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: 2019.07.10 at 12:10:00 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>
99 * <element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
101 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
102 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
104 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
105 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
106 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
108 * </complexContent>
111 * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
113 * <complexContent>
114 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
116 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
117 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
119 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
120 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
121 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
122 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
123 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
125 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
126 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
129 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
130 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
131 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
132 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
133 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
135 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
137 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
139 * </complexContent>
142 * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
144 * <complexContent>
145 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
147 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
148 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
150 * <complexContent>
151 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
152 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
153 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
155 * </complexContent>
158 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
160 * <complexContent>
161 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
162 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
163 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
164 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
166 * </complexContent>
170 * <attGroup ref="{www.jalview.org}swingwindow"/>
171 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
172 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
173 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
174 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
175 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
176 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
177 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
178 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
179 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
180 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
181 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
182 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
183 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
184 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
187 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
188 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
189 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
190 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
191 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
192 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
193 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
194 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
195 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
196 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
197 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
198 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
199 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
200 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
201 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
202 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
203 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
204 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
205 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
206 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
207 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
208 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
209 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
210 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
211 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
212 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
213 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
215 * </complexContent>
218 * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
220 * <complexContent>
221 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
223 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
225 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
227 * </complexContent>
230 * <element name="tree" maxOccurs="unbounded" minOccurs="0">
232 * <complexContent>
233 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
234 * <sequence minOccurs="0">
235 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
236 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
238 * <attGroup ref="{www.jalview.org}swingwindow"/>
239 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
240 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
241 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
242 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
243 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
244 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
245 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
246 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
247 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
248 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
249 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
251 * </complexContent>
254 * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
256 * <complexContent>
257 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
259 * <element name="sequencePoint" maxOccurs="unbounded">
261 * <complexContent>
262 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
263 * <attGroup ref="{www.jalview.org}position"/>
264 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
266 * </complexContent>
269 * <element name="axis" maxOccurs="3" minOccurs="3">
271 * <complexContent>
272 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
273 * <attGroup ref="{www.jalview.org}position"/>
275 * </complexContent>
278 * <element name="seqPointMin">
280 * <complexContent>
281 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
282 * <attGroup ref="{www.jalview.org}position"/>
284 * </complexContent>
287 * <element name="seqPointMax">
289 * <complexContent>
290 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
291 * <attGroup ref="{www.jalview.org}position"/>
293 * </complexContent>
296 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
298 * <attGroup ref="{www.jalview.org}swingwindow"/>
299 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
300 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
301 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
302 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
303 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
304 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
305 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
306 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
307 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
308 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
310 * </complexContent>
313 * <element name="FeatureSettings" minOccurs="0">
315 * <complexContent>
316 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
318 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
320 * <complexContent>
321 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
323 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
324 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
326 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
327 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
328 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
329 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
330 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
331 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
332 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
333 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
334 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
335 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
336 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
337 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
339 * </complexContent>
342 * <element name="group" maxOccurs="unbounded" minOccurs="0">
344 * <complexContent>
345 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
346 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
347 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
349 * </complexContent>
354 * </complexContent>
360 * </complexContent>
366 @XmlAccessorType(XmlAccessType.FIELD)
367 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
379 public class JalviewModel {
381 @XmlElement(required = true)
382 @XmlSchemaType(name = "dateTime")
383 protected XMLGregorianCalendar creationDate;
384 @XmlElement(required = true)
385 protected String version;
386 @XmlElement(required = true)
387 protected VAMSAS vamsasModel;
388 @XmlElement(name = "JSeq")
389 protected List<JalviewModel.JSeq> jSeq;
390 @XmlElement(name = "JGroup")
391 protected List<JalviewModel.JGroup> jGroup;
392 @XmlElement(name = "Viewport")
393 protected List<JalviewModel.Viewport> viewport;
394 @XmlElement(name = "UserColours")
395 protected List<JalviewModel.UserColours> userColours;
396 protected List<JalviewModel.Tree> tree;
397 @XmlElement(name = "PcaViewer")
398 protected List<JalviewModel.PcaViewer> pcaViewer;
399 @XmlElement(name = "FeatureSettings")
400 protected JalviewModel.FeatureSettings featureSettings;
403 * Gets the value of the creationDate property.
407 * {@link XMLGregorianCalendar }
410 public XMLGregorianCalendar getCreationDate() {
415 * Sets the value of the creationDate property.
419 * {@link XMLGregorianCalendar }
422 public void setCreationDate(XMLGregorianCalendar value) {
423 this.creationDate = value;
427 * Gets the value of the version property.
434 public String getVersion() {
439 * Sets the value of the version property.
446 public void setVersion(String value) {
447 this.version = value;
451 * Gets the value of the vamsasModel property.
458 public VAMSAS getVamsasModel() {
463 * Sets the value of the vamsasModel property.
470 public void setVamsasModel(VAMSAS value) {
471 this.vamsasModel = value;
475 * Gets the value of the jSeq property.
478 * This accessor method returns a reference to the live list,
479 * not a snapshot. Therefore any modification you make to the
480 * returned list will be present inside the JAXB object.
481 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
484 * For example, to add a new item, do as follows:
486 * getJSeq().add(newItem);
491 * Objects of the following type(s) are allowed in the list
492 * {@link JalviewModel.JSeq }
496 public List<JalviewModel.JSeq> getJSeq() {
498 jSeq = new ArrayList<JalviewModel.JSeq>();
504 * Gets the value of the jGroup property.
507 * This accessor method returns a reference to the live list,
508 * not a snapshot. Therefore any modification you make to the
509 * returned list will be present inside the JAXB object.
510 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
513 * For example, to add a new item, do as follows:
515 * getJGroup().add(newItem);
520 * Objects of the following type(s) are allowed in the list
521 * {@link JalviewModel.JGroup }
525 public List<JalviewModel.JGroup> getJGroup() {
526 if (jGroup == null) {
527 jGroup = new ArrayList<JalviewModel.JGroup>();
533 * Gets the value of the viewport property.
536 * This accessor method returns a reference to the live list,
537 * not a snapshot. Therefore any modification you make to the
538 * returned list will be present inside the JAXB object.
539 * This is why there is not a <CODE>set</CODE> method for the viewport property.
542 * For example, to add a new item, do as follows:
544 * getViewport().add(newItem);
549 * Objects of the following type(s) are allowed in the list
550 * {@link JalviewModel.Viewport }
554 public List<JalviewModel.Viewport> getViewport() {
555 if (viewport == null) {
556 viewport = new ArrayList<JalviewModel.Viewport>();
558 return this.viewport;
562 * Gets the value of the userColours property.
565 * This accessor method returns a reference to the live list,
566 * not a snapshot. Therefore any modification you make to the
567 * returned list will be present inside the JAXB object.
568 * This is why there is not a <CODE>set</CODE> method for the userColours property.
571 * For example, to add a new item, do as follows:
573 * getUserColours().add(newItem);
578 * Objects of the following type(s) are allowed in the list
579 * {@link JalviewModel.UserColours }
583 public List<JalviewModel.UserColours> getUserColours() {
584 if (userColours == null) {
585 userColours = new ArrayList<JalviewModel.UserColours>();
587 return this.userColours;
591 * Gets the value of the tree property.
594 * This accessor method returns a reference to the live list,
595 * not a snapshot. Therefore any modification you make to the
596 * returned list will be present inside the JAXB object.
597 * This is why there is not a <CODE>set</CODE> method for the tree property.
600 * For example, to add a new item, do as follows:
602 * getTree().add(newItem);
607 * Objects of the following type(s) are allowed in the list
608 * {@link JalviewModel.Tree }
612 public List<JalviewModel.Tree> getTree() {
614 tree = new ArrayList<JalviewModel.Tree>();
620 * Gets the value of the pcaViewer property.
623 * This accessor method returns a reference to the live list,
624 * not a snapshot. Therefore any modification you make to the
625 * returned list will be present inside the JAXB object.
626 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
629 * For example, to add a new item, do as follows:
631 * getPcaViewer().add(newItem);
636 * Objects of the following type(s) are allowed in the list
637 * {@link JalviewModel.PcaViewer }
641 public List<JalviewModel.PcaViewer> getPcaViewer() {
642 if (pcaViewer == null) {
643 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
645 return this.pcaViewer;
649 * Gets the value of the featureSettings property.
653 * {@link JalviewModel.FeatureSettings }
656 public JalviewModel.FeatureSettings getFeatureSettings() {
657 return featureSettings;
661 * Sets the value of the featureSettings property.
665 * {@link JalviewModel.FeatureSettings }
668 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
669 this.featureSettings = value;
674 * <p>Java class for anonymous complex type.
676 * <p>The following schema fragment specifies the expected content contained within this class.
680 * <complexContent>
681 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
683 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
685 * <complexContent>
686 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
688 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
689 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
691 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
692 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
693 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
694 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
695 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
696 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
697 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
698 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
699 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
700 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
701 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
702 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
704 * </complexContent>
707 * <element name="group" maxOccurs="unbounded" minOccurs="0">
709 * <complexContent>
710 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
711 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
712 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
714 * </complexContent>
719 * </complexContent>
725 @XmlAccessorType(XmlAccessType.FIELD)
726 @XmlType(name = "", propOrder = {
730 public static class FeatureSettings {
732 @XmlElement(namespace = "www.jalview.org")
733 protected List<JalviewModel.FeatureSettings.Setting> setting;
734 @XmlElement(namespace = "www.jalview.org")
735 protected List<JalviewModel.FeatureSettings.Group> group;
738 * Gets the value of the setting property.
741 * This accessor method returns a reference to the live list,
742 * not a snapshot. Therefore any modification you make to the
743 * returned list will be present inside the JAXB object.
744 * This is why there is not a <CODE>set</CODE> method for the setting property.
747 * For example, to add a new item, do as follows:
749 * getSetting().add(newItem);
754 * Objects of the following type(s) are allowed in the list
755 * {@link JalviewModel.FeatureSettings.Setting }
759 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
760 if (setting == null) {
761 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
767 * Gets the value of the group property.
770 * This accessor method returns a reference to the live list,
771 * not a snapshot. Therefore any modification you make to the
772 * returned list will be present inside the JAXB object.
773 * This is why there is not a <CODE>set</CODE> method for the group property.
776 * For example, to add a new item, do as follows:
778 * getGroup().add(newItem);
783 * Objects of the following type(s) are allowed in the list
784 * {@link JalviewModel.FeatureSettings.Group }
788 public List<JalviewModel.FeatureSettings.Group> getGroup() {
790 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
797 * <p>Java class for anonymous complex type.
