenominateByShortestLength() {
3629 return denominateByShortestLength;
3633 * Sets the value of the denominateByShortestLength property.
3640 public void setDenominateByShortestLength(Boolean value) {
3641 this.denominateByShortestLength = value;
3645 * Gets the value of the width property.
3648 * possible object is
3652 public Integer getWidth() {
3657 * Sets the value of the width property.
3664 public void setWidth(Integer value) {
3669 * Gets the value of the height property.
3672 * possible object is
3676 public Integer getHeight() {
3681 * Sets the value of the height property.
3688 public void setHeight(Integer value) {
3689 this.height = value;
3693 * Gets the value of the xpos property.
3696 * possible object is
3700 public Integer getXpos() {
3705 * Sets the value of the xpos property.
3712 public void setXpos(Integer value) {
3717 * Gets the value of the ypos property.
3720 * possible object is
3724 public Integer getYpos() {
3729 * Sets the value of the ypos property.
3736 public void setYpos(Integer value) {
3742 * <p>Java class for anonymous complex type.
3744 * <p>The following schema fragment specifies the expected content contained within this class.
3748 * <complexContent>
3749 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3750 * <attGroup ref="{www.jalview.org}position"/>
3752 * </complexContent>
3758 @XmlAccessorType(XmlAccessType.FIELD)
3760 public static class Axis {
3762 @XmlAttribute(name = "xPos")
3763 protected Float xPos;
3764 @XmlAttribute(name = "yPos")
3765 protected Float yPos;
3766 @XmlAttribute(name = "zPos")
3767 protected Float zPos;
3770 * Gets the value of the xPos property.
3773 * possible object is
3777 public Float getXPos() {
3782 * Sets the value of the xPos property.
3789 public void setXPos(Float value) {
3794 * Gets the value of the yPos property.
3797 * possible object is
3801 public Float getYPos() {
3806 * Sets the value of the yPos property.
3813 public void setYPos(Float value) {
3818 * Gets the value of the zPos property.
3821 * possible object is
3825 public Float getZPos() {
3830 * Sets the value of the zPos property.
3837 public void setZPos(Float value) {
3845 * <p>Java class for anonymous complex type.
3847 * <p>The following schema fragment specifies the expected content contained within this class.
3851 * <complexContent>
3852 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3853 * <attGroup ref="{www.jalview.org}position"/>
3855 * </complexContent>
3861 @XmlAccessorType(XmlAccessType.FIELD)
3863 public static class SeqPointMax {
3865 @XmlAttribute(name = "xPos")
3866 protected Float xPos;
3867 @XmlAttribute(name = "yPos")
3868 protected Float yPos;
3869 @XmlAttribute(name = "zPos")
3870 protected Float zPos;
3873 * Gets the value of the xPos property.
3876 * possible object is
3880 public Float getXPos() {
3885 * Sets the value of the xPos property.
3892 public void setXPos(Float value) {
3897 * Gets the value of the yPos property.
3900 * possible object is
3904 public Float getYPos() {
3909 * Sets the value of the yPos property.
3916 public void setYPos(Float value) {
3921 * Gets the value of the zPos property.
3924 * possible object is
3928 public Float getZPos() {
3933 * Sets the value of the zPos property.
3940 public void setZPos(Float value) {
3948 * <p>Java class for anonymous complex type.
3950 * <p>The following schema fragment specifies the expected content contained within this class.
3954 * <complexContent>
3955 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3956 * <attGroup ref="{www.jalview.org}position"/>
3958 * </complexContent>
3964 @XmlAccessorType(XmlAccessType.FIELD)
3966 public static class SeqPointMin {
3968 @XmlAttribute(name = "xPos")
3969 protected Float xPos;
3970 @XmlAttribute(name = "yPos")
3971 protected Float yPos;
3972 @XmlAttribute(name = "zPos")
3973 protected Float zPos;
3976 * Gets the value of the xPos property.
3979 * possible object is
3983 public Float getXPos() {
3988 * Sets the value of the xPos property.
3995 public void setXPos(Float value) {
4000 * Gets the value of the yPos property.
4003 * possible object is
4007 public Float getYPos() {
4012 * Sets the value of the yPos property.
4019 public void setYPos(Float value) {
4024 * Gets the value of the zPos property.
4027 * possible object is
4031 public Float getZPos() {
4036 * Sets the value of the zPos property.
4043 public void setZPos(Float value) {
4051 * <p>Java class for anonymous complex type.
4053 * <p>The following schema fragment specifies the expected content contained within this class.
4057 * <complexContent>
4058 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4059 * <attGroup ref="{www.jalview.org}position"/>
4060 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4062 * </complexContent>
4068 @XmlAccessorType(XmlAccessType.FIELD)
4070 public static class SequencePoint {
4072 @XmlAttribute(name = "sequenceRef")
4073 protected String sequenceRef;
4074 @XmlAttribute(name = "xPos")
4075 protected Float xPos;
4076 @XmlAttribute(name = "yPos")
4077 protected Float yPos;
4078 @XmlAttribute(name = "zPos")
4079 protected Float zPos;
4082 * Gets the value of the sequenceRef property.
