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: 2019.11.07 at 02:47:42 PM GMT
9 package jalview.xml.binding.jalview;
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
27 * <p>Java class for JalviewModel complex type.
29 * <p>The following schema fragment specifies the expected content contained within this class.
32 * <complexType name="JalviewModel">
34 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
36 * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
37 * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
38 * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
40 * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
43 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
45 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
46 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
49 * <extension base="{www.jalview.org}pdbentry">
51 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
54 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
55 * <attGroup ref="{www.jalview.org}swingwindow"/>
56 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
57 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
58 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
59 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
60 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
61 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
68 * </complexContent>
71 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
72 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
75 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
77 * <element name="secondaryStructure" maxOccurs="unbounded">
80 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
81 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
82 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
83 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
84 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
86 * </complexContent>
90 * <attGroup ref="{www.jalview.org}swingwindow"/>
91 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
92 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
93 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
94 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
96 * </complexContent>
100 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
101 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
102 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
104 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
105 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
107 * </complexContent>
110 * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
112 * <complexContent>
113 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
115 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
116 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
118 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
119 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
120 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
121 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
122 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
123 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
125 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
126 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
129 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
130 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
131 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
132 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
133 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
135 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
138 * </complexContent>
141 * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
143 * <complexContent>
144 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
146 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
147 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
149 * <complexContent>
150 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
151 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
152 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
154 * </complexContent>
157 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
159 * <complexContent>
160 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
161 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
162 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
163 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
165 * </complexContent>
169 * <attGroup ref="{www.jalview.org}swingwindow"/>
170 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
171 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
172 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
173 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
174 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
175 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
176 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
177 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
178 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
179 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
180 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
181 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
182 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
183 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
184 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
187 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
188 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
189 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
190 * <attribute name="showAutocalcAbove" type="{http://www.w3.org/2001/XMLSchema}boolean" />
191 * <attribute name="sortAnnotationsBy" type="{http://www.w3.org/2001/XMLSchema}string" />
192 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
193 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
194 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
195 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
196 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
197 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
198 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
199 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
200 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
201 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
202 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
203 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
204 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
205 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
206 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
207 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
208 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
209 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
210 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
211 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
212 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
214 * </complexContent>
217 * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
219 * <complexContent>
220 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
222 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
224 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
226 * </complexContent>
229 * <element name="tree" maxOccurs="unbounded" minOccurs="0">
231 * <complexContent>
232 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
233 * <sequence minOccurs="0">
234 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
235 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
237 * <attGroup ref="{www.jalview.org}swingwindow"/>
238 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
239 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
240 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
241 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
242 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
243 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
244 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
245 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
246 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
247 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
248 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
250 * </complexContent>
253 * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
255 * <complexContent>
256 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
258 * <element name="sequencePoint" maxOccurs="unbounded">
260 * <complexContent>
261 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
262 * <attGroup ref="{www.jalview.org}position"/>
263 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
265 * </complexContent>
268 * <element name="axis" maxOccurs="3" minOccurs="3">
270 * <complexContent>
271 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
272 * <attGroup ref="{www.jalview.org}position"/>
274 * </complexContent>
277 * <element name="seqPointMin">
279 * <complexContent>
280 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
281 * <attGroup ref="{www.jalview.org}position"/>
283 * </complexContent>
286 * <element name="seqPointMax">
288 * <complexContent>
289 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
290 * <attGroup ref="{www.jalview.org}position"/>
292 * </complexContent>
295 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
297 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
298 * <attGroup ref="{www.jalview.org}swingwindow"/>
299 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
300 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
301 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
302 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
303 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
304 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
305 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
306 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
307 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
309 * </complexContent>
312 * <element name="FeatureSettings" minOccurs="0">
314 * <complexContent>
315 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
317 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
319 * <complexContent>
320 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
322 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
323 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
325 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
326 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
327 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
328 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
329 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
330 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
331 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
332 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
333 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
334 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
335 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
336 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
338 * </complexContent>
341 * <element name="group" maxOccurs="unbounded" minOccurs="0">
343 * <complexContent>
344 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
345 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
346 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
348 * </complexContent>
353 * </complexContent>
359 * </complexContent>
365 @XmlAccessorType(XmlAccessType.FIELD)
366 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
378 public class JalviewModel {
380 @XmlElement(required = true)
381 @XmlSchemaType(name = "dateTime")
382 protected XMLGregorianCalendar creationDate;
383 @XmlElement(required = true)
384 protected String version;
385 @XmlElement(required = true)
386 protected VAMSAS vamsasModel;
387 @XmlElement(name = "JSeq")
388 protected List<JalviewModel.JSeq> jSeq;
389 @XmlElement(name = "JGroup")
390 protected List<JalviewModel.JGroup> jGroup;
391 @XmlElement(name = "Viewport")
392 protected List<JalviewModel.Viewport> viewport;
393 @XmlElement(name = "UserColours")
394 protected List<JalviewModel.UserColours> userColours;
395 protected List<JalviewModel.Tree> tree;
396 @XmlElement(name = "PcaViewer")
397 protected List<JalviewModel.PcaViewer> pcaViewer;
398 @XmlElement(name = "FeatureSettings")
399 protected JalviewModel.FeatureSettings featureSettings;
402 * Gets the value of the creationDate property.
406 * {@link XMLGregorianCalendar }
409 public XMLGregorianCalendar getCreationDate() {
414 * Sets the value of the creationDate property.
418 * {@link XMLGregorianCalendar }
421 public void setCreationDate(XMLGregorianCalendar value) {
422 this.creationDate = value;
426 * Gets the value of the version property.
433 public String getVersion() {
438 * Sets the value of the version property.
445 public void setVersion(String value) {
446 this.version = value;
450 * Gets the value of the vamsasModel property.
457 public VAMSAS getVamsasModel() {
462 * Sets the value of the vamsasModel property.
469 public void setVamsasModel(VAMSAS value) {
470 this.vamsasModel = value;
474 * Gets the value of the jSeq property.
477 * This accessor method returns a reference to the live list,
478 * not a snapshot. Therefore any modification you make to the
479 * returned list will be present inside the JAXB object.
480 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
483 * For example, to add a new item, do as follows:
485 * getJSeq().add(newItem);
490 * Objects of the following type(s) are allowed in the list
491 * {@link JalviewModel.JSeq }
495 public List<JalviewModel.JSeq> getJSeq() {
497 jSeq = new ArrayList<JalviewModel.JSeq>();
503 * Gets the value of the jGroup property.
506 * This accessor method returns a reference to the live list,
507 * not a snapshot. Therefore any modification you make to the
508 * returned list will be present inside the JAXB object.
509 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
512 * For example, to add a new item, do as follows:
514 * getJGroup().add(newItem);
519 * Objects of the following type(s) are allowed in the list
520 * {@link JalviewModel.JGroup }
524 public List<JalviewModel.JGroup> getJGroup() {
525 if (jGroup == null) {
526 jGroup = new ArrayList<JalviewModel.JGroup>();
532 * Gets the value of the viewport property.
535 * This accessor method returns a reference to the live list,
536 * not a snapshot. Therefore any modification you make to the
537 * returned list will be present inside the JAXB object.
538 * This is why there is not a <CODE>set</CODE> method for the viewport property.
541 * For example, to add a new item, do as follows:
543 * getViewport().add(newItem);
548 * Objects of the following type(s) are allowed in the list
549 * {@link JalviewModel.Viewport }
553 public List<JalviewModel.Viewport> getViewport() {
554 if (viewport == null) {
555 viewport = new ArrayList<JalviewModel.Viewport>();
557 return this.viewport;
561 * Gets the value of the userColours property.
564 * This accessor method returns a reference to the live list,
565 * not a snapshot. Therefore any modification you make to the
566 * returned list will be present inside the JAXB object.
567 * This is why there is not a <CODE>set</CODE> method for the userColours property.
570 * For example, to add a new item, do as follows:
572 * getUserColours().add(newItem);
577 * Objects of the following type(s) are allowed in the list
578 * {@link JalviewModel.UserColours }
582 public List<JalviewModel.UserColours> getUserColours() {
583 if (userColours == null) {
584 userColours = new ArrayList<JalviewModel.UserColours>();
586 return this.userColours;
590 * Gets the value of the tree property.
593 * This accessor method returns a reference to the live list,
594 * not a snapshot. Therefore any modification you make to the
595 * returned list will be present inside the JAXB object.
596 * This is why there is not a <CODE>set</CODE> method for the tree property.
599 * For example, to add a new item, do as follows:
601 * getTree().add(newItem);
606 * Objects of the following type(s) are allowed in the list
607 * {@link JalviewModel.Tree }
611 public List<JalviewModel.Tree> getTree() {
613 tree = new ArrayList<JalviewModel.Tree>();
619 * Gets the value of the pcaViewer property.
622 * This accessor method returns a reference to the live list,
623 * not a snapshot. Therefore any modification you make to the
624 * returned list will be present inside the JAXB object.
625 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
628 * For example, to add a new item, do as follows:
630 * getPcaViewer().add(newItem);
635 * Objects of the following type(s) are allowed in the list
636 * {@link JalviewModel.PcaViewer }
640 public List<JalviewModel.PcaViewer> getPcaViewer() {
641 if (pcaViewer == null) {
642 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
644 return this.pcaViewer;
648 * Gets the value of the featureSettings property.
652 * {@link JalviewModel.FeatureSettings }
655 public JalviewModel.FeatureSettings getFeatureSettings() {
656 return featureSettings;
660 * Sets the value of the featureSettings property.
664 * {@link JalviewModel.FeatureSettings }
667 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
668 this.featureSettings = value;
673 * <p>Java class for anonymous complex type.
675 * <p>The following schema fragment specifies the expected content contained within this class.
679 * <complexContent>
680 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
682 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
684 * <complexContent>
685 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
687 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
688 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
690 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
691 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
692 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
693 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
694 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
695 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
696 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
697 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
698 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
699 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
700 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
701 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
703 * </complexContent>
706 * <element name="group" maxOccurs="unbounded" minOccurs="0">
708 * <complexContent>
709 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
710 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
711 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
713 * </complexContent>
718 * </complexContent>
724 @XmlAccessorType(XmlAccessType.FIELD)
725 @XmlType(name = "", propOrder = {
729 public static class FeatureSettings {
731 @XmlElement(namespace = "www.jalview.org")
732 protected List<JalviewModel.FeatureSettings.Setting> setting;
733 @XmlElement(namespace = "www.jalview.org")
734 protected List<JalviewModel.FeatureSettings.Group> group;
737 * Gets the value of the setting property.
