2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
4 // Any modifications to this file will be lost upon recompilation of the source schema.
5 // Generated on: 2023.05.13 at 06:58:41 PM BST
8 package jalview.xml.binding.jalview;
10 import java.util.ArrayList;
11 import java.util.List;
12 import javax.xml.bind.annotation.XmlAccessType;
13 import javax.xml.bind.annotation.XmlAccessorType;
14 import javax.xml.bind.annotation.XmlAttribute;
15 import javax.xml.bind.annotation.XmlElement;
16 import javax.xml.bind.annotation.XmlID;
17 import javax.xml.bind.annotation.XmlSchemaType;
18 import javax.xml.bind.annotation.XmlType;
19 import javax.xml.bind.annotation.XmlValue;
20 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
21 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
22 import javax.xml.datatype.XMLGregorianCalendar;
26 * Java class for JalviewModel complex type.
29 * The following schema fragment specifies the expected content contained within
33 * <complexType name="JalviewModel">
35 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
37 * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
38 * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
39 * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
41 * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
44 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
46 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
47 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
50 * <extension base="{www.jalview.org}pdbentry">
52 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
55 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
56 * <attGroup ref="{www.jalview.org}swingwindow"/>
57 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
58 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
59 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
60 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
61 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
62 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
69 * </complexContent>
72 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
73 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
76 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
78 * <element name="secondaryStructure" maxOccurs="unbounded">
81 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
82 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
83 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
84 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
85 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
87 * </complexContent>
91 * <attGroup ref="{www.jalview.org}swingwindow"/>
92 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
93 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
94 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
95 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
97 * </complexContent>
101 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
102 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
103 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
104 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
105 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
106 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
108 * </complexContent>
111 * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
113 * <complexContent>
114 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
116 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
117 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
119 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
120 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
121 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
122 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
123 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
124 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
125 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
126 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
127 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
128 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
129 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
130 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
131 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
132 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
133 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
134 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
135 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
136 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
137 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
139 * </complexContent>
142 * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
144 * <complexContent>
145 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
147 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
148 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
150 * <complexContent>
151 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
152 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
153 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
155 * </complexContent>
158 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
160 * <complexContent>
161 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
162 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
163 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
164 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
166 * </complexContent>
169 * <element name="overview" minOccurs="0">
171 * <complexContent>
172 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
173 * <attGroup ref="{www.jalview.org}swingwindow"/>
174 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
175 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
176 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
177 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
178 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
180 * </complexContent>
184 * <attGroup ref="{www.jalview.org}swingwindow"/>
185 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
187 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
188 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
189 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
190 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
191 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
192 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
193 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
194 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
195 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
196 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
197 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
198 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
199 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
200 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
201 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
202 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
203 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
204 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
205 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
206 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
207 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
208 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
209 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
210 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
211 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
212 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
213 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
214 * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
215 * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
216 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
217 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
218 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
219 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
220 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
221 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
222 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
223 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
224 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
225 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
226 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
227 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
228 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
229 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
231 * </complexContent>
234 * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
236 * <complexContent>
237 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
239 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
241 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
243 * </complexContent>