4085 * possible object is
4089 public String getSequenceRef() {
4094 * Sets the value of the sequenceRef property.
4101 public void setSequenceRef(String value) {
4102 this.sequenceRef = value;
4106 * Gets the value of the xPos property.
4109 * possible object is
4113 public Float getXPos() {
4118 * Sets the value of the xPos property.
4125 public void setXPos(Float value) {
4130 * Gets the value of the yPos property.
4133 * possible object is
4137 public Float getYPos() {
4142 * Sets the value of the yPos property.
4149 public void setYPos(Float value) {
4154 * Gets the value of the zPos property.
4157 * possible object is
4161 public Float getZPos() {
4166 * Sets the value of the zPos property.
4173 public void setZPos(Float value) {
4183 * <p>Java class for anonymous complex type.
4185 * <p>The following schema fragment specifies the expected content contained within this class.
4189 * <complexContent>
4190 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4191 * <sequence minOccurs="0">
4192 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4193 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4195 * <attGroup ref="{www.jalview.org}swingwindow"/>
4196 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4197 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4198 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4199 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4200 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4201 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4202 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4203 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4204 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4205 * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4206 * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
4207 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4208 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4210 * </complexContent>
4216 @XmlAccessorType(XmlAccessType.FIELD)
4217 @XmlType(name = "", propOrder = {
4221 public static class Tree {
4223 @XmlElement(namespace = "www.jalview.org")
4224 protected String title;
4225 @XmlElement(namespace = "www.jalview.org")
4226 protected String newick;
4227 @XmlAttribute(name = "fontName")
4228 protected String fontName;
4229 @XmlAttribute(name = "fontSize")
4230 protected Integer fontSize;
4231 @XmlAttribute(name = "fontStyle")
4232 protected Integer fontStyle;
4233 @XmlAttribute(name = "threshold")
4234 protected Float threshold;
4235 @XmlAttribute(name = "showBootstrap")
4236 protected Boolean showBootstrap;
4237 @XmlAttribute(name = "showDistances")
4238 protected Boolean showDistances;
4239 @XmlAttribute(name = "markUnlinked")
4240 protected Boolean markUnlinked;
4241 @XmlAttribute(name = "fitToWindow")
4242 protected Boolean fitToWindow;
4243 @XmlAttribute(name = "currentTree")
4244 protected Boolean currentTree;
4245 @XmlAttribute(name = "columnWise")
4246 protected Boolean columnWise;
4247 @XmlAttribute(name = "columnReference")
4248 protected String columnReference;
4249 @XmlAttribute(name = "id")
4250 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4252 @XmlSchemaType(name = "ID")
4253 protected String id;
4254 @XmlAttribute(name = "linkToAllViews")
4255 protected Boolean linkToAllViews;
4256 @XmlAttribute(name = "width")
4257 protected Integer width;
4258 @XmlAttribute(name = "height")
4259 protected Integer height;
4260 @XmlAttribute(name = "xpos")
4261 protected Integer xpos;
4262 @XmlAttribute(name = "ypos")
4263 protected Integer ypos;
4266 * Gets the value of the title property.
4269 * possible object is
4273 public String getTitle() {
4278 * Sets the value of the title property.
4285 public void setTitle(String value) {
4290 * Gets the value of the newick property.
4293 * possible object is
4297 public String getNewick() {
4302 * Sets the value of the newick property.
4309 public void setNewick(String value) {
4310 this.newick = value;
4314 * Gets the value of the fontName property.
4317 * possible object is
4321 public String getFontName() {
4326 * Sets the value of the fontName property.
4333 public void setFontName(String value) {
4334 this.fontName = value;
4338 * Gets the value of the fontSize property.
4341 * possible object is
4345 public Integer getFontSize() {
4350 * Sets the value of the fontSize property.
4357 public void setFontSize(Integer value) {
4358 this.fontSize = value;
4362 * Gets the value of the fontStyle property.
4365 * possible object is
4369 public Integer getFontStyle() {
4374 * Sets the value of the fontStyle property.
4381 public void setFontStyle(Integer value) {
4382 this.fontStyle = value;
4386 * Gets the value of the threshold property.
4389 * possible object is
4393 public Float getThreshold() {
4398 * Sets the value of the threshold property.
4405 public void setThreshold(Float value) {
4406 this.threshold = value;
4410 * Gets the value of the showBootstrap property.
4413 * possible object is
4417 public Boolean isShowBootstrap() {
4418 return showBootstrap;
4422 * Sets the value of the showBootstrap property.
4429 public void setShowBootstrap(Boolean value) {
4430 this.showBootstrap = value;
4434 * Gets the value of the showDistances property.
4437 * possible object is
4441 public Boolean isShowDistances() {
4442 return showDistances;
4446 * Sets the value of the showDistances property.
4453 public void setShowDistances(Boolean value) {
4454 this.showDistances = value;
4458 * Gets the value of the markUnlinked property.
4461 * possible object is
4465 public Boolean isMarkUnlinked() {
4466 return markUnlinked;
4470 * Sets the value of the markUnlinked property.