740 * This accessor method returns a reference to the live list,
741 * not a snapshot. Therefore any modification you make to the
742 * returned list will be present inside the JAXB object.
743 * This is why there is not a <CODE>set</CODE> method for the setting property.
746 * For example, to add a new item, do as follows:
748 * getSetting().add(newItem);
753 * Objects of the following type(s) are allowed in the list
754 * {@link JalviewModel.FeatureSettings.Setting }
758 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
759 if (setting == null) {
760 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
766 * Gets the value of the group property.
769 * This accessor method returns a reference to the live list,
770 * not a snapshot. Therefore any modification you make to the
771 * returned list will be present inside the JAXB object.
772 * This is why there is not a <CODE>set</CODE> method for the group property.
775 * For example, to add a new item, do as follows:
777 * getGroup().add(newItem);
782 * Objects of the following type(s) are allowed in the list
783 * {@link JalviewModel.FeatureSettings.Group }
787 public List<JalviewModel.FeatureSettings.Group> getGroup() {
789 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
796 * <p>Java class for anonymous complex type.
798 * <p>The following schema fragment specifies the expected content contained within this class.
802 * <complexContent>
803 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
804 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
805 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
807 * </complexContent>
813 @XmlAccessorType(XmlAccessType.FIELD)
815 public static class Group {
817 @XmlAttribute(name = "name", required = true)
818 protected String name;
819 @XmlAttribute(name = "display", required = true)
820 protected boolean display;
823 * Gets the value of the name property.
830 public String getName() {
835 * Sets the value of the name property.
842 public void setName(String value) {
847 * Gets the value of the display property.
850 public boolean isDisplay() {
855 * Sets the value of the display property.
858 public void setDisplay(boolean value) {
859 this.display = value;
866 * <p>Java class for anonymous complex type.
868 * <p>The following schema fragment specifies the expected content contained within this class.
872 * <complexContent>
873 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
875 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
876 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
878 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
879 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
880 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
881 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
882 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
883 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
884 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
885 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
886 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
887 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
888 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
889 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
891 * </complexContent>
897 @XmlAccessorType(XmlAccessType.FIELD)
898 @XmlType(name = "", propOrder = {
902 public static class Setting {
904 @XmlElement(namespace = "www.jalview.org")
905 protected List<String> attributeName;
906 @XmlElement(namespace = "www.jalview.org")
907 protected FeatureMatcherSet matcherSet;
908 @XmlAttribute(name = "type", required = true)
909 protected String type;
910 @XmlAttribute(name = "colour", required = true)
911 protected int colour;
912 @XmlAttribute(name = "display", required = true)
913 protected boolean display;
914 @XmlAttribute(name = "order")
915 protected Float order;
916 @XmlAttribute(name = "mincolour")
917 protected Integer mincolour;
918 @XmlAttribute(name = "noValueColour")
919 protected NoValueColour noValueColour;
920 @XmlAttribute(name = "threshold")
921 protected Float threshold;
922 @XmlAttribute(name = "threshstate")
923 protected Integer threshstate;
924 @XmlAttribute(name = "max")
926 @XmlAttribute(name = "min")
928 @XmlAttribute(name = "colourByLabel")
929 protected Boolean colourByLabel;
930 @XmlAttribute(name = "autoScale")
931 protected Boolean autoScale;
934 * Gets the value of the attributeName property.
937 * This accessor method returns a reference to the live list,
938 * not a snapshot. Therefore any modification you make to the
939 * returned list will be present inside the JAXB object.
940 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
943 * For example, to add a new item, do as follows:
945 * getAttributeName().add(newItem);
950 * Objects of the following type(s) are allowed in the list
955 public List<String> getAttributeName() {
956 if (attributeName == null) {
957 attributeName = new ArrayList<String>();
959 return this.attributeName;
963 * Gets the value of the matcherSet property.
967 * {@link FeatureMatcherSet }
970 public FeatureMatcherSet getMatcherSet() {
975 * Sets the value of the matcherSet property.
979 * {@link FeatureMatcherSet }
982 public void setMatcherSet(FeatureMatcherSet value) {
983 this.matcherSet = value;
987 * Gets the value of the type property.
994 public String getType() {
999 * Sets the value of the type property.
1006 public void setType(String value) {
1011 * Gets the value of the colour property.
1014 public int getColour() {
1019 * Sets the value of the colour property.
1022 public void setColour(int value) {
1023 this.colour = value;
1027 * Gets the value of the display property.
1030 public boolean isDisplay() {
1035 * Sets the value of the display property.
1038 public void setDisplay(boolean value) {
1039 this.display = value;
1043 * Gets the value of the order property.
1046 * possible object is
1050 public Float getOrder() {
1055 * Sets the value of the order property.
1062 public void setOrder(Float value) {
1067 * Gets the value of the mincolour property.
1070 * possible object is
1074 public Integer getMincolour() {
1079 * Sets the value of the mincolour property.
1086 public void setMincolour(Integer value) {
1087 this.mincolour = value;
1091 * Gets the value of the noValueColour property.
1094 * possible object is
1095 * {@link NoValueColour }
1098 public NoValueColour getNoValueColour() {
1099 if (noValueColour == null) {
1100 return NoValueColour.MIN;
1102 return noValueColour;
1107 * Sets the value of the noValueColour property.
1111 * {@link NoValueColour }
1114 public void setNoValueColour(NoValueColour value) {
1115 this.noValueColour = value;
1119 * Gets the value of the threshold property.
1122 * possible object is
1126 public Float getThreshold() {
1131 * Sets the value of the threshold property.
1138 public void setThreshold(Float value) {
1139 this.threshold = value;
1143 * Gets the value of the threshstate property.
1146 * possible object is
1150 public Integer getThreshstate() {
1155 * Sets the value of the threshstate property.
1162 public void setThreshstate(Integer value) {
1163 this.threshstate = value;
1167 * Gets the value of the max property.
1170 * possible object is
1174 public Float getMax() {
1179 * Sets the value of the max property.
1186 public void setMax(Float value) {
1191 * Gets the value of the min property.
1194 * possible object is
1198 public Float getMin() {
1203 * Sets the value of the min property.
1210 public void setMin(Float value) {
1215 * Gets the value of the colourByLabel property.
1218 * possible object is
1222 public Boolean isColourByLabel() {
1223 return colourByLabel;
1227 * Sets the value of the colourByLabel property.
1234 public void setColourByLabel(Boolean value) {
1235 this.colourByLabel = value;
1239 * Gets the value of the autoScale property.
1242 * possible object is
1246 public Boolean isAutoScale() {
1251 * Sets the value of the autoScale property.
1258 public void setAutoScale(Boolean value) {
1259 this.autoScale = value;
1268 * <p>Java class for anonymous complex type.
1270 * <p>The following schema fragment specifies the expected content contained within this class.
1274 * <complexContent>
1275 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1277 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1278 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1280 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1281 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1282 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1283 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1284 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1285 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1286 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1287 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1288 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1289 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1290 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1291 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1292 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1293 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1294 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1295 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1296 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1297 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1298 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1300 * </complexContent>
1306 @XmlAccessorType(XmlAccessType.FIELD)
1307 @XmlType(name = "", propOrder = {
1311 public static class JGroup {
1313 @XmlElement(namespace = "www.jalview.org", required = true)
1314 protected List<String> seq;
1315 @XmlElement(namespace = "www.jalview.org")
1316 protected AnnotationColourScheme annotationColours;
1317 @XmlAttribute(name = "start")
1318 protected Integer start;
1319 @XmlAttribute(name = "end")
1320 protected Integer end;
1321 @XmlAttribute(name = "name")
1322 protected String name;
1323 @XmlAttribute(name = "colour")
1324 protected String colour;
1325 @XmlAttribute(name = "consThreshold")
1326 protected Integer consThreshold;
1327 @XmlAttribute(name = "pidThreshold")
1328 protected Integer pidThreshold;
1329 @XmlAttribute(name = "outlineColour")
1330 protected Integer outlineColour;
1331 @XmlAttribute(name = "displayBoxes")
1332 protected Boolean displayBoxes;
1333 @XmlAttribute(name = "displayText")
1334 protected Boolean displayText;
1335 @XmlAttribute(name = "colourText")
1336 protected Boolean colourText;
1337 @XmlAttribute(name = "textCol1")
1338 protected Integer textCol1;
1339 @XmlAttribute(name = "textCol2")
1340 protected Integer textCol2;
1341 @XmlAttribute(name = "textColThreshold")
1342 protected Integer textColThreshold;
1343 @XmlAttribute(name = "showUnconserved")
1344 protected Boolean showUnconserved;
1345 @XmlAttribute(name = "ignoreGapsinConsensus")
1346 protected Boolean ignoreGapsinConsensus;
1347 @XmlAttribute(name = "showConsensusHistogram")
1348 protected Boolean showConsensusHistogram;
1349 @XmlAttribute(name = "showSequenceLogo")
1350 protected Boolean showSequenceLogo;
1351 @XmlAttribute(name = "normaliseSequenceLogo")
1352 protected Boolean normaliseSequenceLogo;
1353 @XmlAttribute(name = "id")
1354 protected String id;
1357 * Gets the value of the seq property.
1360 * This accessor method returns a reference to the live list,
1361 * not a snapshot. Therefore any modification you make to the
1362 * returned list will be present inside the JAXB object.
1363 * This is why there is not a <CODE>set</CODE> method for the seq property.
1366 * For example, to add a new item, do as follows:
1368 * getSeq().add(newItem);
1373 * Objects of the following type(s) are allowed in the list
1378 public List<String> getSeq() {
1380 seq = new ArrayList<String>();
1386 * Gets the value of the annotationColours property.
1389 * possible object is
1390 * {@link AnnotationColourScheme }
1393 public AnnotationColourScheme getAnnotationColours() {
1394 return annotationColours;
1398 * Sets the value of the annotationColours property.
1402 * {@link AnnotationColourScheme }
1405 public void setAnnotationColours(AnnotationColourScheme value) {
1406 this.annotationColours = value;
1410 * Gets the value of the start property.
1413 * possible object is
1417 public Integer getStart() {
1422 * Sets the value of the start property.
1429 public void setStart(Integer value) {
1434 * Gets the value of the end property.
1437 * possible object is
1441 public Integer getEnd() {
1446 * Sets the value of the end property.