799 * <p>The following schema fragment specifies the expected content contained within this class.
803 * <complexContent>
804 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
805 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
806 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
808 * </complexContent>
814 @XmlAccessorType(XmlAccessType.FIELD)
816 public static class Group {
818 @XmlAttribute(name = "name", required = true)
819 protected String name;
820 @XmlAttribute(name = "display", required = true)
821 protected boolean display;
824 * Gets the value of the name property.
831 public String getName() {
836 * Sets the value of the name property.
843 public void setName(String value) {
848 * Gets the value of the display property.
851 public boolean isDisplay() {
856 * Sets the value of the display property.
859 public void setDisplay(boolean value) {
860 this.display = value;
867 * <p>Java class for anonymous complex type.
869 * <p>The following schema fragment specifies the expected content contained within this class.
873 * <complexContent>
874 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
876 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
877 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
879 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
880 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
881 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
882 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
883 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
884 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
885 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
886 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
887 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
888 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
889 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
890 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
892 * </complexContent>
898 @XmlAccessorType(XmlAccessType.FIELD)
899 @XmlType(name = "", propOrder = {
903 public static class Setting {
905 @XmlElement(namespace = "www.jalview.org")
906 protected List<String> attributeName;
907 @XmlElement(namespace = "www.jalview.org")
908 protected FeatureMatcherSet matcherSet;
909 @XmlAttribute(name = "type", required = true)
910 protected String type;
911 @XmlAttribute(name = "colour", required = true)
912 protected int colour;
913 @XmlAttribute(name = "display", required = true)
914 protected boolean display;
915 @XmlAttribute(name = "order")
916 protected Float order;
917 @XmlAttribute(name = "mincolour")
918 protected Integer mincolour;
919 @XmlAttribute(name = "noValueColour")
920 protected NoValueColour noValueColour;
921 @XmlAttribute(name = "threshold")
922 protected Float threshold;
923 @XmlAttribute(name = "threshstate")
924 protected Integer threshstate;
925 @XmlAttribute(name = "max")
927 @XmlAttribute(name = "min")
929 @XmlAttribute(name = "colourByLabel")
930 protected Boolean colourByLabel;
931 @XmlAttribute(name = "autoScale")
932 protected Boolean autoScale;
935 * Gets the value of the attributeName property.
938 * This accessor method returns a reference to the live list,
939 * not a snapshot. Therefore any modification you make to the
940 * returned list will be present inside the JAXB object.
941 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
944 * For example, to add a new item, do as follows:
946 * getAttributeName().add(newItem);
951 * Objects of the following type(s) are allowed in the list
956 public List<String> getAttributeName() {
957 if (attributeName == null) {
958 attributeName = new ArrayList<String>();
960 return this.attributeName;
964 * Gets the value of the matcherSet property.
968 * {@link FeatureMatcherSet }
971 public FeatureMatcherSet getMatcherSet() {
976 * Sets the value of the matcherSet property.
980 * {@link FeatureMatcherSet }
983 public void setMatcherSet(FeatureMatcherSet value) {
984 this.matcherSet = value;
988 * Gets the value of the type property.
995 public String getType() {
1000 * Sets the value of the type property.
1007 public void setType(String value) {
1012 * Gets the value of the colour property.
1015 public int getColour() {
1020 * Sets the value of the colour property.
1023 public void setColour(int value) {
1024 this.colour = value;
1028 * Gets the value of the display property.
1031 public boolean isDisplay() {
1036 * Sets the value of the display property.
1039 public void setDisplay(boolean value) {
1040 this.display = value;
1044 * Gets the value of the order property.
1047 * possible object is
1051 public Float getOrder() {
1056 * Sets the value of the order property.
1063 public void setOrder(Float value) {
1068 * Gets the value of the mincolour property.
1071 * possible object is
1075 public Integer getMincolour() {
1080 * Sets the value of the mincolour property.
1087 public void setMincolour(Integer value) {
1088 this.mincolour = value;
1092 * Gets the value of the noValueColour property.
1095 * possible object is
1096 * {@link NoValueColour }
1099 public NoValueColour getNoValueColour() {
1100 if (noValueColour == null) {
1101 return NoValueColour.MIN;
1103 return noValueColour;
1108 * Sets the value of the noValueColour property.
1112 * {@link NoValueColour }
1115 public void setNoValueColour(NoValueColour value) {
1116 this.noValueColour = value;
1120 * Gets the value of the threshold property.
1123 * possible object is
1127 public Float getThreshold() {
1132 * Sets the value of the threshold property.
1139 public void setThreshold(Float value) {
1140 this.threshold = value;
1144 * Gets the value of the threshstate property.
1147 * possible object is
1151 public Integer getThreshstate() {
1156 * Sets the value of the threshstate property.
1163 public void setThreshstate(Integer value) {
1164 this.threshstate = value;
1168 * Gets the value of the max property.
1171 * possible object is
1175 public Float getMax() {
1180 * Sets the value of the max property.
1187 public void setMax(Float value) {
1192 * Gets the value of the min property.
1195 * possible object is
1199 public Float getMin() {
1204 * Sets the value of the min property.
1211 public void setMin(Float value) {
1216 * Gets the value of the colourByLabel property.
1219 * possible object is
1223 public Boolean isColourByLabel() {
1224 return colourByLabel;
1228 * Sets the value of the colourByLabel property.
1235 public void setColourByLabel(Boolean value) {
1236 this.colourByLabel = value;
1240 * Gets the value of the autoScale property.
1243 * possible object is
1247 public Boolean isAutoScale() {
1252 * Sets the value of the autoScale property.
1259 public void setAutoScale(Boolean value) {
1260 this.autoScale = value;
1269 * <p>Java class for anonymous complex type.
1271 * <p>The following schema fragment specifies the expected content contained within this class.
1275 * <complexContent>
1276 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1278 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1279 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1281 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1282 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1283 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1284 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1285 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1286 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1287 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1288 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1289 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1290 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1291 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1292 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1293 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1294 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1295 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1296 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1297 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1298 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1299 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1301 * </complexContent>
1307 @XmlAccessorType(XmlAccessType.FIELD)
1308 @XmlType(name = "", propOrder = {
1312 public static class JGroup {
1314 @XmlElement(namespace = "www.jalview.org", required = true)
1315 protected List<String> seq;
1316 @XmlElement(namespace = "www.jalview.org")
1317 protected AnnotationColourScheme annotationColours;
1318 @XmlAttribute(name = "start")
1319 protected Integer start;
1320 @XmlAttribute(name = "end")
1321 protected Integer end;
1322 @XmlAttribute(name = "name")
1323 protected String name;
1324 @XmlAttribute(name = "colour")
1325 protected String colour;
1326 @XmlAttribute(name = "consThreshold")
1327 protected Integer consThreshold;
1328 @XmlAttribute(name = "pidThreshold")
1329 protected Integer pidThreshold;
1330 @XmlAttribute(name = "outlineColour")
1331 protected Integer outlineColour;
1332 @XmlAttribute(name = "displayBoxes")
1333 protected Boolean displayBoxes;
1334 @XmlAttribute(name = "displayText")
1335 protected Boolean displayText;
1336 @XmlAttribute(name = "colourText")
1337 protected Boolean colourText;
1338 @XmlAttribute(name = "textCol1")
1339 protected Integer textCol1;
1340 @XmlAttribute(name = "textCol2")
1341 protected Integer textCol2;
1342 @XmlAttribute(name = "textColThreshold")
1343 protected Integer textColThreshold;
1344 @XmlAttribute(name = "showUnconserved")
1345 protected Boolean showUnconserved;
1346 @XmlAttribute(name = "ignoreGapsinConsensus")
1347 protected Boolean ignoreGapsinConsensus;
1348 @XmlAttribute(name = "showConsensusHistogram")
1349 protected Boolean showConsensusHistogram;
1350 @XmlAttribute(name = "showSequenceLogo")
1351 protected Boolean showSequenceLogo;
1352 @XmlAttribute(name = "normaliseSequenceLogo")
1353 protected Boolean normaliseSequenceLogo;
1354 @XmlAttribute(name = "id")
1355 protected String id;
1358 * Gets the value of the seq property.
1361 * This accessor method returns a reference to the live list,
1362 * not a snapshot. Therefore any modification you make to the
1363 * returned list will be present inside the JAXB object.
1364 * This is why there is not a <CODE>set</CODE> method for the seq property.
1367 * For example, to add a new item, do as follows:
1369 * getSeq().add(newItem);
1374 * Objects of the following type(s) are allowed in the list
1379 public List<String> getSeq() {
1381 seq = new ArrayList<String>();
1387 * Gets the value of the annotationColours property.
1390 * possible object is
1391 * {@link AnnotationColourScheme }
1394 public AnnotationColourScheme getAnnotationColours() {
1395 return annotationColours;
1399 * Sets the value of the annotationColours property.
1403 * {@link AnnotationColourScheme }
1406 public void setAnnotationColours(AnnotationColourScheme value) {
1407 this.annotationColours = value;
1411 * Gets the value of the start property.
1414 * possible object is
1418 public Integer getStart() {
1423 * Sets the value of the start property.
1430 public void setStart(Integer value) {
1435 * Gets the value of the end property.
1438 * possible object is
1442 public Integer getEnd() {
1447 * Sets the value of the end property.
1454 public void setEnd(Integer value) {
1459 * Gets the value of the name property.
1462 * possible object is
1466 public String getName() {
1471 * Sets the value of the name property.
1478 public void setName(String value) {
1483 * Gets the value of the colour property.
1486 * possible object is
1490 public String getColour() {
1495 * Sets the value of the colour property.
1502 public void setColour(String value) {
1503 this.colour = value;
1507 * Gets the value of the consThreshold property.
1510 * possible object is
1514 public Integer getConsThreshold() {
1515 return consThreshold;
1519 * Sets the value of the consThreshold property.
1526 public void setConsThreshold(Integer value) {
1527 this.consThreshold = value;
1531 * Gets the value of the pidThreshold property.
1534 * possible object is
1538 public Integer getPidThreshold() {
1539 return pidThreshold;
1543 * Sets the value of the pidThreshold property.
1550 public void setPidThreshold(Integer value) {
1551 this.pidThreshold = value;
1555 * Gets the value of the outlineColour property.