4477 public void setMarkUnlinked(Boolean value) {
4478 this.markUnlinked = value;
4482 * Gets the value of the fitToWindow property.
4485 * possible object is
4489 public Boolean isFitToWindow() {
4494 * Sets the value of the fitToWindow property.
4501 public void setFitToWindow(Boolean value) {
4502 this.fitToWindow = value;
4506 * Gets the value of the currentTree property.
4509 * possible object is
4513 public Boolean isCurrentTree() {
4518 * Sets the value of the currentTree property.
4525 public void setCurrentTree(Boolean value) {
4526 this.currentTree = value;
4530 * Gets the value of the columnWise property.
4533 * possible object is
4537 public boolean isColumnWise() {
4538 if (columnWise == null) {
4546 * Sets the value of the columnWise property.
4553 public void setColumnWise(Boolean value) {
4554 this.columnWise = value;
4558 * Gets the value of the columnReference property.
4561 * possible object is
4565 public String getColumnReference() {
4566 return columnReference;
4570 * Sets the value of the columnReference property.
4577 public void setColumnReference(String value) {
4578 this.columnReference = value;
4582 * Gets the value of the id property.
4585 * possible object is
4589 public String getId() {
4594 * Sets the value of the id property.
4601 public void setId(String value) {
4606 * Gets the value of the linkToAllViews property.
4609 * possible object is
4613 public boolean isLinkToAllViews() {
4614 if (linkToAllViews == null) {
4617 return linkToAllViews;
4622 * Sets the value of the linkToAllViews property.
4629 public void setLinkToAllViews(Boolean value) {
4630 this.linkToAllViews = value;
4634 * Gets the value of the width property.
4637 * possible object is
4641 public Integer getWidth() {
4646 * Sets the value of the width property.
4653 public void setWidth(Integer value) {
4658 * Gets the value of the height property.
4661 * possible object is
4665 public Integer getHeight() {
4670 * Sets the value of the height property.
4677 public void setHeight(Integer value) {
4678 this.height = value;
4682 * Gets the value of the xpos property.
4685 * possible object is
4689 public Integer getXpos() {
4694 * Sets the value of the xpos property.
4701 public void setXpos(Integer value) {
4706 * Gets the value of the ypos property.
4709 * possible object is
4713 public Integer getYpos() {
4718 * Sets the value of the ypos property.
4725 public void setYpos(Integer value) {
4733 * <p>Java class for anonymous complex type.
4735 * <p>The following schema fragment specifies the expected content contained within this class.
4739 * <complexContent>
4740 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4742 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4744 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4746 * </complexContent>
4752 @XmlAccessorType(XmlAccessType.FIELD)
4753 @XmlType(name = "", propOrder = {
4756 public static class UserColours {
4758 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4759 protected JalviewUserColours userColourScheme;
4760 @XmlAttribute(name = "id")
4761 protected String id;
4764 * Gets the value of the userColourScheme property.
4767 * possible object is
4768 * {@link JalviewUserColours }
4771 public JalviewUserColours getUserColourScheme() {
4772 return userColourScheme;
4776 * Sets the value of the userColourScheme property.
4780 * {@link JalviewUserColours }
4783 public void setUserColourScheme(JalviewUserColours value) {
4784 this.userColourScheme = value;
4788 * Gets the value of the id property.
4791 * possible object is
4795 public String getId() {
4800 * Sets the value of the id property.
4807 public void setId(String value) {
4815 * <p>Java class for anonymous complex type.
4817 * <p>The following schema fragment specifies the expected content contained within this class.
4821 * <complexContent>
4822 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4824 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4825 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4827 * <complexContent>
4828 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4829 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4830 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4832 * </complexContent>
4835 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4837 * <complexContent>
4838 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4839 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4840 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4841 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4843 * </complexContent>
4846 * <element name="overview" minOccurs="0">
4848 * <complexContent>
4849 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4850 * <attGroup ref="{www.jalview.org}swingwindow"/>
4851 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4852 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4853 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4854 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4855 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4857 * </complexContent>
4861 * <attGroup ref="{www.jalview.org}swingwindow"/>
4862 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4863 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4864 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4865 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4866 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4867 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4868 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4869 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4870 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4871 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4872 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4873 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4874 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4875 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4876 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4877 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4878 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4879 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4880 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4881 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4882 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4883 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4884 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4885 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4886 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4887 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4888 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4889 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4890 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4891 * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