246 * <element name="tree" maxOccurs="unbounded" minOccurs="0">
248 * <complexContent>
249 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
250 * <sequence minOccurs="0">
251 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
252 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
254 * <attGroup ref="{www.jalview.org}swingwindow"/>
255 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
256 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
257 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
258 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
259 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
260 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
261 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
262 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
263 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
264 * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
265 * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
266 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
267 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
269 * </complexContent>
272 * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
274 * <complexContent>
275 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
277 * <element name="sequencePoint" maxOccurs="unbounded">
279 * <complexContent>
280 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
281 * <attGroup ref="{www.jalview.org}position"/>
282 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
284 * </complexContent>
287 * <element name="axis" maxOccurs="3" minOccurs="3">
289 * <complexContent>
290 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
291 * <attGroup ref="{www.jalview.org}position"/>
293 * </complexContent>
296 * <element name="seqPointMin">
298 * <complexContent>
299 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
300 * <attGroup ref="{www.jalview.org}position"/>
302 * </complexContent>
305 * <element name="seqPointMax">
307 * <complexContent>
308 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
309 * <attGroup ref="{www.jalview.org}position"/>
311 * </complexContent>
314 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
316 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
317 * <attGroup ref="{www.jalview.org}swingwindow"/>
318 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
319 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
320 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
321 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
322 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
323 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
324 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
325 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
326 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
328 * </complexContent>
331 * <element name="FeatureSettings" minOccurs="0">
333 * <complexContent>
334 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
336 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
338 * <complexContent>
339 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
341 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
342 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
344 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
345 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
346 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
347 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
348 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
349 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
350 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
351 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
352 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
353 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
354 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
355 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
357 * </complexContent>
360 * <element name="group" maxOccurs="unbounded" minOccurs="0">
362 * <complexContent>
363 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
364 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
365 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
367 * </complexContent>
372 * </complexContent>
378 * </complexContent>
384 @XmlAccessorType(XmlAccessType.FIELD)
386 name = "JalviewModel",
387 namespace = "www.jalview.org",
389 { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
390 "userColours", "tree", "pcaViewer", "featureSettings" })
391 public class JalviewModel
394 @XmlElement(required = true)
395 @XmlSchemaType(name = "dateTime")
396 protected XMLGregorianCalendar creationDate;
398 @XmlElement(required = true)
399 protected String version;
401 @XmlElement(required = true)
402 protected VAMSAS vamsasModel;
404 @XmlElement(name = "JSeq")
405 protected List<JalviewModel.JSeq> jSeq;
407 @XmlElement(name = "JGroup")
408 protected List<JalviewModel.JGroup> jGroup;
410 @XmlElement(name = "Viewport")
411 protected List<JalviewModel.Viewport> viewport;
413 @XmlElement(name = "UserColours")
414 protected List<JalviewModel.UserColours> userColours;
416 protected List<JalviewModel.Tree> tree;
418 @XmlElement(name = "PcaViewer")
419 protected List<JalviewModel.PcaViewer> pcaViewer;
421 @XmlElement(name = "FeatureSettings")
422 protected JalviewModel.FeatureSettings featureSettings;
425 * Gets the value of the creationDate property.
427 * @return possible object is {@link XMLGregorianCalendar }
430 public XMLGregorianCalendar getCreationDate()
436 * Sets the value of the creationDate property.
439 * allowed object is {@link XMLGregorianCalendar }
442 public void setCreationDate(XMLGregorianCalendar value)
444 this.creationDate = value;
448 * Gets the value of the version property.
450 * @return possible object is {@link String }
453 public String getVersion()
459 * Sets the value of the version property.
462 * allowed object is {@link String }
465 public void setVersion(String value)
467 this.version = value;
471 * Gets the value of the vamsasModel property.
473 * @return possible object is {@link VAMSAS }
476 public VAMSAS getVamsasModel()
482 * Sets the value of the vamsasModel property.
485 * allowed object is {@link VAMSAS }
488 public void setVamsasModel(VAMSAS value)
490 this.vamsasModel = value;
494 * Gets the value of the jSeq property.
497 * This accessor method returns a reference to the live list, not a snapshot.
498 * Therefore any modification you make to the returned list will be present
499 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
500 * for the jSeq property.
503 * For example, to add a new item, do as follows:
506 * getJSeq().add(newItem);
511 * Objects of the following type(s) are allowed in the list
512 * {@link JalviewModel.JSeq }
516 public List<JalviewModel.JSeq> getJSeq()
520 jSeq = new ArrayList<JalviewModel.JSeq>();
526 * Gets the value of the jGroup property.
529 * This accessor method returns a reference to the live list, not a snapshot.
530 * Therefore any modification you make to the returned list will be present
531 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
532 * for the jGroup property.
535 * For example, to add a new item, do as follows:
538 * getJGroup().add(newItem);
543 * Objects of the following type(s) are allowed in the list
544 * {@link JalviewModel.JGroup }
548 public List<JalviewModel.JGroup> getJGroup()
552 jGroup = new ArrayList<JalviewModel.JGroup>();
558 * Gets the value of the viewport property.
561 * This accessor method returns a reference to the live list, not a snapshot.
562 * Therefore any modification you make to the returned list will be present
563 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
564 * for the viewport property.
567 * For example, to add a new item, do as follows:
570 * getViewport().add(newItem);
575 * Objects of the following type(s) are allowed in the list
576 * {@link JalviewModel.Viewport }
580 public List<JalviewModel.Viewport> getViewport()
582 if (viewport == null)
584 viewport = new ArrayList<JalviewModel.Viewport>();
586 return this.viewport;
590 * Gets the value of the userColours property.
593 * This accessor method returns a reference to the live list, not a snapshot.
594 * Therefore any modification you make to the returned list will be present
595 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
596 * for the userColours property.
599 * For example, to add a new item, do as follows:
602 * getUserColours().add(newItem);
607 * Objects of the following type(s) are allowed in the list
608 * {@link JalviewModel.UserColours }
612 public List<JalviewModel.UserColours> getUserColours()
614 if (userColours == null)
616 userColours = new ArrayList<JalviewModel.UserColours>();
618 return this.userColours;
622 * Gets the value of the tree property.
625 * This accessor method returns a reference to the live list, not a snapshot.