1558 * possible object is
1562 public Integer getOutlineColour() {
1563 return outlineColour;
1567 * Sets the value of the outlineColour property.
1574 public void setOutlineColour(Integer value) {
1575 this.outlineColour = value;
1579 * Gets the value of the displayBoxes property.
1582 * possible object is
1586 public Boolean isDisplayBoxes() {
1587 return displayBoxes;
1591 * Sets the value of the displayBoxes property.
1598 public void setDisplayBoxes(Boolean value) {
1599 this.displayBoxes = value;
1603 * Gets the value of the displayText property.
1606 * possible object is
1610 public Boolean isDisplayText() {
1615 * Sets the value of the displayText property.
1622 public void setDisplayText(Boolean value) {
1623 this.displayText = value;
1627 * Gets the value of the colourText property.
1630 * possible object is
1634 public Boolean isColourText() {
1639 * Sets the value of the colourText property.
1646 public void setColourText(Boolean value) {
1647 this.colourText = value;
1651 * Gets the value of the textCol1 property.
1654 * possible object is
1658 public Integer getTextCol1() {
1663 * Sets the value of the textCol1 property.
1670 public void setTextCol1(Integer value) {
1671 this.textCol1 = value;
1675 * Gets the value of the textCol2 property.
1678 * possible object is
1682 public Integer getTextCol2() {
1687 * Sets the value of the textCol2 property.
1694 public void setTextCol2(Integer value) {
1695 this.textCol2 = value;
1699 * Gets the value of the textColThreshold property.
1702 * possible object is
1706 public Integer getTextColThreshold() {
1707 return textColThreshold;
1711 * Sets the value of the textColThreshold property.
1718 public void setTextColThreshold(Integer value) {
1719 this.textColThreshold = value;
1723 * Gets the value of the showUnconserved property.
1726 * possible object is
1730 public Boolean isShowUnconserved() {
1731 return showUnconserved;
1735 * Sets the value of the showUnconserved property.
1742 public void setShowUnconserved(Boolean value) {
1743 this.showUnconserved = value;
1747 * Gets the value of the ignoreGapsinConsensus property.
1750 * possible object is
1754 public boolean isIgnoreGapsinConsensus() {
1755 if (ignoreGapsinConsensus == null) {
1758 return ignoreGapsinConsensus;
1763 * Sets the value of the ignoreGapsinConsensus property.
1770 public void setIgnoreGapsinConsensus(Boolean value) {
1771 this.ignoreGapsinConsensus = value;
1775 * Gets the value of the showConsensusHistogram property.
1778 * possible object is
1782 public boolean isShowConsensusHistogram() {
1783 if (showConsensusHistogram == null) {
1786 return showConsensusHistogram;
1791 * Sets the value of the showConsensusHistogram property.
1798 public void setShowConsensusHistogram(Boolean value) {
1799 this.showConsensusHistogram = value;
1803 * Gets the value of the showSequenceLogo property.
1806 * possible object is
1810 public boolean isShowSequenceLogo() {
1811 if (showSequenceLogo == null) {
1814 return showSequenceLogo;
1819 * Sets the value of the showSequenceLogo property.
1826 public void setShowSequenceLogo(Boolean value) {
1827 this.showSequenceLogo = value;
1831 * Gets the value of the normaliseSequenceLogo property.
1834 * possible object is
1838 public boolean isNormaliseSequenceLogo() {
1839 if (normaliseSequenceLogo == null) {
1842 return normaliseSequenceLogo;
1847 * Sets the value of the normaliseSequenceLogo property.
1854 public void setNormaliseSequenceLogo(Boolean value) {
1855 this.normaliseSequenceLogo = value;
1859 * Gets the value of the id property.
1862 * possible object is
1866 public String getId() {
1871 * Sets the value of the id property.
1878 public void setId(String value) {
1886 * <p>Java class for anonymous complex type.
1888 * <p>The following schema fragment specifies the expected content contained within this class.
1892 * <complexContent>
1893 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1895 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1896 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1898 * <complexContent>
1899 * <extension base="{www.jalview.org}pdbentry">
1901 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1903 * <simpleContent>
1904 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1905 * <attGroup ref="{www.jalview.org}swingwindow"/>
1906 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1907 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1908 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1909 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1910 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1911 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1913 * </simpleContent>
1918 * </complexContent>
1921 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1922 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1924 * <complexContent>
1925 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1927 * <element name="secondaryStructure" maxOccurs="unbounded">
1929 * <complexContent>
1930 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1931 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1932 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1933 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1934 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1936 * </complexContent>
1940 * <attGroup ref="{www.jalview.org}swingwindow"/>
1941 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1942 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1943 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1944 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1946 * </complexContent>
1949 * <element name="hmmerProfile" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
1951 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1952 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1953 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1954 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1955 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1956 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1958 * </complexContent>
1964 @XmlAccessorType(XmlAccessType.FIELD)
1965 @XmlType(name = "", propOrder = {
1972 public static class JSeq {
1974 @XmlElement(namespace = "www.jalview.org")
1975 protected List<Feature> features;
1976 @XmlElement(namespace = "www.jalview.org")
1977 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1978 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1979 protected List<Integer> hiddenSequences;
1980 @XmlElement(namespace = "www.jalview.org")
1981 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1982 @XmlElement(namespace = "www.jalview.org")
1983 protected String hmmerProfile;
1984 @XmlAttribute(name = "colour")
1985 protected Integer colour;
1986 @XmlAttribute(name = "start", required = true)
1987 protected int start;
1988 @XmlAttribute(name = "end", required = true)
1990 @XmlAttribute(name = "id", required = true)
1991 protected String id;
1992 @XmlAttribute(name = "hidden")
1993 protected Boolean hidden;
1994 @XmlAttribute(name = "viewreference")
1995 protected Boolean viewreference;
1998 * Gets the value of the features property.
2001 * This accessor method returns a reference to the live list,
2002 * not a snapshot. Therefore any modification you make to the
2003 * returned list will be present inside the JAXB object.
2004 * This is why there is not a <CODE>set</CODE> method for the features property.
2007 * For example, to add a new item, do as follows:
2009 * getFeatures().add(newItem);
2014 * Objects of the following type(s) are allowed in the list
2019 public List<Feature> getFeatures() {
2020 if (features == null) {
2021 features = new ArrayList<Feature>();
2023 return this.features;
2027 * Gets the value of the pdbids property.
2030 * This accessor method returns a reference to the live list,
2031 * not a snapshot. Therefore any modification you make to the
2032 * returned list will be present inside the JAXB object.
2033 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2036 * For example, to add a new item, do as follows:
2038 * getPdbids().add(newItem);
2043 * Objects of the following type(s) are allowed in the list
2044 * {@link JalviewModel.JSeq.Pdbids }
2048 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2049 if (pdbids == null) {
2050 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2056 * Gets the value of the hiddenSequences property.
2059 * This accessor method returns a reference to the live list,
2060 * not a snapshot. Therefore any modification you make to the
2061 * returned list will be present inside the JAXB object.
2062 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2065 * For example, to add a new item, do as follows:
2067 * getHiddenSequences().add(newItem);
2072 * Objects of the following type(s) are allowed in the list
2077 public List<Integer> getHiddenSequences() {
2078 if (hiddenSequences == null) {
2079 hiddenSequences = new ArrayList<Integer>();
2081 return this.hiddenSequences;
2085 * Gets the value of the rnaViewer property.
2088 * This accessor method returns a reference to the live list,
2089 * not a snapshot. Therefore any modification you make to the
2090 * returned list will be present inside the JAXB object.
2091 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2094 * For example, to add a new item, do as follows:
2096 * getRnaViewer().add(newItem);
2101 * Objects of the following type(s) are allowed in the list
2102 * {@link JalviewModel.JSeq.RnaViewer }
2106 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2107 if (rnaViewer == null) {
2108 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2110 return this.rnaViewer;
2114 * Gets the value of the hmmerProfile property.
2117 * possible object is
2121 public String getHmmerProfile() {
2122 return hmmerProfile;
2126 * Sets the value of the hmmerProfile property.
2133 public void setHmmerProfile(String value) {
2134 this.hmmerProfile = value;
2138 * Gets the value of the colour property.
2141 * possible object is
2145 public Integer getColour() {
2150 * Sets the value of the colour property.
2157 public void setColour(Integer value) {
2158 this.colour = value;
2162 * Gets the value of the start property.
2165 public int getStart() {
2170 * Sets the value of the start property.
2173 public void setStart(int value) {
2178 * Gets the value of the end property.
2181 public int getEnd() {
2186 * Sets the value of the end property.
2189 public void setEnd(int value) {
2194 * Gets the value of the id property.
2197 * possible object is
2201 public String getId() {
2206 * Sets the value of the id property.
2213 public void setId(String value) {
2218 * Gets the value of the hidden property.
2221 * possible object is
2225 public Boolean isHidden() {
2230 * Sets the value of the hidden property.
2237 public void setHidden(Boolean value) {
2238 this.hidden = value;
2242 * Gets the value of the viewreference property.
2245 * possible object is
2249 public Boolean isViewreference() {
2250 return viewreference;
2254 * Sets the value of the viewreference property.
2261 public void setViewreference(Boolean value) {
2262 this.viewreference = value;
2267 * <p>Java class for anonymous complex type.
2269 * <p>The following schema fragment specifies the expected content contained within this class.
2273 * <complexContent>
2274 * <extension base="{www.jalview.org}pdbentry">
2276 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2278 * <simpleContent>
2279 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2280 * <attGroup ref="{www.jalview.org}swingwindow"/>
2281 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2282 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2283 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2284 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2285 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2286 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2288 * </simpleContent>
2293 * </complexContent>
2299 @XmlAccessorType(XmlAccessType.FIELD)
2300 @XmlType(name = "", propOrder = {
2303 public static class Pdbids
2307 @XmlElement(namespace = "www.jalview.org")
2308 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2311 * Gets the value of the structureState property.
2314 * This accessor method returns a reference to the live list,
2315 * not a snapshot. Therefore any modification you make to the
2316 * returned list will be present inside the JAXB object.
2317 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2320 * For example, to add a new item, do as follows:
2322 * getStructureState().add(newItem);
2327 * Objects of the following type(s) are allowed in the list
2328 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2332 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2333 if (structureState == null) {
2334 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2336 return this.structureState;
2341 * <p>Java class for anonymous complex type.
2343 * <p>The following schema fragment specifies the expected content contained within this class.