4892 * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
4893 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4894 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4895 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4896 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4897 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4898 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4899 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4900 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4901 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4902 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4903 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4904 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4905 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4906 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4908 * </complexContent>
4914 @XmlAccessorType(XmlAccessType.FIELD)
4915 @XmlType(name = "", propOrder = {
4916 "annotationColours",
4921 public static class Viewport {
4923 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4924 protected AnnotationColourScheme annotationColours;
4925 @XmlElement(namespace = "www.jalview.org")
4926 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4927 @XmlElement(namespace = "www.jalview.org")
4928 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4929 @XmlElement(namespace = "www.jalview.org")
4930 protected JalviewModel.Viewport.Overview overview;
4931 @XmlAttribute(name = "conservationSelected")
4932 protected Boolean conservationSelected;
4933 @XmlAttribute(name = "pidSelected")
4934 protected Boolean pidSelected;
4935 @XmlAttribute(name = "bgColour")
4936 protected String bgColour;
4937 @XmlAttribute(name = "consThreshold")
4938 protected Integer consThreshold;
4939 @XmlAttribute(name = "pidThreshold")
4940 protected Integer pidThreshold;
4941 @XmlAttribute(name = "title")
4942 protected String title;
4943 @XmlAttribute(name = "showFullId")
4944 protected Boolean showFullId;
4945 @XmlAttribute(name = "rightAlignIds")
4946 protected Boolean rightAlignIds;
4947 @XmlAttribute(name = "showText")
4948 protected Boolean showText;
4949 @XmlAttribute(name = "showColourText")
4950 protected Boolean showColourText;
4951 @XmlAttribute(name = "showUnconserved")
4952 protected Boolean showUnconserved;
4953 @XmlAttribute(name = "showBoxes")
4954 protected Boolean showBoxes;
4955 @XmlAttribute(name = "wrapAlignment")
4956 protected Boolean wrapAlignment;
4957 @XmlAttribute(name = "renderGaps")
4958 protected Boolean renderGaps;
4959 @XmlAttribute(name = "showSequenceFeatures")
4960 protected Boolean showSequenceFeatures;
4961 @XmlAttribute(name = "showNPfeatureTooltip")
4962 protected Boolean showNPfeatureTooltip;
4963 @XmlAttribute(name = "showDbRefTooltip")
4964 protected Boolean showDbRefTooltip;
4965 @XmlAttribute(name = "followHighlight")
4966 protected Boolean followHighlight;
4967 @XmlAttribute(name = "followSelection")
4968 protected Boolean followSelection;
4969 @XmlAttribute(name = "showAnnotation")
4970 protected Boolean showAnnotation;
4971 @XmlAttribute(name = "centreColumnLabels")
4972 protected Boolean centreColumnLabels;
4973 @XmlAttribute(name = "showGroupConservation")
4974 protected Boolean showGroupConservation;
4975 @XmlAttribute(name = "showGroupConsensus")
4976 protected Boolean showGroupConsensus;
4977 @XmlAttribute(name = "showConsensusHistogram")
4978 protected Boolean showConsensusHistogram;
4979 @XmlAttribute(name = "showSequenceLogo")
4980 protected Boolean showSequenceLogo;
4981 @XmlAttribute(name = "normaliseSequenceLogo")
4982 protected Boolean normaliseSequenceLogo;
4983 @XmlAttribute(name = "ignoreGapsinConsensus")
4984 protected Boolean ignoreGapsinConsensus;
4985 @XmlAttribute(name = "startRes")
4986 protected Integer startRes;
4987 @XmlAttribute(name = "startSeq")
4988 protected Integer startSeq;
4989 @XmlAttribute(name = "charWidth")
4990 protected Integer charWidth;
4991 @XmlAttribute(name = "charHeight")
4992 protected Integer charHeight;
4993 @XmlAttribute(name = "fontName")
4994 protected String fontName;
4995 @XmlAttribute(name = "fontSize")
4996 protected Integer fontSize;
4997 @XmlAttribute(name = "fontStyle")
4998 protected Integer fontStyle;
4999 @XmlAttribute(name = "scaleProteinAsCdna")
5000 protected Boolean scaleProteinAsCdna;
5001 @XmlAttribute(name = "viewName")
5002 protected String viewName;
5003 @XmlAttribute(name = "sequenceSetId")
5004 protected String sequenceSetId;
5005 @XmlAttribute(name = "gatheredViews")
5006 protected Boolean gatheredViews;
5007 @XmlAttribute(name = "textCol1")
5008 protected Integer textCol1;
5009 @XmlAttribute(name = "textCol2")
5010 protected Integer textCol2;
5011 @XmlAttribute(name = "textColThreshold")
5012 protected Integer textColThreshold;
5013 @XmlAttribute(name = "id")
5014 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5016 @XmlSchemaType(name = "ID")
5017 protected String id;
5018 @XmlAttribute(name = "complementId")
5019 protected String complementId;
5020 @XmlAttribute(name = "showComplementFeatures")
5021 protected Boolean showComplementFeatures;
5022 @XmlAttribute(name = "showComplementFeaturesOnTop")
5023 protected Boolean showComplementFeaturesOnTop;
5024 @XmlAttribute(name = "width")
5025 protected Integer width;
5026 @XmlAttribute(name = "height")
5027 protected Integer height;
5028 @XmlAttribute(name = "xpos")
5029 protected Integer xpos;
5030 @XmlAttribute(name = "ypos")
5031 protected Integer ypos;
5034 * Gets the value of the annotationColours property.
5037 * possible object is
5038 * {@link AnnotationColourScheme }
5041 public AnnotationColourScheme getAnnotationColours() {
5042 return annotationColours;
5046 * Sets the value of the annotationColours property.
5050 * {@link AnnotationColourScheme }
5053 public void setAnnotationColours(AnnotationColourScheme value) {
5054 this.annotationColours = value;
5058 * Gets the value of the hiddenColumns property.