1453 public void setEnd(Integer value) {
1458 * Gets the value of the name property.
1461 * possible object is
1465 public String getName() {
1470 * Sets the value of the name property.
1477 public void setName(String value) {
1482 * Gets the value of the colour property.
1485 * possible object is
1489 public String getColour() {
1494 * Sets the value of the colour property.
1501 public void setColour(String value) {
1502 this.colour = value;
1506 * Gets the value of the consThreshold property.
1509 * possible object is
1513 public Integer getConsThreshold() {
1514 return consThreshold;
1518 * Sets the value of the consThreshold property.
1525 public void setConsThreshold(Integer value) {
1526 this.consThreshold = value;
1530 * Gets the value of the pidThreshold property.
1533 * possible object is
1537 public Integer getPidThreshold() {
1538 return pidThreshold;
1542 * Sets the value of the pidThreshold property.
1549 public void setPidThreshold(Integer value) {
1550 this.pidThreshold = value;
1554 * Gets the value of the outlineColour property.
1557 * possible object is
1561 public Integer getOutlineColour() {
1562 return outlineColour;
1566 * Sets the value of the outlineColour property.
1573 public void setOutlineColour(Integer value) {
1574 this.outlineColour = value;
1578 * Gets the value of the displayBoxes property.
1581 * possible object is
1585 public Boolean isDisplayBoxes() {
1586 return displayBoxes;
1590 * Sets the value of the displayBoxes property.
1597 public void setDisplayBoxes(Boolean value) {
1598 this.displayBoxes = value;
1602 * Gets the value of the displayText property.
1605 * possible object is
1609 public Boolean isDisplayText() {
1614 * Sets the value of the displayText property.
1621 public void setDisplayText(Boolean value) {
1622 this.displayText = value;
1626 * Gets the value of the colourText property.
1629 * possible object is
1633 public Boolean isColourText() {
1638 * Sets the value of the colourText property.
1645 public void setColourText(Boolean value) {
1646 this.colourText = value;
1650 * Gets the value of the textCol1 property.
1653 * possible object is
1657 public Integer getTextCol1() {
1662 * Sets the value of the textCol1 property.
1669 public void setTextCol1(Integer value) {
1670 this.textCol1 = value;
1674 * Gets the value of the textCol2 property.
1677 * possible object is
1681 public Integer getTextCol2() {
1686 * Sets the value of the textCol2 property.
1693 public void setTextCol2(Integer value) {
1694 this.textCol2 = value;
1698 * Gets the value of the textColThreshold property.
1701 * possible object is
1705 public Integer getTextColThreshold() {
1706 return textColThreshold;
1710 * Sets the value of the textColThreshold property.
1717 public void setTextColThreshold(Integer value) {
1718 this.textColThreshold = value;
1722 * Gets the value of the showUnconserved property.
1725 * possible object is
1729 public Boolean isShowUnconserved() {
1730 return showUnconserved;
1734 * Sets the value of the showUnconserved property.
1741 public void setShowUnconserved(Boolean value) {
1742 this.showUnconserved = value;
1746 * Gets the value of the ignoreGapsinConsensus property.
1749 * possible object is
1753 public boolean isIgnoreGapsinConsensus() {
1754 if (ignoreGapsinConsensus == null) {
1757 return ignoreGapsinConsensus;
1762 * Sets the value of the ignoreGapsinConsensus property.
1769 public void setIgnoreGapsinConsensus(Boolean value) {
1770 this.ignoreGapsinConsensus = value;
1774 * Gets the value of the showConsensusHistogram property.
1777 * possible object is
1781 public boolean isShowConsensusHistogram() {
1782 if (showConsensusHistogram == null) {
1785 return showConsensusHistogram;
1790 * Sets the value of the showConsensusHistogram property.
1797 public void setShowConsensusHistogram(Boolean value) {
1798 this.showConsensusHistogram = value;
1802 * Gets the value of the showSequenceLogo property.
1805 * possible object is
1809 public boolean isShowSequenceLogo() {
1810 if (showSequenceLogo == null) {
1813 return showSequenceLogo;
1818 * Sets the value of the showSequenceLogo property.
1825 public void setShowSequenceLogo(Boolean value) {
1826 this.showSequenceLogo = value;
1830 * Gets the value of the normaliseSequenceLogo property.
1833 * possible object is
1837 public boolean isNormaliseSequenceLogo() {
1838 if (normaliseSequenceLogo == null) {
1841 return normaliseSequenceLogo;
1846 * Sets the value of the normaliseSequenceLogo property.
1853 public void setNormaliseSequenceLogo(Boolean value) {
1854 this.normaliseSequenceLogo = value;
1858 * Gets the value of the id property.
1861 * possible object is
1865 public String getId() {
1870 * Sets the value of the id property.
1877 public void setId(String value) {
1885 * <p>Java class for anonymous complex type.
1887 * <p>The following schema fragment specifies the expected content contained within this class.
1891 * <complexContent>
1892 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1894 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1895 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1897 * <complexContent>
1898 * <extension base="{www.jalview.org}pdbentry">
1900 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1902 * <simpleContent>
1903 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1904 * <attGroup ref="{www.jalview.org}swingwindow"/>
1905 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1906 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1907 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1908 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1909 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1910 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1912 * </simpleContent>
1917 * </complexContent>
1920 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1921 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1923 * <complexContent>
1924 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1926 * <element name="secondaryStructure" maxOccurs="unbounded">
1928 * <complexContent>
1929 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1930 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1931 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1932 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1933 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1935 * </complexContent>
1939 * <attGroup ref="{www.jalview.org}swingwindow"/>
1940 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1941 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1942 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1943 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1945 * </complexContent>
1949 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1950 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1951 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1952 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1953 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1954 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1956 * </complexContent>
1962 @XmlAccessorType(XmlAccessType.FIELD)
1963 @XmlType(name = "", propOrder = {
1969 public static class JSeq {
1971 @XmlElement(namespace = "www.jalview.org")
1972 protected List<Feature> features;
1973 @XmlElement(namespace = "www.jalview.org")
1974 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1975 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1976 protected List<Integer> hiddenSequences;
1977 @XmlElement(namespace = "www.jalview.org")
1978 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1979 @XmlAttribute(name = "colour")
1980 protected Integer colour;
1981 @XmlAttribute(name = "start", required = true)
1982 protected int start;
1983 @XmlAttribute(name = "end", required = true)
1985 @XmlAttribute(name = "id", required = true)
1986 protected String id;
1987 @XmlAttribute(name = "hidden")
1988 protected Boolean hidden;
1989 @XmlAttribute(name = "viewreference")
1990 protected Boolean viewreference;
1993 * Gets the value of the features property.
1996 * This accessor method returns a reference to the live list,
1997 * not a snapshot. Therefore any modification you make to the
1998 * returned list will be present inside the JAXB object.
1999 * This is why there is not a <CODE>set</CODE> method for the features property.
2002 * For example, to add a new item, do as follows:
2004 * getFeatures().add(newItem);
2009 * Objects of the following type(s) are allowed in the list
2014 public List<Feature> getFeatures() {
2015 if (features == null) {
2016 features = new ArrayList<Feature>();
2018 return this.features;
2022 * Gets the value of the pdbids property.
2025 * This accessor method returns a reference to the live list,
2026 * not a snapshot. Therefore any modification you make to the
2027 * returned list will be present inside the JAXB object.
2028 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2031 * For example, to add a new item, do as follows:
2033 * getPdbids().add(newItem);
2038 * Objects of the following type(s) are allowed in the list
2039 * {@link JalviewModel.JSeq.Pdbids }
2043 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2044 if (pdbids == null) {
2045 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2051 * Gets the value of the hiddenSequences property.
2054 * This accessor method returns a reference to the live list,
2055 * not a snapshot. Therefore any modification you make to the
2056 * returned list will be present inside the JAXB object.
2057 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2060 * For example, to add a new item, do as follows:
2062 * getHiddenSequences().add(newItem);
2067 * Objects of the following type(s) are allowed in the list
2072 public List<Integer> getHiddenSequences() {
2073 if (hiddenSequences == null) {
2074 hiddenSequences = new ArrayList<Integer>();
2076 return this.hiddenSequences;
2080 * Gets the value of the rnaViewer property.
2083 * This accessor method returns a reference to the live list,
2084 * not a snapshot. Therefore any modification you make to the
2085 * returned list will be present inside the JAXB object.
2086 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2089 * For example, to add a new item, do as follows:
2091 * getRnaViewer().add(newItem);
2096 * Objects of the following type(s) are allowed in the list
2097 * {@link JalviewModel.JSeq.RnaViewer }
2101 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2102 if (rnaViewer == null) {
2103 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2105 return this.rnaViewer;
2109 * Gets the value of the colour property.
2112 * possible object is
2116 public Integer getColour() {
2121 * Sets the value of the colour property.
2128 public void setColour(Integer value) {
2129 this.colour = value;
2133 * Gets the value of the start property.
2136 public int getStart() {
2141 * Sets the value of the start property.
2144 public void setStart(int value) {
2149 * Gets the value of the end property.
2152 public int getEnd() {
2157 * Sets the value of the end property.
2160 public void setEnd(int value) {
2165 * Gets the value of the id property.
2168 * possible object is
2172 public String getId() {
2177 * Sets the value of the id property.
2184 public void setId(String value) {
2189 * Gets the value of the hidden property.
2192 * possible object is
2196 public Boolean isHidden() {
2201 * Sets the value of the hidden property.
2208 public void setHidden(Boolean value) {
2209 this.hidden = value;
2213 * Gets the value of the viewreference property.
2216 * possible object is
2220 public Boolean isViewreference() {
2221 return viewreference;
2225 * Sets the value of the viewreference property.
2232 public void setViewreference(Boolean value) {
2233 this.viewreference = value;
2238 * <p>Java class for anonymous complex type.
2240 * <p>The following schema fragment specifies the expected content contained within this class.
2244 * <complexContent>
2245 * <extension base="{www.jalview.org}pdbentry">
2247 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2249 * <simpleContent>
2250 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2251 * <attGroup ref="{www.jalview.org}swingwindow"/>
2252 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2253 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2254 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2255 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2256 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2257 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2259 * </simpleContent>
2264 * </complexContent>
2270 @XmlAccessorType(XmlAccessType.FIELD)
2271 @XmlType(name = "", propOrder = {
2274 public static class Pdbids
2278 @XmlElement(namespace = "www.jalview.org")
2279 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2282 * Gets the value of the structureState property.