2347 * <simpleContent>
2348 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2349 * <attGroup ref="{www.jalview.org}swingwindow"/>
2350 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2351 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2352 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2353 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2354 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2355 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2357 * </simpleContent>
2363 @XmlAccessorType(XmlAccessType.FIELD)
2364 @XmlType(name = "", propOrder = {
2367 public static class StructureState {
2370 protected String value;
2371 @XmlAttribute(name = "visible")
2372 protected Boolean visible;
2373 @XmlAttribute(name = "viewId")
2374 protected String viewId;
2375 @XmlAttribute(name = "alignwithAlignPanel")
2376 protected Boolean alignwithAlignPanel;
2377 @XmlAttribute(name = "colourwithAlignPanel")
2378 protected Boolean colourwithAlignPanel;
2379 @XmlAttribute(name = "colourByJmol")
2380 protected Boolean colourByJmol;
2381 @XmlAttribute(name = "type")
2382 protected String type;
2383 @XmlAttribute(name = "width")
2384 protected Integer width;
2385 @XmlAttribute(name = "height")
2386 protected Integer height;
2387 @XmlAttribute(name = "xpos")
2388 protected Integer xpos;
2389 @XmlAttribute(name = "ypos")
2390 protected Integer ypos;
2393 * Gets the value of the value property.
2396 * possible object is
2400 public String getValue() {
2405 * Sets the value of the value property.
2412 public void setValue(String value) {
2417 * Gets the value of the visible property.
2420 * possible object is
2424 public Boolean isVisible() {
2429 * Sets the value of the visible property.
2436 public void setVisible(Boolean value) {
2437 this.visible = value;
2441 * Gets the value of the viewId property.
2444 * possible object is
2448 public String getViewId() {
2453 * Sets the value of the viewId property.
2460 public void setViewId(String value) {
2461 this.viewId = value;
2465 * Gets the value of the alignwithAlignPanel property.
2468 * possible object is
2472 public boolean isAlignwithAlignPanel() {
2473 if (alignwithAlignPanel == null) {
2476 return alignwithAlignPanel;
2481 * Sets the value of the alignwithAlignPanel property.
2488 public void setAlignwithAlignPanel(Boolean value) {
2489 this.alignwithAlignPanel = value;
2493 * Gets the value of the colourwithAlignPanel property.
2496 * possible object is
2500 public boolean isColourwithAlignPanel() {
2501 if (colourwithAlignPanel == null) {
2504 return colourwithAlignPanel;
2509 * Sets the value of the colourwithAlignPanel property.
2516 public void setColourwithAlignPanel(Boolean value) {
2517 this.colourwithAlignPanel = value;
2521 * Gets the value of the colourByJmol property.
2524 * possible object is
2528 public boolean isColourByJmol() {
2529 if (colourByJmol == null) {
2532 return colourByJmol;
2537 * Sets the value of the colourByJmol property.
2544 public void setColourByJmol(Boolean value) {
2545 this.colourByJmol = value;
2549 * Gets the value of the type property.
2552 * possible object is
2556 public String getType() {
2561 * Sets the value of the type property.
2568 public void setType(String value) {
2573 * Gets the value of the width property.
2576 * possible object is
2580 public Integer getWidth() {
2585 * Sets the value of the width property.
2592 public void setWidth(Integer value) {
2597 * Gets the value of the height property.
2600 * possible object is
2604 public Integer getHeight() {
2609 * Sets the value of the height property.
2616 public void setHeight(Integer value) {
2617 this.height = value;
2621 * Gets the value of the xpos property.
2624 * possible object is
2628 public Integer getXpos() {
2633 * Sets the value of the xpos property.
2640 public void setXpos(Integer value) {
2645 * Gets the value of the ypos property.
2648 * possible object is
2652 public Integer getYpos() {
2657 * Sets the value of the ypos property.
2664 public void setYpos(Integer value) {
2674 * <p>Java class for anonymous complex type.
2676 * <p>The following schema fragment specifies the expected content contained within this class.
2680 * <complexContent>
2681 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2683 * <element name="secondaryStructure" maxOccurs="unbounded">
2685 * <complexContent>
2686 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2687 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2688 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2689 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2690 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2692 * </complexContent>
2696 * <attGroup ref="{www.jalview.org}swingwindow"/>
2697 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2698 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2699 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2700 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2702 * </complexContent>
2708 @XmlAccessorType(XmlAccessType.FIELD)
2709 @XmlType(name = "", propOrder = {
2710 "secondaryStructure"
2712 public static class RnaViewer {
2714 @XmlElement(namespace = "www.jalview.org", required = true)
2715 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2716 @XmlAttribute(name = "title")
2717 protected String title;
2718 @XmlAttribute(name = "viewId")
2719 protected String viewId;
2720 @XmlAttribute(name = "dividerLocation")
2721 protected Integer dividerLocation;
2722 @XmlAttribute(name = "selectedRna")
2723 protected Integer selectedRna;
2724 @XmlAttribute(name = "width")
2725 protected Integer width;
2726 @XmlAttribute(name = "height")
2727 protected Integer height;
2728 @XmlAttribute(name = "xpos")
2729 protected Integer xpos;
2730 @XmlAttribute(name = "ypos")
2731 protected Integer ypos;
2734 * Gets the value of the secondaryStructure property.
2737 * This accessor method returns a reference to the live list,
2738 * not a snapshot. Therefore any modification you make to the
2739 * returned list will be present inside the JAXB object.
2740 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2743 * For example, to add a new item, do as follows:
2745 * getSecondaryStructure().add(newItem);
2750 * Objects of the following type(s) are allowed in the list
2751 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2755 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2756 if (secondaryStructure == null) {
2757 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2759 return this.secondaryStructure;
2763 * Gets the value of the title property.
2766 * possible object is
2770 public String getTitle() {
2775 * Sets the value of the title property.
2782 public void setTitle(String value) {
2787 * Gets the value of the viewId property.
2790 * possible object is
2794 public String getViewId() {
2799 * Sets the value of the viewId property.
2806 public void setViewId(String value) {
2807 this.viewId = value;
2811 * Gets the value of the dividerLocation property.
2814 * possible object is
2818 public Integer getDividerLocation() {
2819 return dividerLocation;
2823 * Sets the value of the dividerLocation property.
2830 public void setDividerLocation(Integer value) {
2831 this.dividerLocation = value;
2835 * Gets the value of the selectedRna property.
2838 * possible object is
2842 public Integer getSelectedRna() {
2847 * Sets the value of the selectedRna property.
2854 public void setSelectedRna(Integer value) {
2855 this.selectedRna = value;
2859 * Gets the value of the width property.
2862 * possible object is
2866 public Integer getWidth() {
2871 * Sets the value of the width property.
2878 public void setWidth(Integer value) {
2883 * Gets the value of the height property.
2886 * possible object is
2890 public Integer getHeight() {
2895 * Sets the value of the height property.
2902 public void setHeight(Integer value) {
2903 this.height = value;
2907 * Gets the value of the xpos property.
2910 * possible object is
2914 public Integer getXpos() {
2919 * Sets the value of the xpos property.
2926 public void setXpos(Integer value) {
2931 * Gets the value of the ypos property.
2934 * possible object is
2938 public Integer getYpos() {
2943 * Sets the value of the ypos property.
2950 public void setYpos(Integer value) {
2956 * <p>Java class for anonymous complex type.
2958 * <p>The following schema fragment specifies the expected content contained within this class.
2962 * <complexContent>
2963 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2964 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2965 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2966 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2967 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2969 * </complexContent>
2975 @XmlAccessorType(XmlAccessType.FIELD)
2977 public static class SecondaryStructure {
2979 @XmlAttribute(name = "title")
2980 protected String title;
2981 @XmlAttribute(name = "annotationId", required = true)
2982 protected String annotationId;
2983 @XmlAttribute(name = "gapped")
2984 protected Boolean gapped;
2985 @XmlAttribute(name = "viewerState")
2986 protected String viewerState;
2989 * Gets the value of the title property.
2992 * possible object is
2996 public String getTitle() {
3001 * Sets the value of the title property.
3008 public void setTitle(String value) {
3013 * Gets the value of the annotationId property.
3016 * possible object is
3020 public String getAnnotationId() {
3021 return annotationId;
3025 * Sets the value of the annotationId property.
3032 public void setAnnotationId(String value) {
3033 this.annotationId = value;
3037 * Gets the value of the gapped property.
3040 * possible object is
3044 public Boolean isGapped() {
3049 * Sets the value of the gapped property.
3056 public void setGapped(Boolean value) {
3057 this.gapped = value;
3061 * Gets the value of the viewerState property.
3064 * possible object is
3068 public String getViewerState() {
3073 * Sets the value of the viewerState property.
3080 public void setViewerState(String value) {
3081 this.viewerState = value;
3092 * <p>Java class for anonymous complex type.
3094 * <p>The following schema fragment specifies the expected content contained within this class.