5061 * This accessor method returns a reference to the live list,
5062 * not a snapshot. Therefore any modification you make to the
5063 * returned list will be present inside the JAXB object.
5064 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
5067 * For example, to add a new item, do as follows:
5069 * getHiddenColumns().add(newItem);
5074 * Objects of the following type(s) are allowed in the list
5075 * {@link JalviewModel.Viewport.HiddenColumns }
5079 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5080 if (hiddenColumns == null) {
5081 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5083 return this.hiddenColumns;
5087 * Gets the value of the calcIdParam property.
5090 * This accessor method returns a reference to the live list,
5091 * not a snapshot. Therefore any modification you make to the
5092 * returned list will be present inside the JAXB object.
5093 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5096 * For example, to add a new item, do as follows:
5098 * getCalcIdParam().add(newItem);
5103 * Objects of the following type(s) are allowed in the list
5104 * {@link JalviewModel.Viewport.CalcIdParam }
5108 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5109 if (calcIdParam == null) {
5110 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5112 return this.calcIdParam;
5116 * Gets the value of the overview property.
5119 * possible object is
5120 * {@link JalviewModel.Viewport.Overview }
5123 public JalviewModel.Viewport.Overview getOverview() {
5128 * Sets the value of the overview property.
5132 * {@link JalviewModel.Viewport.Overview }
5135 public void setOverview(JalviewModel.Viewport.Overview value) {
5136 this.overview = value;
5140 * Gets the value of the conservationSelected property.
5143 * possible object is
5147 public Boolean isConservationSelected() {
5148 return conservationSelected;
5152 * Sets the value of the conservationSelected property.
5159 public void setConservationSelected(Boolean value) {
5160 this.conservationSelected = value;
5164 * Gets the value of the pidSelected property.
5167 * possible object is
5171 public Boolean isPidSelected() {
5176 * Sets the value of the pidSelected property.
5183 public void setPidSelected(Boolean value) {
5184 this.pidSelected = value;
5188 * Gets the value of the bgColour property.
5191 * possible object is
5195 public String getBgColour() {
5200 * Sets the value of the bgColour property.
5207 public void setBgColour(String value) {
5208 this.bgColour = value;
5212 * Gets the value of the consThreshold property.
5215 * possible object is
5219 public Integer getConsThreshold() {
5220 return consThreshold;
5224 * Sets the value of the consThreshold property.
5231 public void setConsThreshold(Integer value) {
5232 this.consThreshold = value;
5236 * Gets the value of the pidThreshold property.
5239 * possible object is
5243 public Integer getPidThreshold() {
5244 return pidThreshold;
5248 * Sets the value of the pidThreshold property.
5255 public void setPidThreshold(Integer value) {
5256 this.pidThreshold = value;
5260 * Gets the value of the title property.
5263 * possible object is
5267 public String getTitle() {
5272 * Sets the value of the title property.
5279 public void setTitle(String value) {
5284 * Gets the value of the showFullId property.
5287 * possible object is
5291 public Boolean isShowFullId() {
5296 * Sets the value of the showFullId property.
5303 public void setShowFullId(Boolean value) {
5304 this.showFullId = value;
5308 * Gets the value of the rightAlignIds property.
5311 * possible object is
5315 public Boolean isRightAlignIds() {
5316 return rightAlignIds;
5320 * Sets the value of the rightAlignIds property.
5327 public void setRightAlignIds(Boolean value) {
5328 this.rightAlignIds = value;
5332 * Gets the value of the showText property.
5335 * possible object is
5339 public Boolean isShowText() {
5344 * Sets the value of the showText property.
5351 public void setShowText(Boolean value) {
5352 this.showText = value;
5356 * Gets the value of the showColourText property.
5359 * possible object is
5363 public Boolean isShowColourText() {
5364 return showColourText;
5368 * Sets the value of the showColourText property.
5375 public void setShowColourText(Boolean value) {
5376 this.showColourText = value;
5380 * Gets the value of the showUnconserved property.
5383 * possible object is
5387 public boolean isShowUnconserved() {
5388 if (showUnconserved == null) {
5391 return showUnconserved;
5396 * Sets the value of the showUnconserved property.
5403 public void setShowUnconserved(Boolean value) {
5404 this.showUnconserved = value;
5408 * Gets the value of the showBoxes property.
5411 * possible object is
5415 public Boolean isShowBoxes() {
5420 * Sets the value of the showBoxes property.
5427 public void setShowBoxes(Boolean value) {
5428 this.showBoxes = value;
5432 * Gets the value of the wrapAlignment property.
5435 * possible object is
5439 public Boolean isWrapAlignment() {
5440 return wrapAlignment;
5444 * Sets the value of the wrapAlignment property.
5451 public void setWrapAlignment(Boolean value) {
5452 this.wrapAlignment = value;
5456 * Gets the value of the renderGaps property.
5459 * possible object is
5463 public Boolean isRenderGaps() {
5468 * Sets the value of the renderGaps property.
5475 public void setRenderGaps(Boolean value) {
5476 this.renderGaps = value;
5480 * Gets the value of the showSequenceFeatures property.