2285 * This accessor method returns a reference to the live list,
2286 * not a snapshot. Therefore any modification you make to the
2287 * returned list will be present inside the JAXB object.
2288 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2291 * For example, to add a new item, do as follows:
2293 * getStructureState().add(newItem);
2298 * Objects of the following type(s) are allowed in the list
2299 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2303 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2304 if (structureState == null) {
2305 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2307 return this.structureState;
2312 * <p>Java class for anonymous complex type.
2314 * <p>The following schema fragment specifies the expected content contained within this class.
2318 * <simpleContent>
2319 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2320 * <attGroup ref="{www.jalview.org}swingwindow"/>
2321 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2322 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2323 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2324 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2325 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2326 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2328 * </simpleContent>
2334 @XmlAccessorType(XmlAccessType.FIELD)
2335 @XmlType(name = "", propOrder = {
2338 public static class StructureState {
2341 protected String value;
2342 @XmlAttribute(name = "visible")
2343 protected Boolean visible;
2344 @XmlAttribute(name = "viewId")
2345 protected String viewId;
2346 @XmlAttribute(name = "alignwithAlignPanel")
2347 protected Boolean alignwithAlignPanel;
2348 @XmlAttribute(name = "colourwithAlignPanel")
2349 protected Boolean colourwithAlignPanel;
2350 @XmlAttribute(name = "colourByJmol")
2351 protected Boolean colourByJmol;
2352 @XmlAttribute(name = "type")
2353 protected String type;
2354 @XmlAttribute(name = "width")
2355 protected Integer width;
2356 @XmlAttribute(name = "height")
2357 protected Integer height;
2358 @XmlAttribute(name = "xpos")
2359 protected Integer xpos;
2360 @XmlAttribute(name = "ypos")
2361 protected Integer ypos;
2364 * Gets the value of the value property.
2367 * possible object is
2371 public String getValue() {
2376 * Sets the value of the value property.
2383 public void setValue(String value) {
2388 * Gets the value of the visible property.
2391 * possible object is
2395 public Boolean isVisible() {
2400 * Sets the value of the visible property.
2407 public void setVisible(Boolean value) {
2408 this.visible = value;
2412 * Gets the value of the viewId property.
2415 * possible object is
2419 public String getViewId() {
2424 * Sets the value of the viewId property.
2431 public void setViewId(String value) {
2432 this.viewId = value;
2436 * Gets the value of the alignwithAlignPanel property.
2439 * possible object is
2443 public boolean isAlignwithAlignPanel() {
2444 if (alignwithAlignPanel == null) {
2447 return alignwithAlignPanel;
2452 * Sets the value of the alignwithAlignPanel property.
2459 public void setAlignwithAlignPanel(Boolean value) {
2460 this.alignwithAlignPanel = value;
2464 * Gets the value of the colourwithAlignPanel property.
2467 * possible object is
2471 public boolean isColourwithAlignPanel() {
2472 if (colourwithAlignPanel == null) {
2475 return colourwithAlignPanel;
2480 * Sets the value of the colourwithAlignPanel property.
2487 public void setColourwithAlignPanel(Boolean value) {
2488 this.colourwithAlignPanel = value;
2492 * Gets the value of the colourByJmol property.
2495 * possible object is
2499 public boolean isColourByJmol() {
2500 if (colourByJmol == null) {
2503 return colourByJmol;
2508 * Sets the value of the colourByJmol property.
2515 public void setColourByJmol(Boolean value) {
2516 this.colourByJmol = value;
2520 * Gets the value of the type property.
2523 * possible object is
2527 public String getType() {
2532 * Sets the value of the type property.
2539 public void setType(String value) {
2544 * Gets the value of the width property.
2547 * possible object is
2551 public Integer getWidth() {
2556 * Sets the value of the width property.
2563 public void setWidth(Integer value) {
2568 * Gets the value of the height property.
2571 * possible object is
2575 public Integer getHeight() {
2580 * Sets the value of the height property.
2587 public void setHeight(Integer value) {
2588 this.height = value;
2592 * Gets the value of the xpos property.
2595 * possible object is
2599 public Integer getXpos() {
2604 * Sets the value of the xpos property.
2611 public void setXpos(Integer value) {
2616 * Gets the value of the ypos property.
2619 * possible object is
2623 public Integer getYpos() {
2628 * Sets the value of the ypos property.
2635 public void setYpos(Integer value) {
2645 * <p>Java class for anonymous complex type.
2647 * <p>The following schema fragment specifies the expected content contained within this class.
2651 * <complexContent>
2652 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2654 * <element name="secondaryStructure" maxOccurs="unbounded">
2656 * <complexContent>
2657 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2658 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2659 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2660 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2661 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2663 * </complexContent>
2667 * <attGroup ref="{www.jalview.org}swingwindow"/>
2668 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2669 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2670 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2671 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2673 * </complexContent>
2679 @XmlAccessorType(XmlAccessType.FIELD)
2680 @XmlType(name = "", propOrder = {
2681 "secondaryStructure"
2683 public static class RnaViewer {
2685 @XmlElement(namespace = "www.jalview.org", required = true)
2686 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2687 @XmlAttribute(name = "title")
2688 protected String title;
2689 @XmlAttribute(name = "viewId")
2690 protected String viewId;
2691 @XmlAttribute(name = "dividerLocation")
2692 protected Integer dividerLocation;
2693 @XmlAttribute(name = "selectedRna")
2694 protected Integer selectedRna;
2695 @XmlAttribute(name = "width")
2696 protected Integer width;
2697 @XmlAttribute(name = "height")
2698 protected Integer height;
2699 @XmlAttribute(name = "xpos")
2700 protected Integer xpos;
2701 @XmlAttribute(name = "ypos")
2702 protected Integer ypos;
2705 * Gets the value of the secondaryStructure property.
2708 * This accessor method returns a reference to the live list,
2709 * not a snapshot. Therefore any modification you make to the
2710 * returned list will be present inside the JAXB object.
2711 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2714 * For example, to add a new item, do as follows:
2716 * getSecondaryStructure().add(newItem);
2721 * Objects of the following type(s) are allowed in the list
2722 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2726 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2727 if (secondaryStructure == null) {
2728 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2730 return this.secondaryStructure;
2734 * Gets the value of the title property.
2737 * possible object is
2741 public String getTitle() {
2746 * Sets the value of the title property.
2753 public void setTitle(String value) {
2758 * Gets the value of the viewId property.
2761 * possible object is
2765 public String getViewId() {
2770 * Sets the value of the viewId property.
2777 public void setViewId(String value) {
2778 this.viewId = value;
2782 * Gets the value of the dividerLocation property.
2785 * possible object is
2789 public Integer getDividerLocation() {
2790 return dividerLocation;
2794 * Sets the value of the dividerLocation property.
2801 public void setDividerLocation(Integer value) {
2802 this.dividerLocation = value;
2806 * Gets the value of the selectedRna property.
2809 * possible object is
2813 public Integer getSelectedRna() {
2818 * Sets the value of the selectedRna property.
2825 public void setSelectedRna(Integer value) {
2826 this.selectedRna = value;
2830 * Gets the value of the width property.
2833 * possible object is
2837 public Integer getWidth() {
2842 * Sets the value of the width property.
2849 public void setWidth(Integer value) {
2854 * Gets the value of the height property.
2857 * possible object is
2861 public Integer getHeight() {
2866 * Sets the value of the height property.
2873 public void setHeight(Integer value) {
2874 this.height = value;
2878 * Gets the value of the xpos property.
2881 * possible object is
2885 public Integer getXpos() {
2890 * Sets the value of the xpos property.
2897 public void setXpos(Integer value) {
2902 * Gets the value of the ypos property.
2905 * possible object is
2909 public Integer getYpos() {
2914 * Sets the value of the ypos property.
2921 public void setYpos(Integer value) {
2927 * <p>Java class for anonymous complex type.
2929 * <p>The following schema fragment specifies the expected content contained within this class.
2933 * <complexContent>
2934 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2935 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2936 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2937 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2938 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2940 * </complexContent>
2946 @XmlAccessorType(XmlAccessType.FIELD)
2948 public static class SecondaryStructure {
2950 @XmlAttribute(name = "title")
2951 protected String title;
2952 @XmlAttribute(name = "annotationId", required = true)
2953 protected String annotationId;
2954 @XmlAttribute(name = "gapped")
2955 protected Boolean gapped;
2956 @XmlAttribute(name = "viewerState")
2957 protected String viewerState;
2960 * Gets the value of the title property.
2963 * possible object is
2967 public String getTitle() {
2972 * Sets the value of the title property.
2979 public void setTitle(String value) {
2984 * Gets the value of the annotationId property.
2987 * possible object is
2991 public String getAnnotationId() {
2992 return annotationId;
2996 * Sets the value of the annotationId property.
3003 public void setAnnotationId(String value) {
3004 this.annotationId = value;
3008 * Gets the value of the gapped property.
3011 * possible object is
3015 public Boolean isGapped() {
3020 * Sets the value of the gapped property.
3027 public void setGapped(Boolean value) {
3028 this.gapped = value;
3032 * Gets the value of the viewerState property.
3035 * possible object is
3039 public String getViewerState() {
3044 * Sets the value of the viewerState property.
3051 public void setViewerState(String value) {
3052 this.viewerState = value;
3063 * <p>Java class for anonymous complex type.
3065 * <p>The following schema fragment specifies the expected content contained within this class.