3098 * <complexContent>
3099 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3101 * <element name="sequencePoint" maxOccurs="unbounded">
3103 * <complexContent>
3104 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3105 * <attGroup ref="{www.jalview.org}position"/>
3106 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3108 * </complexContent>
3111 * <element name="axis" maxOccurs="3" minOccurs="3">
3113 * <complexContent>
3114 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3115 * <attGroup ref="{www.jalview.org}position"/>
3117 * </complexContent>
3120 * <element name="seqPointMin">
3122 * <complexContent>
3123 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3124 * <attGroup ref="{www.jalview.org}position"/>
3126 * </complexContent>
3129 * <element name="seqPointMax">
3131 * <complexContent>
3132 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3133 * <attGroup ref="{www.jalview.org}position"/>
3135 * </complexContent>
3138 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3140 * <attGroup ref="{www.jalview.org}swingwindow"/>
3141 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
3142 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3143 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3144 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3145 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3146 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3147 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3148 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3149 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3150 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3152 * </complexContent>
3158 @XmlAccessorType(XmlAccessType.FIELD)
3159 @XmlType(name = "", propOrder = {
3166 public static class PcaViewer {
3168 @XmlElement(namespace = "www.jalview.org", required = true)
3169 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3170 @XmlElement(namespace = "www.jalview.org", required = true)
3171 protected List<JalviewModel.PcaViewer.Axis> axis;
3172 @XmlElement(namespace = "www.jalview.org", required = true)
3173 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3174 @XmlElement(namespace = "www.jalview.org", required = true)
3175 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3176 @XmlElement(namespace = "www.jalview.org", required = true)
3177 protected PcaDataType pcaData;
3178 @XmlAttribute(name = "title")
3179 protected String title;
3180 @XmlAttribute(name = "scoreModelName")
3181 protected String scoreModelName;
3182 @XmlAttribute(name = "xDim")
3183 protected Integer xDim;
3184 @XmlAttribute(name = "yDim")
3185 protected Integer yDim;
3186 @XmlAttribute(name = "zDim")
3187 protected Integer zDim;
3188 @XmlAttribute(name = "bgColour")
3189 protected Integer bgColour;
3190 @XmlAttribute(name = "scaleFactor")
3191 protected Float scaleFactor;
3192 @XmlAttribute(name = "showLabels")
3193 protected Boolean showLabels;
3194 @XmlAttribute(name = "linkToAllViews")
3195 protected Boolean linkToAllViews;
3196 @XmlAttribute(name = "width")
3197 protected Integer width;
3198 @XmlAttribute(name = "height")
3199 protected Integer height;
3200 @XmlAttribute(name = "xpos")
3201 protected Integer xpos;
3202 @XmlAttribute(name = "ypos")
3203 protected Integer ypos;
3204 @XmlAttribute(name = "includeGaps")
3205 protected Boolean includeGaps;
3206 @XmlAttribute(name = "matchGaps")
3207 protected Boolean matchGaps;
3208 @XmlAttribute(name = "includeGappedColumns")
3209 protected Boolean includeGappedColumns;
3210 @XmlAttribute(name = "denominateByShortestLength")
3211 protected Boolean denominateByShortestLength;
3214 * Gets the value of the sequencePoint property.
3217 * This accessor method returns a reference to the live list,
3218 * not a snapshot. Therefore any modification you make to the
3219 * returned list will be present inside the JAXB object.
3220 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3223 * For example, to add a new item, do as follows:
3225 * getSequencePoint().add(newItem);
3230 * Objects of the following type(s) are allowed in the list
3231 * {@link JalviewModel.PcaViewer.SequencePoint }
3235 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3236 if (sequencePoint == null) {
3237 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3239 return this.sequencePoint;
3243 * Gets the value of the axis property.
3246 * This accessor method returns a reference to the live list,
3247 * not a snapshot. Therefore any modification you make to the
3248 * returned list will be present inside the JAXB object.
3249 * This is why there is not a <CODE>set</CODE> method for the axis property.
3252 * For example, to add a new item, do as follows:
3254 * getAxis().add(newItem);
3259 * Objects of the following type(s) are allowed in the list
3260 * {@link JalviewModel.PcaViewer.Axis }
3264 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3266 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3272 * Gets the value of the seqPointMin property.
3275 * possible object is
3276 * {@link JalviewModel.PcaViewer.SeqPointMin }
3279 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3284 * Sets the value of the seqPointMin property.
3288 * {@link JalviewModel.PcaViewer.SeqPointMin }
3291 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3292 this.seqPointMin = value;
3296 * Gets the value of the seqPointMax property.
3299 * possible object is
3300 * {@link JalviewModel.PcaViewer.SeqPointMax }
3303 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3308 * Sets the value of the seqPointMax property.
3312 * {@link JalviewModel.PcaViewer.SeqPointMax }
3315 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3316 this.seqPointMax = value;
3320 * Gets the value of the pcaData property.
3323 * possible object is
3324 * {@link PcaDataType }
3327 public PcaDataType getPcaData() {
3332 * Sets the value of the pcaData property.
3336 * {@link PcaDataType }
3339 public void setPcaData(PcaDataType value) {
3340 this.pcaData = value;
3344 * Gets the value of the title property.
3347 * possible object is
3351 public String getTitle() {
3356 * Sets the value of the title property.
3363 public void setTitle(String value) {
3368 * Gets the value of the scoreModelName property.
3371 * possible object is
3375 public String getScoreModelName() {
3376 return scoreModelName;
3380 * Sets the value of the scoreModelName property.
3387 public void setScoreModelName(String value) {
3388 this.scoreModelName = value;
3392 * Gets the value of the xDim property.
3395 * possible object is
3399 public Integer getXDim() {
3404 * Sets the value of the xDim property.
3411 public void setXDim(Integer value) {
3416 * Gets the value of the yDim property.
3419 * possible object is
3423 public Integer getYDim() {
3428 * Sets the value of the yDim property.
3435 public void setYDim(Integer value) {
3440 * Gets the value of the zDim property.
3443 * possible object is
3447 public Integer getZDim() {
3452 * Sets the value of the zDim property.
3459 public void setZDim(Integer value) {
3464 * Gets the value of the bgColour property.
3467 * possible object is
3471 public Integer getBgColour() {
3476 * Sets the value of the bgColour property.
3483 public void setBgColour(Integer value) {
3484 this.bgColour = value;
3488 * Gets the value of the scaleFactor property.
3491 * possible object is
3495 public Float getScaleFactor() {
3500 * Sets the value of the scaleFactor property.
3507 public void setScaleFactor(Float value) {
3508 this.scaleFactor = value;
3512 * Gets the value of the showLabels property.
3515 * possible object is
3519 public Boolean isShowLabels() {
3524 * Sets the value of the showLabels property.
3531 public void setShowLabels(Boolean value) {
3532 this.showLabels = value;
3536 * Gets the value of the linkToAllViews property.
3539 * possible object is
3543 public Boolean isLinkToAllViews() {
3544 return linkToAllViews;
3548 * Sets the value of the linkToAllViews property.
3555 public void setLinkToAllViews(Boolean value) {
3556 this.linkToAllViews = value;
3560 * Gets the value of the width property.
3563 * possible object is
3567 public Integer getWidth() {
3572 * Sets the value of the width property.
3579 public void setWidth(Integer value) {
3584 * Gets the value of the height property.
3587 * possible object is
3591 public Integer getHeight() {
3596 * Sets the value of the height property.
3603 public void setHeight(Integer value) {
3604 this.height = value;
3608 * Gets the value of the xpos property.
3611 * possible object is
3615 public Integer getXpos() {
3620 * Sets the value of the xpos property.
3627 public void setXpos(Integer value) {
3632 * Gets the value of the ypos property.
3635 * possible object is
3639 public Integer getYpos() {
3644 * Sets the value of the ypos property.
3651 public void setYpos(Integer value) {
3656 * Gets the value of the includeGaps property.
3659 * possible object is
3663 public Boolean isIncludeGaps() {
3668 * Sets the value of the includeGaps property.
3675 public void setIncludeGaps(Boolean value) {
3676 this.includeGaps = value;
3680 * Gets the value of the matchGaps property.
3683 * possible object is
3687 public Boolean isMatchGaps() {
3692 * Sets the value of the matchGaps property.
3699 public void setMatchGaps(Boolean value) {
3700 this.matchGaps = value;
3704 * Gets the value of the includeGappedColumns property.
3707 * possible object is
3711 public Boolean isIncludeGappedColumns() {
3712 return includeGappedColumns;
3716 * Sets the value of the includeGappedColumns property.
3723 public void setIncludeGappedColumns(Boolean value) {
3724 this.includeGappedColumns = value;
3728 * Gets the value of the denominateByShortestLength property.
3731 * possible object is
3735 public Boolean isDenominateByShortestLength() {
3736 return denominateByShortestLength;
3740 * Sets the value of the denominateByShortestLength property.
3747 public void setDenominateByShortestLength(Boolean value) {
3748 this.denominateByShortestLength = value;
3753 * <p>Java class for anonymous complex type.
3755 * <p>The following schema fragment specifies the expected content contained within this class.
3759 * <complexContent>
3760 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3761 * <attGroup ref="{www.jalview.org}position"/>
3763 * </complexContent>
3769 @XmlAccessorType(XmlAccessType.FIELD)
3771 public static class Axis {
3773 @XmlAttribute(name = "xPos")
3774 protected Float xPos;
3775 @XmlAttribute(name = "yPos")
3776 protected Float yPos;
3777 @XmlAttribute(name = "zPos")
3778 protected Float zPos;
3781 * Gets the value of the xPos property.
3784 * possible object is
3788 public Float getXPos() {
3793 * Sets the value of the xPos property.
3800 public void setXPos(Float value) {
3805 * Gets the value of the yPos property.
3808 * possible object is
3812 public Float getYPos() {
3817 * Sets the value of the yPos property.
3824 public void setYPos(Float value) {
3829 * Gets the value of the zPos property.
3832 * possible object is
3836 public Float getZPos() {
3841 * Sets the value of the zPos property.
3848 public void setZPos(Float value) {
3856 * <p>Java class for anonymous complex type.
3858 * <p>The following schema fragment specifies the expected content contained within this class.
3862 * <complexContent>
3863 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3864 * <attGroup ref="{www.jalview.org}position"/>
3866 * </complexContent>
3872 @XmlAccessorType(XmlAccessType.FIELD)
3874 public static class SeqPointMax {
3876 @XmlAttribute(name = "xPos")
3877 protected Float xPos;
3878 @XmlAttribute(name = "yPos")
3879 protected Float yPos;
3880 @XmlAttribute(name = "zPos")
3881 protected Float zPos;
3884 * Gets the value of the xPos property.
3887 * possible object is
3891 public Float getXPos() {
3896 * Sets the value of the xPos property.
3903 public void setXPos(Float value) {
3908 * Gets the value of the yPos property.
3911 * possible object is
3915 public Float getYPos() {
3920 * Sets the value of the yPos property.
3927 public void setYPos(Float value) {
3932 * Gets the value of the zPos property.
3935 * possible object is
3939 public Float getZPos() {
3944 * Sets the value of the zPos property.
3951 public void setZPos(Float value) {
3959 * <p>Java class for anonymous complex type.
3961 * <p>The following schema fragment specifies the expected content contained within this class.
3965 * <complexContent>
3966 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3967 * <attGroup ref="{www.jalview.org}position"/>
3969 * </complexContent>
3975 @XmlAccessorType(XmlAccessType.FIELD)
3977 public static class SeqPointMin {
3979 @XmlAttribute(name = "xPos")
3980 protected Float xPos;
3981 @XmlAttribute(name = "yPos")
3982 protected Float yPos;
3983 @XmlAttribute(name = "zPos")
3984 protected Float zPos;
3987 * Gets the value of the xPos property.
3990 * possible object is
3994 public Float getXPos() {
3999 * Sets the value of the xPos property.