5483 * possible object is
5487 public Boolean isShowSequenceFeatures() {
5488 return showSequenceFeatures;
5492 * Sets the value of the showSequenceFeatures property.
5499 public void setShowSequenceFeatures(Boolean value) {
5500 this.showSequenceFeatures = value;
5504 * Gets the value of the showNPfeatureTooltip property.
5507 * possible object is
5511 public Boolean isShowNPfeatureTooltip() {
5512 return showNPfeatureTooltip;
5516 * Sets the value of the showNPfeatureTooltip property.
5523 public void setShowNPfeatureTooltip(Boolean value) {
5524 this.showNPfeatureTooltip = value;
5528 * Gets the value of the showDbRefTooltip property.
5531 * possible object is
5535 public Boolean isShowDbRefTooltip() {
5536 return showDbRefTooltip;
5540 * Sets the value of the showDbRefTooltip property.
5547 public void setShowDbRefTooltip(Boolean value) {
5548 this.showDbRefTooltip = value;
5552 * Gets the value of the followHighlight property.
5555 * possible object is
5559 public boolean isFollowHighlight() {
5560 if (followHighlight == null) {
5563 return followHighlight;
5568 * Sets the value of the followHighlight property.
5575 public void setFollowHighlight(Boolean value) {
5576 this.followHighlight = value;
5580 * Gets the value of the followSelection property.
5583 * possible object is
5587 public boolean isFollowSelection() {
5588 if (followSelection == null) {
5591 return followSelection;
5596 * Sets the value of the followSelection property.
5603 public void setFollowSelection(Boolean value) {
5604 this.followSelection = value;
5608 * Gets the value of the showAnnotation property.
5611 * possible object is
5615 public Boolean isShowAnnotation() {
5616 return showAnnotation;
5620 * Sets the value of the showAnnotation property.
5627 public void setShowAnnotation(Boolean value) {
5628 this.showAnnotation = value;
5632 * Gets the value of the centreColumnLabels property.
5635 * possible object is
5639 public boolean isCentreColumnLabels() {
5640 if (centreColumnLabels == null) {
5643 return centreColumnLabels;
5648 * Sets the value of the centreColumnLabels property.
5655 public void setCentreColumnLabels(Boolean value) {
5656 this.centreColumnLabels = value;
5660 * Gets the value of the showGroupConservation property.
5663 * possible object is
5667 public boolean isShowGroupConservation() {
5668 if (showGroupConservation == null) {
5671 return showGroupConservation;
5676 * Sets the value of the showGroupConservation property.
5683 public void setShowGroupConservation(Boolean value) {
5684 this.showGroupConservation = value;
5688 * Gets the value of the showGroupConsensus property.
5691 * possible object is
5695 public boolean isShowGroupConsensus() {
5696 if (showGroupConsensus == null) {
5699 return showGroupConsensus;
5704 * Sets the value of the showGroupConsensus property.
5711 public void setShowGroupConsensus(Boolean value) {
5712 this.showGroupConsensus = value;
5716 * Gets the value of the showConsensusHistogram property.
5719 * possible object is
5723 public boolean isShowConsensusHistogram() {
5724 if (showConsensusHistogram == null) {
5727 return showConsensusHistogram;
5732 * Sets the value of the showConsensusHistogram property.
5739 public void setShowConsensusHistogram(Boolean value) {
5740 this.showConsensusHistogram = value;
5744 * Gets the value of the showSequenceLogo property.
5747 * possible object is
5751 public boolean isShowSequenceLogo() {
5752 if (showSequenceLogo == null) {
5755 return showSequenceLogo;
5760 * Sets the value of the showSequenceLogo property.
5767 public void setShowSequenceLogo(Boolean value) {
5768 this.showSequenceLogo = value;
5772 * Gets the value of the normaliseSequenceLogo property.
5775 * possible object is
5779 public boolean isNormaliseSequenceLogo() {
5780 if (normaliseSequenceLogo == null) {
5783 return normaliseSequenceLogo;
5788 * Sets the value of the normaliseSequenceLogo property.
5795 public void setNormaliseSequenceLogo(Boolean value) {
5796 this.normaliseSequenceLogo = value;
5800 * Gets the value of the ignoreGapsinConsensus property.
5803 * possible object is
5807 public boolean isIgnoreGapsinConsensus() {
5808 if (ignoreGapsinConsensus == null) {
5811 return ignoreGapsinConsensus;
5816 * Sets the value of the ignoreGapsinConsensus property.
5823 public void setIgnoreGapsinConsensus(Boolean value) {
5824 this.ignoreGapsinConsensus = value;
5828 * Gets the value of the startRes property.
5831 * possible object is
5835 public Integer getStartRes() {
5840 * Sets the value of the startRes property.
5847 public void setStartRes(Integer value) {
5848 this.startRes = value;
5852 * Gets the value of the startSeq property.
5855 * possible object is
5859 public Integer getStartSeq() {
5864 * Sets the value of the startSeq property.
5871 public void setStartSeq(Integer value) {
5872 this.startSeq = value;
5876 * Gets the value of the charWidth property.