3069 * <complexContent>
3070 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3072 * <element name="sequencePoint" maxOccurs="unbounded">
3074 * <complexContent>
3075 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3076 * <attGroup ref="{www.jalview.org}position"/>
3077 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3079 * </complexContent>
3082 * <element name="axis" maxOccurs="3" minOccurs="3">
3084 * <complexContent>
3085 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3086 * <attGroup ref="{www.jalview.org}position"/>
3088 * </complexContent>
3091 * <element name="seqPointMin">
3093 * <complexContent>
3094 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3095 * <attGroup ref="{www.jalview.org}position"/>
3097 * </complexContent>
3100 * <element name="seqPointMax">
3102 * <complexContent>
3103 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3104 * <attGroup ref="{www.jalview.org}position"/>
3106 * </complexContent>
3109 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3111 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
3112 * <attGroup ref="{www.jalview.org}swingwindow"/>
3113 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3114 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3115 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3116 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3117 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3118 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3119 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3120 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3121 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3123 * </complexContent>
3129 @XmlAccessorType(XmlAccessType.FIELD)
3130 @XmlType(name = "", propOrder = {
3137 public static class PcaViewer {
3139 @XmlElement(namespace = "www.jalview.org", required = true)
3140 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3141 @XmlElement(namespace = "www.jalview.org", required = true)
3142 protected List<JalviewModel.PcaViewer.Axis> axis;
3143 @XmlElement(namespace = "www.jalview.org", required = true)
3144 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3145 @XmlElement(namespace = "www.jalview.org", required = true)
3146 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3147 @XmlElement(namespace = "www.jalview.org", required = true)
3148 protected PcaDataType pcaData;
3149 @XmlAttribute(name = "title")
3150 protected String title;
3151 @XmlAttribute(name = "scoreModelName")
3152 protected String scoreModelName;
3153 @XmlAttribute(name = "xDim")
3154 protected Integer xDim;
3155 @XmlAttribute(name = "yDim")
3156 protected Integer yDim;
3157 @XmlAttribute(name = "zDim")
3158 protected Integer zDim;
3159 @XmlAttribute(name = "bgColour")
3160 protected Integer bgColour;
3161 @XmlAttribute(name = "scaleFactor")
3162 protected Float scaleFactor;
3163 @XmlAttribute(name = "showLabels")
3164 protected Boolean showLabels;
3165 @XmlAttribute(name = "linkToAllViews")
3166 protected Boolean linkToAllViews;
3167 @XmlAttribute(name = "includeGaps")
3168 protected Boolean includeGaps;
3169 @XmlAttribute(name = "matchGaps")
3170 protected Boolean matchGaps;
3171 @XmlAttribute(name = "includeGappedColumns")
3172 protected Boolean includeGappedColumns;
3173 @XmlAttribute(name = "denominateByShortestLength")
3174 protected Boolean denominateByShortestLength;
3175 @XmlAttribute(name = "width")
3176 protected Integer width;
3177 @XmlAttribute(name = "height")
3178 protected Integer height;
3179 @XmlAttribute(name = "xpos")
3180 protected Integer xpos;
3181 @XmlAttribute(name = "ypos")
3182 protected Integer ypos;
3185 * Gets the value of the sequencePoint property.
3188 * This accessor method returns a reference to the live list,
3189 * not a snapshot. Therefore any modification you make to the
3190 * returned list will be present inside the JAXB object.
3191 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3194 * For example, to add a new item, do as follows:
3196 * getSequencePoint().add(newItem);
3201 * Objects of the following type(s) are allowed in the list
3202 * {@link JalviewModel.PcaViewer.SequencePoint }
3206 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3207 if (sequencePoint == null) {
3208 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3210 return this.sequencePoint;
3214 * Gets the value of the axis 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 axis property.
3223 * For example, to add a new item, do as follows:
3225 * getAxis().add(newItem);
3230 * Objects of the following type(s) are allowed in the list
3231 * {@link JalviewModel.PcaViewer.Axis }
3235 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3237 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3243 * Gets the value of the seqPointMin property.
3246 * possible object is
3247 * {@link JalviewModel.PcaViewer.SeqPointMin }
3250 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3255 * Sets the value of the seqPointMin property.
3259 * {@link JalviewModel.PcaViewer.SeqPointMin }
3262 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3263 this.seqPointMin = value;
3267 * Gets the value of the seqPointMax property.
3270 * possible object is
3271 * {@link JalviewModel.PcaViewer.SeqPointMax }
3274 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3279 * Sets the value of the seqPointMax property.
3283 * {@link JalviewModel.PcaViewer.SeqPointMax }
3286 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3287 this.seqPointMax = value;
3291 * Gets the value of the pcaData property.
3294 * possible object is
3295 * {@link PcaDataType }
3298 public PcaDataType getPcaData() {
3303 * Sets the value of the pcaData property.
3307 * {@link PcaDataType }
3310 public void setPcaData(PcaDataType value) {
3311 this.pcaData = value;
3315 * Gets the value of the title property.
3318 * possible object is
3322 public String getTitle() {
3327 * Sets the value of the title property.
3334 public void setTitle(String value) {
3339 * Gets the value of the scoreModelName property.
3342 * possible object is
3346 public String getScoreModelName() {
3347 return scoreModelName;
3351 * Sets the value of the scoreModelName property.
3358 public void setScoreModelName(String value) {
3359 this.scoreModelName = value;
3363 * Gets the value of the xDim property.
3366 * possible object is
3370 public Integer getXDim() {
3375 * Sets the value of the xDim property.
3382 public void setXDim(Integer value) {
3387 * Gets the value of the yDim property.
3390 * possible object is
3394 public Integer getYDim() {
3399 * Sets the value of the yDim property.
3406 public void setYDim(Integer value) {
3411 * Gets the value of the zDim property.
3414 * possible object is
3418 public Integer getZDim() {
3423 * Sets the value of the zDim property.
3430 public void setZDim(Integer value) {
3435 * Gets the value of the bgColour property.
3438 * possible object is
3442 public Integer getBgColour() {
3447 * Sets the value of the bgColour property.
3454 public void setBgColour(Integer value) {
3455 this.bgColour = value;
3459 * Gets the value of the scaleFactor property.
3462 * possible object is
3466 public Float getScaleFactor() {
3471 * Sets the value of the scaleFactor property.
3478 public void setScaleFactor(Float value) {
3479 this.scaleFactor = value;
3483 * Gets the value of the showLabels property.
3486 * possible object is
3490 public Boolean isShowLabels() {
3495 * Sets the value of the showLabels property.
3502 public void setShowLabels(Boolean value) {
3503 this.showLabels = value;
3507 * Gets the value of the linkToAllViews property.
3510 * possible object is
3514 public Boolean isLinkToAllViews() {
3515 return linkToAllViews;
3519 * Sets the value of the linkToAllViews property.
3526 public void setLinkToAllViews(Boolean value) {
3527 this.linkToAllViews = value;
3531 * Gets the value of the includeGaps property.
3534 * possible object is
3538 public Boolean isIncludeGaps() {
3543 * Sets the value of the includeGaps property.
3550 public void setIncludeGaps(Boolean value) {
3551 this.includeGaps = value;
3555 * Gets the value of the matchGaps property.
3558 * possible object is
3562 public Boolean isMatchGaps() {
3567 * Sets the value of the matchGaps property.
3574 public void setMatchGaps(Boolean value) {
3575 this.matchGaps = value;
3579 * Gets the value of the includeGappedColumns property.
3582 * possible object is
3586 public Boolean isIncludeGappedColumns() {
3587 return includeGappedColumns;
3591 * Sets the value of the includeGappedColumns property.
3598 public void setIncludeGappedColumns(Boolean value) {
3599 this.includeGappedColumns = value;
3603 * Gets the value of the denominateByShortestLength property.
3606 * possible object is
3610 public Boolean isDenominateByShortestLength() {
3611 return denominateByShortestLength;
3615 * Sets the value of the denominateByShortestLength property.
3622 public void setDenominateByShortestLength(Boolean value) {
3623 this.denominateByShortestLength = value;
3627 * Gets the value of the width property.
3630 * possible object is
3634 public Integer getWidth() {
3639 * Sets the value of the width property.
3646 public void setWidth(Integer value) {
3651 * Gets the value of the height property.
3654 * possible object is
3658 public Integer getHeight() {
3663 * Sets the value of the height property.
3670 public void setHeight(Integer value) {
3671 this.height = value;
3675 * Gets the value of the xpos property.
3678 * possible object is
3682 public Integer getXpos() {
3687 * Sets the value of the xpos property.
3694 public void setXpos(Integer value) {
3699 * Gets the value of the ypos property.
3702 * possible object is
3706 public Integer getYpos() {
3711 * Sets the value of the ypos property.
3718 public void setYpos(Integer value) {
3724 * <p>Java class for anonymous complex type.
3726 * <p>The following schema fragment specifies the expected content contained within this class.
3730 * <complexContent>
3731 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3732 * <attGroup ref="{www.jalview.org}position"/>
3734 * </complexContent>
3740 @XmlAccessorType(XmlAccessType.FIELD)
3742 public static class Axis {
3744 @XmlAttribute(name = "xPos")
3745 protected Float xPos;
3746 @XmlAttribute(name = "yPos")
3747 protected Float yPos;
3748 @XmlAttribute(name = "zPos")
3749 protected Float zPos;
3752 * Gets the value of the xPos property.
3755 * possible object is
3759 public Float getXPos() {
3764 * Sets the value of the xPos property.
3771 public void setXPos(Float value) {
3776 * Gets the value of the yPos property.
3779 * possible object is
3783 public Float getYPos() {
3788 * Sets the value of the yPos property.
3795 public void setYPos(Float value) {
3800 * Gets the value of the zPos property.
3803 * possible object is
3807 public Float getZPos() {
3812 * Sets the value of the zPos property.
3819 public void setZPos(Float value) {
3827 * <p>Java class for anonymous complex type.
3829 * <p>The following schema fragment specifies the expected content contained within this class.
3833 * <complexContent>
3834 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3835 * <attGroup ref="{www.jalview.org}position"/>
3837 * </complexContent>
3843 @XmlAccessorType(XmlAccessType.FIELD)
3845 public static class SeqPointMax {
3847 @XmlAttribute(name = "xPos")
3848 protected Float xPos;
3849 @XmlAttribute(name = "yPos")
3850 protected Float yPos;
3851 @XmlAttribute(name = "zPos")
3852 protected Float zPos;
3855 * Gets the value of the xPos property.
3858 * possible object is
3862 public Float getXPos() {
3867 * Sets the value of the xPos property.
3874 public void setXPos(Float value) {
3879 * Gets the value of the yPos property.
3882 * possible object is
3886 public Float getYPos() {
3891 * Sets the value of the yPos property.
3898 public void setYPos(Float value) {
3903 * Gets the value of the zPos property.
3906 * possible object is
3910 public Float getZPos() {
3915 * Sets the value of the zPos property.
3922 public void setZPos(Float value) {
3930 * <p>Java class for anonymous complex type.
3932 * <p>The following schema fragment specifies the expected content contained within this class.
3936 * <complexContent>
3937 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3938 * <attGroup ref="{www.jalview.org}position"/>
3940 * </complexContent>
3946 @XmlAccessorType(XmlAccessType.FIELD)
3948 public static class SeqPointMin {
3950 @XmlAttribute(name = "xPos")
3951 protected Float xPos;
3952 @XmlAttribute(name = "yPos")
3953 protected Float yPos;
3954 @XmlAttribute(name = "zPos")
3955 protected Float zPos;
3958 * Gets the value of the xPos property.