4006 public void setXPos(Float value) {
4011 * Gets the value of the yPos property.
4014 * possible object is
4018 public Float getYPos() {
4023 * Sets the value of the yPos property.
4030 public void setYPos(Float value) {
4035 * Gets the value of the zPos property.
4038 * possible object is
4042 public Float getZPos() {
4047 * Sets the value of the zPos property.
4054 public void setZPos(Float value) {
4062 * <p>Java class for anonymous complex type.
4064 * <p>The following schema fragment specifies the expected content contained within this class.
4068 * <complexContent>
4069 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4070 * <attGroup ref="{www.jalview.org}position"/>
4071 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4073 * </complexContent>
4079 @XmlAccessorType(XmlAccessType.FIELD)
4081 public static class SequencePoint {
4083 @XmlAttribute(name = "sequenceRef")
4084 protected String sequenceRef;
4085 @XmlAttribute(name = "xPos")
4086 protected Float xPos;
4087 @XmlAttribute(name = "yPos")
4088 protected Float yPos;
4089 @XmlAttribute(name = "zPos")
4090 protected Float zPos;
4093 * Gets the value of the sequenceRef property.
4096 * possible object is
4100 public String getSequenceRef() {
4105 * Sets the value of the sequenceRef property.
4112 public void setSequenceRef(String value) {
4113 this.sequenceRef = value;
4117 * Gets the value of the xPos property.
4120 * possible object is
4124 public Float getXPos() {
4129 * Sets the value of the xPos property.
4136 public void setXPos(Float value) {
4141 * Gets the value of the yPos property.
4144 * possible object is
4148 public Float getYPos() {
4153 * Sets the value of the yPos property.
4160 public void setYPos(Float value) {
4165 * Gets the value of the zPos property.
4168 * possible object is
4172 public Float getZPos() {
4177 * Sets the value of the zPos property.
4184 public void setZPos(Float value) {
4194 * <p>Java class for anonymous complex type.
4196 * <p>The following schema fragment specifies the expected content contained within this class.
4200 * <complexContent>
4201 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4202 * <sequence minOccurs="0">
4203 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4204 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4206 * <attGroup ref="{www.jalview.org}swingwindow"/>
4207 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4208 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4209 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4210 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4211 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4212 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4213 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4214 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4215 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4216 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4217 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4219 * </complexContent>
4225 @XmlAccessorType(XmlAccessType.FIELD)
4226 @XmlType(name = "", propOrder = {
4230 public static class Tree {
4232 @XmlElement(namespace = "www.jalview.org")
4233 protected String title;
4234 @XmlElement(namespace = "www.jalview.org")
4235 protected String newick;
4236 @XmlAttribute(name = "fontName")
4237 protected String fontName;
4238 @XmlAttribute(name = "fontSize")
4239 protected Integer fontSize;
4240 @XmlAttribute(name = "fontStyle")
4241 protected Integer fontStyle;
4242 @XmlAttribute(name = "threshold")
4243 protected Float threshold;
4244 @XmlAttribute(name = "showBootstrap")
4245 protected Boolean showBootstrap;
4246 @XmlAttribute(name = "showDistances")
4247 protected Boolean showDistances;
4248 @XmlAttribute(name = "markUnlinked")
4249 protected Boolean markUnlinked;
4250 @XmlAttribute(name = "fitToWindow")
4251 protected Boolean fitToWindow;
4252 @XmlAttribute(name = "currentTree")
4253 protected Boolean currentTree;
4254 @XmlAttribute(name = "id")
4255 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4257 @XmlSchemaType(name = "ID")
4258 protected String id;
4259 @XmlAttribute(name = "linkToAllViews")
4260 protected Boolean linkToAllViews;
4261 @XmlAttribute(name = "width")
4262 protected Integer width;
4263 @XmlAttribute(name = "height")
4264 protected Integer height;
4265 @XmlAttribute(name = "xpos")
4266 protected Integer xpos;
4267 @XmlAttribute(name = "ypos")
4268 protected Integer ypos;
4271 * Gets the value of the title property.
4274 * possible object is
4278 public String getTitle() {
4283 * Sets the value of the title property.
4290 public void setTitle(String value) {
4295 * Gets the value of the newick property.
4298 * possible object is
4302 public String getNewick() {
4307 * Sets the value of the newick property.
4314 public void setNewick(String value) {
4315 this.newick = value;
4319 * Gets the value of the fontName property.
4322 * possible object is
4326 public String getFontName() {
4331 * Sets the value of the fontName property.
4338 public void setFontName(String value) {
4339 this.fontName = value;
4343 * Gets the value of the fontSize property.
4346 * possible object is
4350 public Integer getFontSize() {
4355 * Sets the value of the fontSize property.
4362 public void setFontSize(Integer value) {
4363 this.fontSize = value;
4367 * Gets the value of the fontStyle property.
4370 * possible object is
4374 public Integer getFontStyle() {
4379 * Sets the value of the fontStyle property.
4386 public void setFontStyle(Integer value) {
4387 this.fontStyle = value;
4391 * Gets the value of the threshold property.
4394 * possible object is
4398 public Float getThreshold() {
4403 * Sets the value of the threshold property.
4410 public void setThreshold(Float value) {
4411 this.threshold = value;
4415 * Gets the value of the showBootstrap property.
4418 * possible object is
4422 public Boolean isShowBootstrap() {
4423 return showBootstrap;
4427 * Sets the value of the showBootstrap property.
4434 public void setShowBootstrap(Boolean value) {
4435 this.showBootstrap = value;
4439 * Gets the value of the showDistances property.
4442 * possible object is
4446 public Boolean isShowDistances() {
4447 return showDistances;
4451 * Sets the value of the showDistances property.
4458 public void setShowDistances(Boolean value) {
4459 this.showDistances = value;
4463 * Gets the value of the markUnlinked property.
4466 * possible object is
4470 public Boolean isMarkUnlinked() {
4471 return markUnlinked;
4475 * Sets the value of the markUnlinked property.
4482 public void setMarkUnlinked(Boolean value) {
4483 this.markUnlinked = value;
4487 * Gets the value of the fitToWindow property.
4490 * possible object is
4494 public Boolean isFitToWindow() {
4499 * Sets the value of the fitToWindow property.
4506 public void setFitToWindow(Boolean value) {
4507 this.fitToWindow = value;
4511 * Gets the value of the currentTree property.
4514 * possible object is
4518 public Boolean isCurrentTree() {
4523 * Sets the value of the currentTree property.
4530 public void setCurrentTree(Boolean value) {
4531 this.currentTree = value;
4535 * Gets the value of the id property.
4538 * possible object is
4542 public String getId() {
4547 * Sets the value of the id property.
4554 public void setId(String value) {
4559 * Gets the value of the linkToAllViews property.
4562 * possible object is
4566 public boolean isLinkToAllViews() {
4567 if (linkToAllViews == null) {
4570 return linkToAllViews;
4575 * Sets the value of the linkToAllViews property.
4582 public void setLinkToAllViews(Boolean value) {
4583 this.linkToAllViews = value;
4587 * Gets the value of the width property.
4590 * possible object is
4594 public Integer getWidth() {
4599 * Sets the value of the width property.
4606 public void setWidth(Integer value) {
4611 * Gets the value of the height property.
4614 * possible object is
4618 public Integer getHeight() {
4623 * Sets the value of the height property.
4630 public void setHeight(Integer value) {
4631 this.height = value;
4635 * Gets the value of the xpos property.
4638 * possible object is
4642 public Integer getXpos() {
4647 * Sets the value of the xpos property.
4654 public void setXpos(Integer value) {
4659 * Gets the value of the ypos property.
4662 * possible object is
4666 public Integer getYpos() {
4671 * Sets the value of the ypos property.
4678 public void setYpos(Integer value) {
4686 * <p>Java class for anonymous complex type.
4688 * <p>The following schema fragment specifies the expected content contained within this class.
4692 * <complexContent>
4693 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4695 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4697 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4699 * </complexContent>
4705 @XmlAccessorType(XmlAccessType.FIELD)
4706 @XmlType(name = "", propOrder = {
4709 public static class UserColours {
4711 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4712 protected JalviewUserColours userColourScheme;
4713 @XmlAttribute(name = "id")
4714 protected String id;
4717 * Gets the value of the userColourScheme property.
4720 * possible object is
4721 * {@link JalviewUserColours }
4724 public JalviewUserColours getUserColourScheme() {
4725 return userColourScheme;
4729 * Sets the value of the userColourScheme property.
4733 * {@link JalviewUserColours }
4736 public void setUserColourScheme(JalviewUserColours value) {
4737 this.userColourScheme = value;
4741 * Gets the value of the id property.
4744 * possible object is
4748 public String getId() {
4753 * Sets the value of the id property.
4760 public void setId(String value) {
4768 * <p>Java class for anonymous complex type.
4770 * <p>The following schema fragment specifies the expected content contained within this class.