5879 * possible object is
5883 public Integer getCharWidth() {
5888 * Sets the value of the charWidth property.
5895 public void setCharWidth(Integer value) {
5896 this.charWidth = value;
5900 * Gets the value of the charHeight property.
5903 * possible object is
5907 public Integer getCharHeight() {
5912 * Sets the value of the charHeight property.
5919 public void setCharHeight(Integer value) {
5920 this.charHeight = value;
5924 * Gets the value of the fontName property.
5927 * possible object is
5931 public String getFontName() {
5936 * Sets the value of the fontName property.
5943 public void setFontName(String value) {
5944 this.fontName = value;
5948 * Gets the value of the fontSize property.
5951 * possible object is
5955 public Integer getFontSize() {
5960 * Sets the value of the fontSize property.
5967 public void setFontSize(Integer value) {
5968 this.fontSize = value;
5972 * Gets the value of the fontStyle property.
5975 * possible object is
5979 public Integer getFontStyle() {
5984 * Sets the value of the fontStyle property.
5991 public void setFontStyle(Integer value) {
5992 this.fontStyle = value;
5996 * Gets the value of the scaleProteinAsCdna property.
5999 * possible object is
6003 public boolean isScaleProteinAsCdna() {
6004 if (scaleProteinAsCdna == null) {
6007 return scaleProteinAsCdna;
6012 * Sets the value of the scaleProteinAsCdna property.
6019 public void setScaleProteinAsCdna(Boolean value) {
6020 this.scaleProteinAsCdna = value;
6024 * Gets the value of the viewName property.
6027 * possible object is
6031 public String getViewName() {
6036 * Sets the value of the viewName property.
6043 public void setViewName(String value) {
6044 this.viewName = value;
6048 * Gets the value of the sequenceSetId property.
6051 * possible object is
6055 public String getSequenceSetId() {
6056 return sequenceSetId;
6060 * Sets the value of the sequenceSetId property.
6067 public void setSequenceSetId(String value) {
6068 this.sequenceSetId = value;
6072 * Gets the value of the gatheredViews property.
6075 * possible object is
6079 public Boolean isGatheredViews() {
6080 return gatheredViews;
6084 * Sets the value of the gatheredViews property.
6091 public void setGatheredViews(Boolean value) {
6092 this.gatheredViews = value;
6096 * Gets the value of the textCol1 property.
6099 * possible object is
6103 public Integer getTextCol1() {
6108 * Sets the value of the textCol1 property.
6115 public void setTextCol1(Integer value) {
6116 this.textCol1 = value;
6120 * Gets the value of the textCol2 property.
6123 * possible object is
6127 public Integer getTextCol2() {
6132 * Sets the value of the textCol2 property.
6139 public void setTextCol2(Integer value) {
6140 this.textCol2 = value;
6144 * Gets the value of the textColThreshold property.
6147 * possible object is
6151 public Integer getTextColThreshold() {
6152 return textColThreshold;
6156 * Sets the value of the textColThreshold property.
6163 public void setTextColThreshold(Integer value) {
6164 this.textColThreshold = value;
6168 * Gets the value of the id property.
6171 * possible object is
6175 public String getId() {
6180 * Sets the value of the id property.
6187 public void setId(String value) {
6192 * Gets the value of the complementId property.
6195 * possible object is
6199 public String getComplementId() {
6200 return complementId;
6204 * Sets the value of the complementId property.
6211 public void setComplementId(String value) {
6212 this.complementId = value;
6216 * Gets the value of the showComplementFeatures property.
6219 * possible object is
6223 public boolean isShowComplementFeatures() {
6224 if (showComplementFeatures == null) {
6227 return showComplementFeatures;
6232 * Sets the value of the showComplementFeatures property.
6239 public void setShowComplementFeatures(Boolean value) {
6240 this.showComplementFeatures = value;
6244 * Gets the value of the showComplementFeaturesOnTop property.
6247 * possible object is
6251 public boolean isShowComplementFeaturesOnTop() {
6252 if (showComplementFeaturesOnTop == null) {
6255 return showComplementFeaturesOnTop;
6260 * Sets the value of the showComplementFeaturesOnTop property.
6267 public void setShowComplementFeaturesOnTop(Boolean value) {
6268 this.showComplementFeaturesOnTop = value;
6272 * Gets the value of the width property.
6275 * possible object is
6279 public Integer getWidth() {
6284 * Sets the value of the width property.
6291 public void setWidth(Integer value) {
6296 * Gets the value of the height property.
6299 * possible object is
6303 public Integer getHeight() {
6308 * Sets the value of the height property.
6315 public void setHeight(Integer value) {
6316 this.height = value;
6320 * Gets the value of the xpos property.
6323 * possible object is
6327 public Integer getXpos() {
6332 * Sets the value of the xpos property.
6339 public void setXpos(Integer value) {
6344 * Gets the value of the ypos property.
6347 * possible object is
6351 public Integer getYpos() {
6356 * Sets the value of the ypos property.
6363 public void setYpos(Integer value) {
6369 * <p>Java class for anonymous complex type.
6371 * <p>The following schema fragment specifies the expected content contained within this class.