3961 * possible object is
3965 public Float getXPos() {
3970 * Sets the value of the xPos property.
3977 public void setXPos(Float value) {
3982 * Gets the value of the yPos property.
3985 * possible object is
3989 public Float getYPos() {
3994 * Sets the value of the yPos property.
4001 public void setYPos(Float value) {
4006 * Gets the value of the zPos property.
4009 * possible object is
4013 public Float getZPos() {
4018 * Sets the value of the zPos property.
4025 public void setZPos(Float value) {
4033 * <p>Java class for anonymous complex type.
4035 * <p>The following schema fragment specifies the expected content contained within this class.
4039 * <complexContent>
4040 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4041 * <attGroup ref="{www.jalview.org}position"/>
4042 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4044 * </complexContent>
4050 @XmlAccessorType(XmlAccessType.FIELD)
4052 public static class SequencePoint {
4054 @XmlAttribute(name = "sequenceRef")
4055 protected String sequenceRef;
4056 @XmlAttribute(name = "xPos")
4057 protected Float xPos;
4058 @XmlAttribute(name = "yPos")
4059 protected Float yPos;
4060 @XmlAttribute(name = "zPos")
4061 protected Float zPos;
4064 * Gets the value of the sequenceRef property.
4067 * possible object is
4071 public String getSequenceRef() {
4076 * Sets the value of the sequenceRef property.
4083 public void setSequenceRef(String value) {
4084 this.sequenceRef = value;
4088 * Gets the value of the xPos property.
4091 * possible object is
4095 public Float getXPos() {
4100 * Sets the value of the xPos property.
4107 public void setXPos(Float value) {
4112 * Gets the value of the yPos property.
4115 * possible object is
4119 public Float getYPos() {
4124 * Sets the value of the yPos property.
4131 public void setYPos(Float value) {
4136 * Gets the value of the zPos property.
4139 * possible object is
4143 public Float getZPos() {
4148 * Sets the value of the zPos property.
4155 public void setZPos(Float value) {
4165 * <p>Java class for anonymous complex type.
4167 * <p>The following schema fragment specifies the expected content contained within this class.
4171 * <complexContent>
4172 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4173 * <sequence minOccurs="0">
4174 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4175 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4177 * <attGroup ref="{www.jalview.org}swingwindow"/>
4178 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4179 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4180 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4181 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4182 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4183 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4184 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4185 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4186 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4187 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4188 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4190 * </complexContent>
4196 @XmlAccessorType(XmlAccessType.FIELD)
4197 @XmlType(name = "", propOrder = {
4201 public static class Tree {
4203 @XmlElement(namespace = "www.jalview.org")
4204 protected String title;
4205 @XmlElement(namespace = "www.jalview.org")
4206 protected String newick;
4207 @XmlAttribute(name = "fontName")
4208 protected String fontName;
4209 @XmlAttribute(name = "fontSize")
4210 protected Integer fontSize;
4211 @XmlAttribute(name = "fontStyle")
4212 protected Integer fontStyle;
4213 @XmlAttribute(name = "threshold")
4214 protected Float threshold;
4215 @XmlAttribute(name = "showBootstrap")
4216 protected Boolean showBootstrap;
4217 @XmlAttribute(name = "showDistances")
4218 protected Boolean showDistances;
4219 @XmlAttribute(name = "markUnlinked")
4220 protected Boolean markUnlinked;
4221 @XmlAttribute(name = "fitToWindow")
4222 protected Boolean fitToWindow;
4223 @XmlAttribute(name = "currentTree")
4224 protected Boolean currentTree;
4225 @XmlAttribute(name = "id")
4226 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4228 @XmlSchemaType(name = "ID")
4229 protected String id;
4230 @XmlAttribute(name = "linkToAllViews")
4231 protected Boolean linkToAllViews;
4232 @XmlAttribute(name = "width")
4233 protected Integer width;
4234 @XmlAttribute(name = "height")
4235 protected Integer height;
4236 @XmlAttribute(name = "xpos")
4237 protected Integer xpos;
4238 @XmlAttribute(name = "ypos")
4239 protected Integer ypos;
4242 * Gets the value of the title property.
4245 * possible object is
4249 public String getTitle() {
4254 * Sets the value of the title property.
4261 public void setTitle(String value) {
4266 * Gets the value of the newick property.
4269 * possible object is
4273 public String getNewick() {
4278 * Sets the value of the newick property.
4285 public void setNewick(String value) {
4286 this.newick = value;
4290 * Gets the value of the fontName property.
4293 * possible object is
4297 public String getFontName() {
4302 * Sets the value of the fontName property.
4309 public void setFontName(String value) {
4310 this.fontName = value;
4314 * Gets the value of the fontSize property.
4317 * possible object is
4321 public Integer getFontSize() {
4326 * Sets the value of the fontSize property.
4333 public void setFontSize(Integer value) {
4334 this.fontSize = value;
4338 * Gets the value of the fontStyle property.
4341 * possible object is
4345 public Integer getFontStyle() {
4350 * Sets the value of the fontStyle property.
4357 public void setFontStyle(Integer value) {
4358 this.fontStyle = value;
4362 * Gets the value of the threshold property.
4365 * possible object is
4369 public Float getThreshold() {
4374 * Sets the value of the threshold property.
4381 public void setThreshold(Float value) {
4382 this.threshold = value;
4386 * Gets the value of the showBootstrap property.
4389 * possible object is
4393 public Boolean isShowBootstrap() {
4394 return showBootstrap;
4398 * Sets the value of the showBootstrap property.
4405 public void setShowBootstrap(Boolean value) {
4406 this.showBootstrap = value;
4410 * Gets the value of the showDistances property.
4413 * possible object is
4417 public Boolean isShowDistances() {
4418 return showDistances;
4422 * Sets the value of the showDistances property.
4429 public void setShowDistances(Boolean value) {
4430 this.showDistances = value;
4434 * Gets the value of the markUnlinked property.
4437 * possible object is
4441 public Boolean isMarkUnlinked() {
4442 return markUnlinked;
4446 * Sets the value of the markUnlinked property.
4453 public void setMarkUnlinked(Boolean value) {
4454 this.markUnlinked = value;
4458 * Gets the value of the fitToWindow property.
4461 * possible object is
4465 public Boolean isFitToWindow() {
4470 * Sets the value of the fitToWindow property.
4477 public void setFitToWindow(Boolean value) {
4478 this.fitToWindow = value;
4482 * Gets the value of the currentTree property.
4485 * possible object is
4489 public Boolean isCurrentTree() {
4494 * Sets the value of the currentTree property.
4501 public void setCurrentTree(Boolean value) {
4502 this.currentTree = value;
4506 * Gets the value of the id property.
4509 * possible object is
4513 public String getId() {
4518 * Sets the value of the id property.
4525 public void setId(String value) {
4530 * Gets the value of the linkToAllViews property.
4533 * possible object is
4537 public boolean isLinkToAllViews() {
4538 if (linkToAllViews == null) {
4541 return linkToAllViews;
4546 * Sets the value of the linkToAllViews property.
4553 public void setLinkToAllViews(Boolean value) {
4554 this.linkToAllViews = value;
4558 * Gets the value of the width property.
4561 * possible object is
4565 public Integer getWidth() {
4570 * Sets the value of the width property.
4577 public void setWidth(Integer value) {
4582 * Gets the value of the height property.
4585 * possible object is
4589 public Integer getHeight() {
4594 * Sets the value of the height property.
4601 public void setHeight(Integer value) {
4602 this.height = value;
4606 * Gets the value of the xpos property.
4609 * possible object is
4613 public Integer getXpos() {
4618 * Sets the value of the xpos property.
4625 public void setXpos(Integer value) {
4630 * Gets the value of the ypos property.
4633 * possible object is
4637 public Integer getYpos() {
4642 * Sets the value of the ypos property.
4649 public void setYpos(Integer value) {
4657 * <p>Java class for anonymous complex type.
4659 * <p>The following schema fragment specifies the expected content contained within this class.
4663 * <complexContent>
4664 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4666 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4668 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4670 * </complexContent>
4676 @XmlAccessorType(XmlAccessType.FIELD)
4677 @XmlType(name = "", propOrder = {
4680 public static class UserColours {
4682 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4683 protected JalviewUserColours userColourScheme;
4684 @XmlAttribute(name = "id")
4685 protected String id;
4688 * Gets the value of the userColourScheme property.
4691 * possible object is
4692 * {@link JalviewUserColours }
4695 public JalviewUserColours getUserColourScheme() {
4696 return userColourScheme;
4700 * Sets the value of the userColourScheme property.
4704 * {@link JalviewUserColours }
4707 public void setUserColourScheme(JalviewUserColours value) {
4708 this.userColourScheme = value;
4712 * Gets the value of the id property.
4715 * possible object is
4719 public String getId() {
4724 * Sets the value of the id property.
4731 public void setId(String value) {
4739 * <p>Java class for anonymous complex type.
4741 * <p>The following schema fragment specifies the expected content contained within this class.