4774 * <complexContent>
4775 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4777 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4778 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4780 * <complexContent>
4781 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4782 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4783 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4785 * </complexContent>
4788 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4790 * <complexContent>
4791 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4792 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4793 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4794 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4796 * </complexContent>
4800 * <attGroup ref="{www.jalview.org}swingwindow"/>
4801 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4802 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4803 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4804 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4805 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4806 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4807 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4808 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4809 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4811 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4812 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4813 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4814 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4815 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4816 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4817 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4818 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4819 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4820 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4821 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4822 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4823 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4824 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4825 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4826 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4827 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4828 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4829 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4830 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4831 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4832 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4833 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4834 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4835 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4836 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4837 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4838 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4839 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4840 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4841 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4842 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4843 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4845 * </complexContent>
4851 @XmlAccessorType(XmlAccessType.FIELD)
4852 @XmlType(name = "", propOrder = {
4853 "annotationColours",
4857 public static class Viewport {
4859 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4860 protected AnnotationColourScheme annotationColours;
4861 @XmlElement(namespace = "www.jalview.org")
4862 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4863 @XmlElement(namespace = "www.jalview.org")
4864 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4865 @XmlAttribute(name = "conservationSelected")
4866 protected Boolean conservationSelected;
4867 @XmlAttribute(name = "pidSelected")
4868 protected Boolean pidSelected;
4869 @XmlAttribute(name = "bgColour")
4870 protected String bgColour;
4871 @XmlAttribute(name = "consThreshold")
4872 protected Integer consThreshold;
4873 @XmlAttribute(name = "pidThreshold")
4874 protected Integer pidThreshold;
4875 @XmlAttribute(name = "title")
4876 protected String title;
4877 @XmlAttribute(name = "showFullId")
4878 protected Boolean showFullId;
4879 @XmlAttribute(name = "rightAlignIds")
4880 protected Boolean rightAlignIds;
4881 @XmlAttribute(name = "showText")
4882 protected Boolean showText;
4883 @XmlAttribute(name = "showColourText")
4884 protected Boolean showColourText;
4885 @XmlAttribute(name = "showUnconserved")
4886 protected Boolean showUnconserved;
4887 @XmlAttribute(name = "showBoxes")
4888 protected Boolean showBoxes;
4889 @XmlAttribute(name = "wrapAlignment")
4890 protected Boolean wrapAlignment;
4891 @XmlAttribute(name = "renderGaps")
4892 protected Boolean renderGaps;
4893 @XmlAttribute(name = "showSequenceFeatures")
4894 protected Boolean showSequenceFeatures;
4895 @XmlAttribute(name = "showNPfeatureTooltip")
4896 protected Boolean showNPfeatureTooltip;
4897 @XmlAttribute(name = "showDbRefTooltip")
4898 protected Boolean showDbRefTooltip;
4899 @XmlAttribute(name = "followHighlight")
4900 protected Boolean followHighlight;
4901 @XmlAttribute(name = "followSelection")
4902 protected Boolean followSelection;
4903 @XmlAttribute(name = "showAnnotation")
4904 protected Boolean showAnnotation;
4905 @XmlAttribute(name = "centreColumnLabels")
4906 protected Boolean centreColumnLabels;
4907 @XmlAttribute(name = "showGroupConservation")
4908 protected Boolean showGroupConservation;
4909 @XmlAttribute(name = "showGroupConsensus")
4910 protected Boolean showGroupConsensus;
4911 @XmlAttribute(name = "showConsensusHistogram")
4912 protected Boolean showConsensusHistogram;
4913 @XmlAttribute(name = "showSequenceLogo")
4914 protected Boolean showSequenceLogo;
4915 @XmlAttribute(name = "normaliseSequenceLogo")
4916 protected Boolean normaliseSequenceLogo;
4917 @XmlAttribute(name = "ignoreGapsinConsensus")
4918 protected Boolean ignoreGapsinConsensus;
4919 @XmlAttribute(name = "startRes")
4920 protected Integer startRes;
4921 @XmlAttribute(name = "startSeq")
4922 protected Integer startSeq;
4923 @XmlAttribute(name = "fontName")
4924 protected String fontName;
4925 @XmlAttribute(name = "fontSize")
4926 protected Integer fontSize;
4927 @XmlAttribute(name = "fontStyle")
4928 protected Integer fontStyle;
4929 @XmlAttribute(name = "scaleProteinAsCdna")
4930 protected Boolean scaleProteinAsCdna;
4931 @XmlAttribute(name = "viewName")
4932 protected String viewName;
4933 @XmlAttribute(name = "sequenceSetId")
4934 protected String sequenceSetId;
4935 @XmlAttribute(name = "gatheredViews")
4936 protected Boolean gatheredViews;
4937 @XmlAttribute(name = "textCol1")
4938 protected Integer textCol1;
4939 @XmlAttribute(name = "textCol2")
4940 protected Integer textCol2;
4941 @XmlAttribute(name = "textColThreshold")
4942 protected Integer textColThreshold;
4943 @XmlAttribute(name = "id")
4944 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4946 @XmlSchemaType(name = "ID")
4947 protected String id;
4948 @XmlAttribute(name = "complementId")
4949 protected String complementId;
4950 @XmlAttribute(name = "showComplementFeatures")
4951 protected Boolean showComplementFeatures;
4952 @XmlAttribute(name = "showComplementFeaturesOnTop")
4953 protected Boolean showComplementFeaturesOnTop;
4954 @XmlAttribute(name = "width")
4955 protected Integer width;
4956 @XmlAttribute(name = "height")
4957 protected Integer height;
4958 @XmlAttribute(name = "xpos")
4959 protected Integer xpos;
4960 @XmlAttribute(name = "ypos")
4961 protected Integer ypos;
4964 * Gets the value of the annotationColours property.
4967 * possible object is
4968 * {@link AnnotationColourScheme }
4971 public AnnotationColourScheme getAnnotationColours() {
4972 return annotationColours;
4976 * Sets the value of the annotationColours property.
4980 * {@link AnnotationColourScheme }
4983 public void setAnnotationColours(AnnotationColourScheme value) {
4984 this.annotationColours = value;
4988 * Gets the value of the hiddenColumns property.
4991 * This accessor method returns a reference to the live list,
4992 * not a snapshot. Therefore any modification you make to the
4993 * returned list will be present inside the JAXB object.
4994 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4997 * For example, to add a new item, do as follows:
4999 * getHiddenColumns().add(newItem);
5004 * Objects of the following type(s) are allowed in the list
5005 * {@link JalviewModel.Viewport.HiddenColumns }
5009 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5010 if (hiddenColumns == null) {
5011 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5013 return this.hiddenColumns;
5017 * Gets the value of the calcIdParam property.
5020 * This accessor method returns a reference to the live list,
5021 * not a snapshot. Therefore any modification you make to the
5022 * returned list will be present inside the JAXB object.
5023 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5026 * For example, to add a new item, do as follows:
5028 * getCalcIdParam().add(newItem);
5033 * Objects of the following type(s) are allowed in the list
5034 * {@link JalviewModel.Viewport.CalcIdParam }
5038 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5039 if (calcIdParam == null) {
5040 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5042 return this.calcIdParam;
5046 * Gets the value of the conservationSelected property.
5049 * possible object is
5053 public Boolean isConservationSelected() {
5054 return conservationSelected;
5058 * Sets the value of the conservationSelected property.
5065 public void setConservationSelected(Boolean value) {
5066 this.conservationSelected = value;
5070 * Gets the value of the pidSelected property.
5073 * possible object is
5077 public Boolean isPidSelected() {
5082 * Sets the value of the pidSelected property.
5089 public void setPidSelected(Boolean value) {
5090 this.pidSelected = value;
5094 * Gets the value of the bgColour property.
5097 * possible object is
5101 public String getBgColour() {
5106 * Sets the value of the bgColour property.
5113 public void setBgColour(String value) {
5114 this.bgColour = value;
5118 * Gets the value of the consThreshold property.
5121 * possible object is
5125 public Integer getConsThreshold() {
5126 return consThreshold;
5130 * Sets the value of the consThreshold property.
5137 public void setConsThreshold(Integer value) {
5138 this.consThreshold = value;
5142 * Gets the value of the pidThreshold property.
5145 * possible object is
5149 public Integer getPidThreshold() {
5150 return pidThreshold;
5154 * Sets the value of the pidThreshold property.
5161 public void setPidThreshold(Integer value) {
5162 this.pidThreshold = value;
5166 * Gets the value of the title property.
5169 * possible object is
5173 public String getTitle() {
5178 * Sets the value of the title property.
5185 public void setTitle(String value) {
5190 * Gets the value of the showFullId property.
5193 * possible object is
5197 public Boolean isShowFullId() {
5202 * Sets the value of the showFullId property.
5209 public void setShowFullId(Boolean value) {
5210 this.showFullId = value;
5214 * Gets the value of the rightAlignIds property.
5217 * possible object is
5221 public Boolean isRightAlignIds() {
5222 return rightAlignIds;
5226 * Sets the value of the rightAlignIds property.
5233 public void setRightAlignIds(Boolean value) {
5234 this.rightAlignIds = value;
5238 * Gets the value of the showText property.
5241 * possible object is
5245 public Boolean isShowText() {
5250 * Sets the value of the showText property.
5257 public void setShowText(Boolean value) {
5258 this.showText = value;
5262 * Gets the value of the showColourText property.
5265 * possible object is
5269 public Boolean isShowColourText() {
5270 return showColourText;
5274 * Sets the value of the showColourText property.
5281 public void setShowColourText(Boolean value) {
5282 this.showColourText = value;
5286 * Gets the value of the showUnconserved property.
5289 * possible object is
5293 public boolean isShowUnconserved() {
5294 if (showUnconserved == null) {
5297 return showUnconserved;
5302 * Sets the value of the showUnconserved property.
5309 public void setShowUnconserved(Boolean value) {
5310 this.showUnconserved = value;
5314 * Gets the value of the showBoxes property.
5317 * possible object is
5321 public Boolean isShowBoxes() {
5326 * Sets the value of the showBoxes property.
5333 public void setShowBoxes(Boolean value) {
5334 this.showBoxes = value;
5338 * Gets the value of the wrapAlignment property.
5341 * possible object is
5345 public Boolean isWrapAlignment() {
5346 return wrapAlignment;
5350 * Sets the value of the wrapAlignment property.
5357 public void setWrapAlignment(Boolean value) {
5358 this.wrapAlignment = value;
5362 * Gets the value of the renderGaps property.
5365 * possible object is
5369 public Boolean isRenderGaps() {
5374 * Sets the value of the renderGaps property.
5381 public void setRenderGaps(Boolean value) {
5382 this.renderGaps = value;
5386 * Gets the value of the showSequenceFeatures property.
5389 * possible object is
5393 public Boolean isShowSequenceFeatures() {
5394 return showSequenceFeatures;
5398 * Sets the value of the showSequenceFeatures property.
5405 public void setShowSequenceFeatures(Boolean value) {
5406 this.showSequenceFeatures = value;
5410 * Gets the value of the showNPfeatureTooltip property.
5413 * possible object is
5417 public Boolean isShowNPfeatureTooltip() {
5418 return showNPfeatureTooltip;
5422 * Sets the value of the showNPfeatureTooltip property.
5429 public void setShowNPfeatureTooltip(Boolean value) {
5430 this.showNPfeatureTooltip = value;
5434 * Gets the value of the showDbRefTooltip property.
5437 * possible object is
5441 public Boolean isShowDbRefTooltip() {
5442 return showDbRefTooltip;
5446 * Sets the value of the showDbRefTooltip property.
5453 public void setShowDbRefTooltip(Boolean value) {
5454 this.showDbRefTooltip = value;
5458 * Gets the value of the followHighlight property.
5461 * possible object is
5465 public boolean isFollowHighlight() {
5466 if (followHighlight == null) {
5469 return followHighlight;
5474 * Sets the value of the followHighlight property.