6375 * <complexContent>
6376 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6377 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6378 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6379 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6381 * </complexContent>
6387 @XmlAccessorType(XmlAccessType.FIELD)
6389 public static class CalcIdParam
6390 extends WebServiceParameterSet
6393 @XmlAttribute(name = "calcId", required = true)
6394 protected String calcId;
6395 @XmlAttribute(name = "needsUpdate")
6396 protected Boolean needsUpdate;
6397 @XmlAttribute(name = "autoUpdate", required = true)
6398 protected boolean autoUpdate;
6401 * Gets the value of the calcId property.
6404 * possible object is
6408 public String getCalcId() {
6413 * Sets the value of the calcId property.
6420 public void setCalcId(String value) {
6421 this.calcId = value;
6425 * Gets the value of the needsUpdate property.
6428 * possible object is
6432 public boolean isNeedsUpdate() {
6433 if (needsUpdate == null) {
6441 * Sets the value of the needsUpdate property.
6448 public void setNeedsUpdate(Boolean value) {
6449 this.needsUpdate = value;
6453 * Gets the value of the autoUpdate property.
6456 public boolean isAutoUpdate() {
6461 * Sets the value of the autoUpdate property.
6464 public void setAutoUpdate(boolean value) {
6465 this.autoUpdate = value;
6472 * <p>Java class for anonymous complex type.
6474 * <p>The following schema fragment specifies the expected content contained within this class.
6478 * <complexContent>
6479 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6480 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6481 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6483 * </complexContent>
6489 @XmlAccessorType(XmlAccessType.FIELD)
6491 public static class HiddenColumns {
6493 @XmlAttribute(name = "start")
6494 protected Integer start;
6495 @XmlAttribute(name = "end")
6496 protected Integer end;
6499 * Gets the value of the start property.
6502 * possible object is
6506 public Integer getStart() {
6511 * Sets the value of the start property.
6518 public void setStart(Integer value) {
6523 * Gets the value of the end property.
6526 * possible object is
6530 public Integer getEnd() {
6535 * Sets the value of the end property.
6542 public void setEnd(Integer value) {
6550 * <p>Java class for anonymous complex type.
6552 * <p>The following schema fragment specifies the expected content contained within this class.
6556 * <complexContent>
6557 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6558 * <attGroup ref="{www.jalview.org}swingwindow"/>
6559 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6560 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6561 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6562 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6563 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
6565 * </complexContent>
6571 @XmlAccessorType(XmlAccessType.FIELD)
6573 public static class Overview {
6575 @XmlAttribute(name = "showHidden")
6576 protected Boolean showHidden;
6577 @XmlAttribute(name = "residueColour")
6578 protected Integer residueColour;
6579 @XmlAttribute(name = "gapColour")
6580 protected Integer gapColour;
6581 @XmlAttribute(name = "hiddenColour")
6582 protected Integer hiddenColour;
6583 @XmlAttribute(name = "title")
6584 protected String title;
6585 @XmlAttribute(name = "width")
6586 protected Integer width;
6587 @XmlAttribute(name = "height")
6588 protected Integer height;
6589 @XmlAttribute(name = "xpos")
6590 protected Integer xpos;
6591 @XmlAttribute(name = "ypos")
6592 protected Integer ypos;
6595 * Gets the value of the showHidden property.
6598 * possible object is
6602 public Boolean isShowHidden() {
6607 * Sets the value of the showHidden property.
6614 public void setShowHidden(Boolean value) {
6615 this.showHidden = value;
6619 * Gets the value of the residueColour property.
6622 * possible object is
6626 public Integer getResidueColour() {
6627 return residueColour;
6631 * Sets the value of the residueColour property.
6638 public void setResidueColour(Integer value) {
6639 this.residueColour = value;
6643 * Gets the value of the gapColour property.
6646 * possible object is
6650 public Integer getGapColour() {
6655 * Sets the value of the gapColour property.
6662 public void setGapColour(Integer value) {
6663 this.gapColour = value;
6667 * Gets the value of the hiddenColour property.
6670 * possible object is
6674 public Integer getHiddenColour() {
6675 return hiddenColour;
6679 * Sets the value of the hiddenColour property.
6686 public void setHiddenColour(Integer value) {
6687 this.hiddenColour = value;
6691 * Gets the value of the title property.
6694 * possible object is
6698 public String getTitle() {
6703 * Sets the value of the title property.
6710 public void setTitle(String value) {
6715 * Gets the value of the width property.
6718 * possible object is
6722 public Integer getWidth() {
6727 * Sets the value of the width property.
6734 public void setWidth(Integer value) {
6739 * Gets the value of the height property.
6742 * possible object is
6746 public Integer getHeight() {
6751 * Sets the value of the height property.
6758 public void setHeight(Integer value) {
6759 this.height = value;
6763 * Gets the value of the xpos property.
6766 * possible object is
6770 public Integer getXpos() {
6775 * Sets the value of the xpos property.
6782 public void setXpos(Integer value) {
6787 * Gets the value of the ypos property.
6790 * possible object is
6794 public Integer getYpos() {
6799 * Sets the value of the ypos property.
6806 public void setYpos(Integer value) {