4745 * <complexContent>
4746 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4748 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4749 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4751 * <complexContent>
4752 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4753 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4754 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4756 * </complexContent>
4759 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4761 * <complexContent>
4762 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4763 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4764 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4765 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4767 * </complexContent>
4771 * <attGroup ref="{www.jalview.org}swingwindow"/>
4772 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4773 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4774 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4775 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4776 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4777 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4778 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4779 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4780 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4781 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4782 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4783 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4784 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4785 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4786 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4787 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4788 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4789 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4790 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4791 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4792 * <attribute name="showAutocalcAbove" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4793 * <attribute name="sortAnnotationsBy" type="{http://www.w3.org/2001/XMLSchema}string" />
4794 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4795 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4796 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4797 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4798 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4799 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4800 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4801 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
4802 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
4803 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4804 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4805 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4806 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4807 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
4808 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
4809 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4810 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
4811 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
4812 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4813 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4814 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
4816 * </complexContent>
4822 @XmlAccessorType(XmlAccessType.FIELD)
4823 @XmlType(name = "", propOrder = {
4824 "annotationColours",
4828 public static class Viewport {
4830 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4831 protected AnnotationColourScheme annotationColours;
4832 @XmlElement(namespace = "www.jalview.org")
4833 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4834 @XmlElement(namespace = "www.jalview.org")
4835 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4836 @XmlAttribute(name = "conservationSelected")
4837 protected Boolean conservationSelected;
4838 @XmlAttribute(name = "pidSelected")
4839 protected Boolean pidSelected;
4840 @XmlAttribute(name = "bgColour")
4841 protected String bgColour;
4842 @XmlAttribute(name = "consThreshold")
4843 protected Integer consThreshold;
4844 @XmlAttribute(name = "pidThreshold")
4845 protected Integer pidThreshold;
4846 @XmlAttribute(name = "title")
4847 protected String title;
4848 @XmlAttribute(name = "showFullId")
4849 protected Boolean showFullId;
4850 @XmlAttribute(name = "rightAlignIds")
4851 protected Boolean rightAlignIds;
4852 @XmlAttribute(name = "showText")
4853 protected Boolean showText;
4854 @XmlAttribute(name = "showColourText")
4855 protected Boolean showColourText;
4856 @XmlAttribute(name = "showUnconserved")
4857 protected Boolean showUnconserved;
4858 @XmlAttribute(name = "showBoxes")
4859 protected Boolean showBoxes;
4860 @XmlAttribute(name = "wrapAlignment")
4861 protected Boolean wrapAlignment;
4862 @XmlAttribute(name = "renderGaps")
4863 protected Boolean renderGaps;
4864 @XmlAttribute(name = "showSequenceFeatures")
4865 protected Boolean showSequenceFeatures;
4866 @XmlAttribute(name = "showNPfeatureTooltip")
4867 protected Boolean showNPfeatureTooltip;
4868 @XmlAttribute(name = "showDbRefTooltip")
4869 protected Boolean showDbRefTooltip;
4870 @XmlAttribute(name = "followHighlight")
4871 protected Boolean followHighlight;
4872 @XmlAttribute(name = "followSelection")
4873 protected Boolean followSelection;
4874 @XmlAttribute(name = "showAnnotation")
4875 protected Boolean showAnnotation;
4876 @XmlAttribute(name = "showAutocalcAbove")
4877 protected Boolean showAutocalcAbove;
4878 @XmlAttribute(name = "sortAnnotationsBy")
4879 protected String sortAnnotationsBy;
4880 @XmlAttribute(name = "centreColumnLabels")
4881 protected Boolean centreColumnLabels;
4882 @XmlAttribute(name = "showGroupConservation")
4883 protected Boolean showGroupConservation;
4884 @XmlAttribute(name = "showGroupConsensus")
4885 protected Boolean showGroupConsensus;
4886 @XmlAttribute(name = "showConsensusHistogram")
4887 protected Boolean showConsensusHistogram;
4888 @XmlAttribute(name = "showSequenceLogo")
4889 protected Boolean showSequenceLogo;
4890 @XmlAttribute(name = "normaliseSequenceLogo")
4891 protected Boolean normaliseSequenceLogo;
4892 @XmlAttribute(name = "ignoreGapsinConsensus")
4893 protected Boolean ignoreGapsinConsensus;
4894 @XmlAttribute(name = "startRes")
4895 protected Integer startRes;
4896 @XmlAttribute(name = "startSeq")
4897 protected Integer startSeq;
4898 @XmlAttribute(name = "fontName")
4899 protected String fontName;
4900 @XmlAttribute(name = "fontSize")
4901 protected Integer fontSize;
4902 @XmlAttribute(name = "fontStyle")
4903 protected Integer fontStyle;
4904 @XmlAttribute(name = "scaleProteinAsCdna")
4905 protected Boolean scaleProteinAsCdna;
4906 @XmlAttribute(name = "viewName")
4907 protected String viewName;
4908 @XmlAttribute(name = "sequenceSetId")
4909 protected String sequenceSetId;
4910 @XmlAttribute(name = "gatheredViews")
4911 protected Boolean gatheredViews;
4912 @XmlAttribute(name = "textCol1")
4913 protected Integer textCol1;
4914 @XmlAttribute(name = "textCol2")
4915 protected Integer textCol2;
4916 @XmlAttribute(name = "textColThreshold")
4917 protected Integer textColThreshold;
4918 @XmlAttribute(name = "id")
4919 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4921 @XmlSchemaType(name = "ID")
4922 protected String id;
4923 @XmlAttribute(name = "complementId")
4924 protected String complementId;
4925 @XmlAttribute(name = "width")
4926 protected Integer width;
4927 @XmlAttribute(name = "height")
4928 protected Integer height;
4929 @XmlAttribute(name = "xpos")
4930 protected Integer xpos;
4931 @XmlAttribute(name = "ypos")
4932 protected Integer ypos;
4935 * Gets the value of the annotationColours property.
4938 * possible object is
4939 * {@link AnnotationColourScheme }
4942 public AnnotationColourScheme getAnnotationColours() {
4943 return annotationColours;
4947 * Sets the value of the annotationColours property.
4951 * {@link AnnotationColourScheme }
4954 public void setAnnotationColours(AnnotationColourScheme value) {
4955 this.annotationColours = value;
4959 * Gets the value of the hiddenColumns property.
4962 * This accessor method returns a reference to the live list,
4963 * not a snapshot. Therefore any modification you make to the
4964 * returned list will be present inside the JAXB object.
4965 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4968 * For example, to add a new item, do as follows:
4970 * getHiddenColumns().add(newItem);
4975 * Objects of the following type(s) are allowed in the list
4976 * {@link JalviewModel.Viewport.HiddenColumns }
4980 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
4981 if (hiddenColumns == null) {
4982 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
4984 return this.hiddenColumns;
4988 * Gets the value of the calcIdParam 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 calcIdParam property.
4997 * For example, to add a new item, do as follows:
4999 * getCalcIdParam().add(newItem);
5004 * Objects of the following type(s) are allowed in the list
5005 * {@link JalviewModel.Viewport.CalcIdParam }
5009 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5010 if (calcIdParam == null) {
5011 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5013 return this.calcIdParam;
5017 * Gets the value of the conservationSelected property.
5020 * possible object is
5024 public Boolean isConservationSelected() {
5025 return conservationSelected;
5029 * Sets the value of the conservationSelected property.
5036 public void setConservationSelected(Boolean value) {
5037 this.conservationSelected = value;
5041 * Gets the value of the pidSelected property.
5044 * possible object is
5048 public Boolean isPidSelected() {
5053 * Sets the value of the pidSelected property.
5060 public void setPidSelected(Boolean value) {
5061 this.pidSelected = value;
5065 * Gets the value of the bgColour property.
5068 * possible object is
5072 public String getBgColour() {
5077 * Sets the value of the bgColour property.
5084 public void setBgColour(String value) {
5085 this.bgColour = value;
5089 * Gets the value of the consThreshold property.
5092 * possible object is
5096 public Integer getConsThreshold() {
5097 return consThreshold;
5101 * Sets the value of the consThreshold property.
5108 public void setConsThreshold(Integer value) {
5109 this.consThreshold = value;
5113 * Gets the value of the pidThreshold property.
5116 * possible object is
5120 public Integer getPidThreshold() {
5121 return pidThreshold;
5125 * Sets the value of the pidThreshold property.
5132 public void setPidThreshold(Integer value) {
5133 this.pidThreshold = value;
5137 * Gets the value of the title property.
5140 * possible object is
5144 public String getTitle() {
5149 * Sets the value of the title property.
5156 public void setTitle(String value) {
5161 * Gets the value of the showFullId property.
5164 * possible object is
5168 public Boolean isShowFullId() {
5173 * Sets the value of the showFullId property.
5180 public void setShowFullId(Boolean value) {
5181 this.showFullId = value;
5185 * Gets the value of the rightAlignIds property.
5188 * possible object is
5192 public Boolean isRightAlignIds() {
5193 return rightAlignIds;
5197 * Sets the value of the rightAlignIds property.
5204 public void setRightAlignIds(Boolean value) {
5205 this.rightAlignIds = value;
5209 * Gets the value of the showText property.
5212 * possible object is
5216 public Boolean isShowText() {
5221 * Sets the value of the showText property.
5228 public void setShowText(Boolean value) {
5229 this.showText = value;
5233 * Gets the value of the showColourText property.
5236 * possible object is
5240 public Boolean isShowColourText() {
5241 return showColourText;
5245 * Sets the value of the showColourText property.
5252 public void setShowColourText(Boolean value) {
5253 this.showColourText = value;
5257 * Gets the value of the showUnconserved property.
5260 * possible object is
5264 public boolean isShowUnconserved() {
5265 if (showUnconserved == null) {
5268 return showUnconserved;
5273 * Sets the value of the showUnconserved property.
5280 public void setShowUnconserved(Boolean value) {
5281 this.showUnconserved = value;
5285 * Gets the value of the showBoxes property.
5288 * possible object is
5292 public Boolean isShowBoxes() {
5297 * Sets the value of the showBoxes property.
5304 public void setShowBoxes(Boolean value) {
5305 this.showBoxes = value;
5309 * Gets the value of the wrapAlignment property.
5312 * possible object is
5316 public Boolean isWrapAlignment() {
5317 return wrapAlignment;
5321 * Sets the value of the wrapAlignment property.
5328 public void setWrapAlignment(Boolean value) {
5329 this.wrapAlignment = value;
5333 * Gets the value of the renderGaps property.
5336 * possible object is
5340 public Boolean isRenderGaps() {
5345 * Sets the value of the renderGaps property.
5352 public void setRenderGaps(Boolean value) {
5353 this.renderGaps = value;
5357 * Gets the value of the showSequenceFeatures property.
5360 * possible object is
5364 public Boolean isShowSequenceFeatures() {
5365 return showSequenceFeatures;
5369 * Sets the value of the showSequenceFeatures property.
5376 public void setShowSequenceFeatures(Boolean value) {
5377 this.showSequenceFeatures = value;
5381 * Gets the value of the showNPfeatureTooltip property.
5384 * possible object is
5388 public Boolean isShowNPfeatureTooltip() {
5389 return showNPfeatureTooltip;
5393 * Sets the value of the showNPfeatureTooltip property.
5400 public void setShowNPfeatureTooltip(Boolean value) {
5401 this.showNPfeatureTooltip = value;
5405 * Gets the value of the showDbRefTooltip property.
5408 * possible object is
5412 public Boolean isShowDbRefTooltip() {
5413 return showDbRefTooltip;
5417 * Sets the value of the showDbRefTooltip property.
5424 public void setShowDbRefTooltip(Boolean value) {
5425 this.showDbRefTooltip = value;
5429 * Gets the value of the followHighlight property.