5481 public void setFollowHighlight(Boolean value) {
5482 this.followHighlight = value;
5486 * Gets the value of the followSelection property.
5489 * possible object is
5493 public boolean isFollowSelection() {
5494 if (followSelection == null) {
5497 return followSelection;
5502 * Sets the value of the followSelection property.
5509 public void setFollowSelection(Boolean value) {
5510 this.followSelection = value;
5514 * Gets the value of the showAnnotation property.
5517 * possible object is
5521 public Boolean isShowAnnotation() {
5522 return showAnnotation;
5526 * Sets the value of the showAnnotation property.
5533 public void setShowAnnotation(Boolean value) {
5534 this.showAnnotation = value;
5538 * Gets the value of the centreColumnLabels property.
5541 * possible object is
5545 public boolean isCentreColumnLabels() {
5546 if (centreColumnLabels == null) {
5549 return centreColumnLabels;
5554 * Sets the value of the centreColumnLabels property.
5561 public void setCentreColumnLabels(Boolean value) {
5562 this.centreColumnLabels = value;
5566 * Gets the value of the showGroupConservation property.
5569 * possible object is
5573 public boolean isShowGroupConservation() {
5574 if (showGroupConservation == null) {
5577 return showGroupConservation;
5582 * Sets the value of the showGroupConservation property.
5589 public void setShowGroupConservation(Boolean value) {
5590 this.showGroupConservation = value;
5594 * Gets the value of the showGroupConsensus property.
5597 * possible object is
5601 public boolean isShowGroupConsensus() {
5602 if (showGroupConsensus == null) {
5605 return showGroupConsensus;
5610 * Sets the value of the showGroupConsensus property.
5617 public void setShowGroupConsensus(Boolean value) {
5618 this.showGroupConsensus = value;
5622 * Gets the value of the showConsensusHistogram property.
5625 * possible object is
5629 public boolean isShowConsensusHistogram() {
5630 if (showConsensusHistogram == null) {
5633 return showConsensusHistogram;
5638 * Sets the value of the showConsensusHistogram property.
5645 public void setShowConsensusHistogram(Boolean value) {
5646 this.showConsensusHistogram = value;
5650 * Gets the value of the showSequenceLogo property.
5653 * possible object is
5657 public boolean isShowSequenceLogo() {
5658 if (showSequenceLogo == null) {
5661 return showSequenceLogo;
5666 * Sets the value of the showSequenceLogo property.
5673 public void setShowSequenceLogo(Boolean value) {
5674 this.showSequenceLogo = value;
5678 * Gets the value of the normaliseSequenceLogo property.
5681 * possible object is
5685 public boolean isNormaliseSequenceLogo() {
5686 if (normaliseSequenceLogo == null) {
5689 return normaliseSequenceLogo;
5694 * Sets the value of the normaliseSequenceLogo property.
5701 public void setNormaliseSequenceLogo(Boolean value) {
5702 this.normaliseSequenceLogo = value;
5706 * Gets the value of the ignoreGapsinConsensus property.
5709 * possible object is
5713 public boolean isIgnoreGapsinConsensus() {
5714 if (ignoreGapsinConsensus == null) {
5717 return ignoreGapsinConsensus;
5722 * Sets the value of the ignoreGapsinConsensus property.
5729 public void setIgnoreGapsinConsensus(Boolean value) {
5730 this.ignoreGapsinConsensus = value;
5734 * Gets the value of the startRes property.
5737 * possible object is
5741 public Integer getStartRes() {
5746 * Sets the value of the startRes property.
5753 public void setStartRes(Integer value) {
5754 this.startRes = value;
5758 * Gets the value of the startSeq property.
5761 * possible object is
5765 public Integer getStartSeq() {
5770 * Sets the value of the startSeq property.
5777 public void setStartSeq(Integer value) {
5778 this.startSeq = value;
5782 * Gets the value of the fontName property.
5785 * possible object is
5789 public String getFontName() {
5794 * Sets the value of the fontName property.
5801 public void setFontName(String value) {
5802 this.fontName = value;
5806 * Gets the value of the fontSize property.
5809 * possible object is
5813 public Integer getFontSize() {
5818 * Sets the value of the fontSize property.
5825 public void setFontSize(Integer value) {
5826 this.fontSize = value;
5830 * Gets the value of the fontStyle property.
5833 * possible object is
5837 public Integer getFontStyle() {
5842 * Sets the value of the fontStyle property.
5849 public void setFontStyle(Integer value) {
5850 this.fontStyle = value;
5854 * Gets the value of the scaleProteinAsCdna property.
5857 * possible object is
5861 public boolean isScaleProteinAsCdna() {
5862 if (scaleProteinAsCdna == null) {
5865 return scaleProteinAsCdna;
5870 * Sets the value of the scaleProteinAsCdna property.
5877 public void setScaleProteinAsCdna(Boolean value) {
5878 this.scaleProteinAsCdna = value;
5882 * Gets the value of the viewName property.
5885 * possible object is
5889 public String getViewName() {
5894 * Sets the value of the viewName property.
5901 public void setViewName(String value) {
5902 this.viewName = value;
5906 * Gets the value of the sequenceSetId property.
5909 * possible object is
5913 public String getSequenceSetId() {
5914 return sequenceSetId;
5918 * Sets the value of the sequenceSetId property.
5925 public void setSequenceSetId(String value) {
5926 this.sequenceSetId = value;
5930 * Gets the value of the gatheredViews property.
5933 * possible object is
5937 public Boolean isGatheredViews() {
5938 return gatheredViews;
5942 * Sets the value of the gatheredViews property.
5949 public void setGatheredViews(Boolean value) {
5950 this.gatheredViews = value;
5954 * Gets the value of the textCol1 property.
5957 * possible object is
5961 public Integer getTextCol1() {
5966 * Sets the value of the textCol1 property.
5973 public void setTextCol1(Integer value) {
5974 this.textCol1 = value;
5978 * Gets the value of the textCol2 property.
5981 * possible object is
5985 public Integer getTextCol2() {
5990 * Sets the value of the textCol2 property.
5997 public void setTextCol2(Integer value) {
5998 this.textCol2 = value;
6002 * Gets the value of the textColThreshold property.
6005 * possible object is
6009 public Integer getTextColThreshold() {
6010 return textColThreshold;
6014 * Sets the value of the textColThreshold property.
6021 public void setTextColThreshold(Integer value) {
6022 this.textColThreshold = value;
6026 * Gets the value of the id property.
6029 * possible object is
6033 public String getId() {
6038 * Sets the value of the id property.
6045 public void setId(String value) {
6050 * Gets the value of the complementId property.
6053 * possible object is
6057 public String getComplementId() {
6058 return complementId;
6062 * Sets the value of the complementId property.
6069 public void setComplementId(String value) {
6070 this.complementId = value;
6074 * Gets the value of the showComplementFeatures property.
6077 * possible object is
6081 public boolean isShowComplementFeatures() {
6082 if (showComplementFeatures == null) {
6085 return showComplementFeatures;
6090 * Sets the value of the showComplementFeatures property.
6097 public void setShowComplementFeatures(Boolean value) {
6098 this.showComplementFeatures = value;
6102 * Gets the value of the showComplementFeaturesOnTop property.
6105 * possible object is
6109 public boolean isShowComplementFeaturesOnTop() {
6110 if (showComplementFeaturesOnTop == null) {
6113 return showComplementFeaturesOnTop;
6118 * Sets the value of the showComplementFeaturesOnTop property.
6125 public void setShowComplementFeaturesOnTop(Boolean value) {
6126 this.showComplementFeaturesOnTop = value;
6130 * Gets the value of the width property.
6133 * possible object is
6137 public Integer getWidth() {
6142 * Sets the value of the width property.
6149 public void setWidth(Integer value) {
6154 * Gets the value of the height property.
6157 * possible object is
6161 public Integer getHeight() {
6166 * Sets the value of the height property.
6173 public void setHeight(Integer value) {
6174 this.height = value;
6178 * Gets the value of the xpos property.
6181 * possible object is
6185 public Integer getXpos() {
6190 * Sets the value of the xpos property.
6197 public void setXpos(Integer value) {
6202 * Gets the value of the ypos property.
6205 * possible object is
6209 public Integer getYpos() {
6214 * Sets the value of the ypos property.
6221 public void setYpos(Integer value) {
6227 * <p>Java class for anonymous complex type.
6229 * <p>The following schema fragment specifies the expected content contained within this class.
6233 * <complexContent>
6234 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6235 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6236 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6237 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6239 * </complexContent>
6245 @XmlAccessorType(XmlAccessType.FIELD)
6247 public static class CalcIdParam
6248 extends WebServiceParameterSet
6251 @XmlAttribute(name = "calcId", required = true)
6252 protected String calcId;
6253 @XmlAttribute(name = "needsUpdate")
6254 protected Boolean needsUpdate;
6255 @XmlAttribute(name = "autoUpdate", required = true)
6256 protected boolean autoUpdate;
6259 * Gets the value of the calcId property.
6262 * possible object is
6266 public String getCalcId() {
6271 * Sets the value of the calcId property.
6278 public void setCalcId(String value) {
6279 this.calcId = value;
6283 * Gets the value of the needsUpdate property.
6286 * possible object is
6290 public boolean isNeedsUpdate() {
6291 if (needsUpdate == null) {
6299 * Sets the value of the needsUpdate property.
6306 public void setNeedsUpdate(Boolean value) {
6307 this.needsUpdate = value;
6311 * Gets the value of the autoUpdate property.
6314 public boolean isAutoUpdate() {
6319 * Sets the value of the autoUpdate property.
6322 public void setAutoUpdate(boolean value) {
6323 this.autoUpdate = value;
6330 * <p>Java class for anonymous complex type.
6332 * <p>The following schema fragment specifies the expected content contained within this class.
6336 * <complexContent>
6337 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6338 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6339 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6341 * </complexContent>
6347 @XmlAccessorType(XmlAccessType.FIELD)
6349 public static class HiddenColumns {
6351 @XmlAttribute(name = "start")
6352 protected Integer start;
6353 @XmlAttribute(name = "end")
6354 protected Integer end;
6357 * Gets the value of the start property.
6360 * possible object is
6364 public Integer getStart() {
6369 * Sets the value of the start property.
6376 public void setStart(Integer value) {
6381 * Gets the value of the end property.
6384 * possible object is
6388 public Integer getEnd() {
6393 * Sets the value of the end property.
6400 public void setEnd(Integer value) {