5432 * possible object is
5436 public boolean isFollowHighlight() {
5437 if (followHighlight == null) {
5440 return followHighlight;
5445 * Sets the value of the followHighlight property.
5452 public void setFollowHighlight(Boolean value) {
5453 this.followHighlight = value;
5457 * Gets the value of the followSelection property.
5460 * possible object is
5464 public boolean isFollowSelection() {
5465 if (followSelection == null) {
5468 return followSelection;
5473 * Sets the value of the followSelection property.
5480 public void setFollowSelection(Boolean value) {
5481 this.followSelection = value;
5485 * Gets the value of the showAnnotation property.
5488 * possible object is
5492 public Boolean isShowAnnotation() {
5493 return showAnnotation;
5497 * Sets the value of the showAnnotation property.
5504 public void setShowAnnotation(Boolean value) {
5505 this.showAnnotation = value;
5509 * Gets the value of the showAutocalcAbove property.
5512 * possible object is
5516 public Boolean isShowAutocalcAbove() {
5517 return showAutocalcAbove;
5521 * Sets the value of the showAutocalcAbove property.
5528 public void setShowAutocalcAbove(Boolean value) {
5529 this.showAutocalcAbove = value;
5533 * Gets the value of the sortAnnotationsBy property.
5536 * possible object is
5540 public String getSortAnnotationsBy() {
5541 return sortAnnotationsBy;
5545 * Sets the value of the sortAnnotationsBy property.
5552 public void setSortAnnotationsBy(String value) {
5553 this.sortAnnotationsBy = value;
5557 * Gets the value of the centreColumnLabels property.
5560 * possible object is
5564 public boolean isCentreColumnLabels() {
5565 if (centreColumnLabels == null) {
5568 return centreColumnLabels;
5573 * Sets the value of the centreColumnLabels property.
5580 public void setCentreColumnLabels(Boolean value) {
5581 this.centreColumnLabels = value;
5585 * Gets the value of the showGroupConservation property.
5588 * possible object is
5592 public boolean isShowGroupConservation() {
5593 if (showGroupConservation == null) {
5596 return showGroupConservation;
5601 * Sets the value of the showGroupConservation property.
5608 public void setShowGroupConservation(Boolean value) {
5609 this.showGroupConservation = value;
5613 * Gets the value of the showGroupConsensus property.
5616 * possible object is
5620 public boolean isShowGroupConsensus() {
5621 if (showGroupConsensus == null) {
5624 return showGroupConsensus;
5629 * Sets the value of the showGroupConsensus property.
5636 public void setShowGroupConsensus(Boolean value) {
5637 this.showGroupConsensus = value;
5641 * Gets the value of the showConsensusHistogram property.
5644 * possible object is
5648 public boolean isShowConsensusHistogram() {
5649 if (showConsensusHistogram == null) {
5652 return showConsensusHistogram;
5657 * Sets the value of the showConsensusHistogram property.
5664 public void setShowConsensusHistogram(Boolean value) {
5665 this.showConsensusHistogram = value;
5669 * Gets the value of the showSequenceLogo property.
5672 * possible object is
5676 public boolean isShowSequenceLogo() {
5677 if (showSequenceLogo == null) {
5680 return showSequenceLogo;
5685 * Sets the value of the showSequenceLogo property.
5692 public void setShowSequenceLogo(Boolean value) {
5693 this.showSequenceLogo = value;
5697 * Gets the value of the normaliseSequenceLogo property.
5700 * possible object is
5704 public boolean isNormaliseSequenceLogo() {
5705 if (normaliseSequenceLogo == null) {
5708 return normaliseSequenceLogo;
5713 * Sets the value of the normaliseSequenceLogo property.
5720 public void setNormaliseSequenceLogo(Boolean value) {
5721 this.normaliseSequenceLogo = value;
5725 * Gets the value of the ignoreGapsinConsensus property.
5728 * possible object is
5732 public boolean isIgnoreGapsinConsensus() {
5733 if (ignoreGapsinConsensus == null) {
5736 return ignoreGapsinConsensus;
5741 * Sets the value of the ignoreGapsinConsensus property.
5748 public void setIgnoreGapsinConsensus(Boolean value) {
5749 this.ignoreGapsinConsensus = value;
5753 * Gets the value of the startRes property.
5756 * possible object is
5760 public Integer getStartRes() {
5765 * Sets the value of the startRes property.
5772 public void setStartRes(Integer value) {
5773 this.startRes = value;
5777 * Gets the value of the startSeq property.
5780 * possible object is
5784 public Integer getStartSeq() {
5789 * Sets the value of the startSeq property.
5796 public void setStartSeq(Integer value) {
5797 this.startSeq = value;
5801 * Gets the value of the fontName property.
5804 * possible object is
5808 public String getFontName() {
5813 * Sets the value of the fontName property.
5820 public void setFontName(String value) {
5821 this.fontName = value;
5825 * Gets the value of the fontSize property.
5828 * possible object is
5832 public Integer getFontSize() {
5837 * Sets the value of the fontSize property.
5844 public void setFontSize(Integer value) {
5845 this.fontSize = value;
5849 * Gets the value of the fontStyle property.
5852 * possible object is
5856 public Integer getFontStyle() {
5861 * Sets the value of the fontStyle property.
5868 public void setFontStyle(Integer value) {
5869 this.fontStyle = value;
5873 * Gets the value of the scaleProteinAsCdna property.
5876 * possible object is
5880 public boolean isScaleProteinAsCdna() {
5881 if (scaleProteinAsCdna == null) {
5884 return scaleProteinAsCdna;
5889 * Sets the value of the scaleProteinAsCdna property.
5896 public void setScaleProteinAsCdna(Boolean value) {
5897 this.scaleProteinAsCdna = value;
5901 * Gets the value of the viewName property.
5904 * possible object is
5908 public String getViewName() {
5913 * Sets the value of the viewName property.
5920 public void setViewName(String value) {
5921 this.viewName = value;
5925 * Gets the value of the sequenceSetId property.
5928 * possible object is
5932 public String getSequenceSetId() {
5933 return sequenceSetId;
5937 * Sets the value of the sequenceSetId property.
5944 public void setSequenceSetId(String value) {
5945 this.sequenceSetId = value;
5949 * Gets the value of the gatheredViews property.
5952 * possible object is
5956 public Boolean isGatheredViews() {
5957 return gatheredViews;
5961 * Sets the value of the gatheredViews property.
5968 public void setGatheredViews(Boolean value) {
5969 this.gatheredViews = value;
5973 * Gets the value of the textCol1 property.
5976 * possible object is
5980 public Integer getTextCol1() {
5985 * Sets the value of the textCol1 property.
5992 public void setTextCol1(Integer value) {
5993 this.textCol1 = value;
5997 * Gets the value of the textCol2 property.
6000 * possible object is
6004 public Integer getTextCol2() {
6009 * Sets the value of the textCol2 property.
6016 public void setTextCol2(Integer value) {
6017 this.textCol2 = value;
6021 * Gets the value of the textColThreshold property.
6024 * possible object is
6028 public Integer getTextColThreshold() {
6029 return textColThreshold;
6033 * Sets the value of the textColThreshold property.
6040 public void setTextColThreshold(Integer value) {
6041 this.textColThreshold = value;
6045 * Gets the value of the id property.
6048 * possible object is
6052 public String getId() {
6057 * Sets the value of the id property.
6064 public void setId(String value) {
6069 * Gets the value of the complementId property.
6072 * possible object is
6076 public String getComplementId() {
6077 return complementId;
6081 * Sets the value of the complementId property.
6088 public void setComplementId(String value) {
6089 this.complementId = value;
6093 * Gets the value of the width property.
6096 * possible object is
6100 public Integer getWidth() {
6105 * Sets the value of the width property.
6112 public void setWidth(Integer value) {
6117 * Gets the value of the height property.
6120 * possible object is
6124 public Integer getHeight() {
6129 * Sets the value of the height property.
6136 public void setHeight(Integer value) {
6137 this.height = value;
6141 * Gets the value of the xpos property.
6144 * possible object is
6148 public Integer getXpos() {
6153 * Sets the value of the xpos property.
6160 public void setXpos(Integer value) {
6165 * Gets the value of the ypos property.
6168 * possible object is
6172 public Integer getYpos() {
6177 * Sets the value of the ypos property.
6184 public void setYpos(Integer value) {
6190 * <p>Java class for anonymous complex type.
6192 * <p>The following schema fragment specifies the expected content contained within this class.
6196 * <complexContent>
6197 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6198 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6199 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6200 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6202 * </complexContent>
6208 @XmlAccessorType(XmlAccessType.FIELD)
6210 public static class CalcIdParam
6211 extends WebServiceParameterSet
6214 @XmlAttribute(name = "calcId", required = true)
6215 protected String calcId;
6216 @XmlAttribute(name = "needsUpdate")
6217 protected Boolean needsUpdate;
6218 @XmlAttribute(name = "autoUpdate", required = true)
6219 protected boolean autoUpdate;
6222 * Gets the value of the calcId property.
6225 * possible object is
6229 public String getCalcId() {
6234 * Sets the value of the calcId property.
6241 public void setCalcId(String value) {
6242 this.calcId = value;
6246 * Gets the value of the needsUpdate property.
6249 * possible object is
6253 public boolean isNeedsUpdate() {
6254 if (needsUpdate == null) {
6262 * Sets the value of the needsUpdate property.
6269 public void setNeedsUpdate(Boolean value) {
6270 this.needsUpdate = value;
6274 * Gets the value of the autoUpdate property.
6277 public boolean isAutoUpdate() {
6282 * Sets the value of the autoUpdate property.
6285 public void setAutoUpdate(boolean value) {
6286 this.autoUpdate = value;
6293 * <p>Java class for anonymous complex type.
6295 * <p>The following schema fragment specifies the expected content contained within this class.
6299 * <complexContent>
6300 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6301 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6302 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6304 * </complexContent>
6310 @XmlAccessorType(XmlAccessType.FIELD)
6312 public static class HiddenColumns {
6314 @XmlAttribute(name = "start")
6315 protected Integer start;
6316 @XmlAttribute(name = "end")
6317 protected Integer end;
6320 * Gets the value of the start property.
6323 * possible object is
6327 public Integer getStart() {
6332 * Sets the value of the start property.
6339 public void setStart(Integer value) {
6344 * Gets the value of the end property.
6347 * possible object is
6351 public Integer getEnd() {
6356 * Sets the value of the end property.
6363 public void setEnd(Integer value) {