626 * Therefore any modification you make to the returned list will be present
627 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
628 * for the tree property.
631 * For example, to add a new item, do as follows:
634 * getTree().add(newItem);
639 * Objects of the following type(s) are allowed in the list
640 * {@link JalviewModel.Tree }
644 public List<JalviewModel.Tree> getTree()
648 tree = new ArrayList<JalviewModel.Tree>();
654 * Gets the value of the pcaViewer property.
657 * This accessor method returns a reference to the live list, not a snapshot.
658 * Therefore any modification you make to the returned list will be present
659 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
660 * for the pcaViewer property.
663 * For example, to add a new item, do as follows:
666 * getPcaViewer().add(newItem);
671 * Objects of the following type(s) are allowed in the list
672 * {@link JalviewModel.PcaViewer }
676 public List<JalviewModel.PcaViewer> getPcaViewer()
678 if (pcaViewer == null)
680 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
682 return this.pcaViewer;
686 * Gets the value of the featureSettings property.
688 * @return possible object is {@link JalviewModel.FeatureSettings }
691 public JalviewModel.FeatureSettings getFeatureSettings()
693 return featureSettings;
697 * Sets the value of the featureSettings property.
700 * allowed object is {@link JalviewModel.FeatureSettings }
703 public void setFeatureSettings(JalviewModel.FeatureSettings value)
705 this.featureSettings = value;
710 * Java class for anonymous complex type.
713 * The following schema fragment specifies the expected content contained
718 * <complexContent>
719 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
721 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
723 * <complexContent>
724 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
726 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
727 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
729 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
730 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
731 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
732 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
733 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
734 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
735 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
736 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
737 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
738 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
739 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
740 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
742 * </complexContent>
745 * <element name="group" maxOccurs="unbounded" minOccurs="0">
747 * <complexContent>
748 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
749 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
750 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
752 * </complexContent>
757 * </complexContent>
763 @XmlAccessorType(XmlAccessType.FIELD)
764 @XmlType(name = "", propOrder = { "setting", "group" })
765 public static class FeatureSettings
768 @XmlElement(namespace = "www.jalview.org")
769 protected List<JalviewModel.FeatureSettings.Setting> setting;
771 @XmlElement(namespace = "www.jalview.org")
772 protected List<JalviewModel.FeatureSettings.Group> group;
775 * Gets the value of the setting property.
778 * This accessor method returns a reference to the live list, not a
779 * snapshot. Therefore any modification you make to the returned list will
780 * be present inside the JAXB object. This is why there is not a
781 * <CODE>set</CODE> method for the setting property.
784 * For example, to add a new item, do as follows:
787 * getSetting().add(newItem);
792 * Objects of the following type(s) are allowed in the list
793 * {@link JalviewModel.FeatureSettings.Setting }
797 public List<JalviewModel.FeatureSettings.Setting> getSetting()
801 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
807 * Gets the value of the group property.
810 * This accessor method returns a reference to the live list, not a
811 * snapshot. Therefore any modification you make to the returned list will
812 * be present inside the JAXB object. This is why there is not a
813 * <CODE>set</CODE> method for the group property.
816 * For example, to add a new item, do as follows:
819 * getGroup().add(newItem);
824 * Objects of the following type(s) are allowed in the list
825 * {@link JalviewModel.FeatureSettings.Group }
829 public List<JalviewModel.FeatureSettings.Group> getGroup()
833 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
840 * Java class for anonymous complex type.
843 * The following schema fragment specifies the expected content contained
848 * <complexContent>
849 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
850 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
851 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
853 * </complexContent>
859 @XmlAccessorType(XmlAccessType.FIELD)
861 public static class Group
864 @XmlAttribute(name = "name", required = true)
865 protected String name;
867 @XmlAttribute(name = "display", required = true)
868 protected boolean display;
871 * Gets the value of the name property.
873 * @return possible object is {@link String }
876 public String getName()
882 * Sets the value of the name property.
885 * allowed object is {@link String }
888 public void setName(String value)
894 * Gets the value of the display property.
897 public boolean isDisplay()
903 * Sets the value of the display property.
906 public void setDisplay(boolean value)
908 this.display = value;
915 * Java class for anonymous complex type.
918 * The following schema fragment specifies the expected content contained
923 * <complexContent>
924 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
926 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
927 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
929 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
930 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
931 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
932 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
933 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
934 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
935 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
936 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
937 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
938 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
939 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
940 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
942 * </complexContent>
948 @XmlAccessorType(XmlAccessType.FIELD)
949 @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
950 public static class Setting
953 @XmlElement(namespace = "www.jalview.org")
954 protected List<String> attributeName;
956 @XmlElement(namespace = "www.jalview.org")
957 protected FeatureMatcherSet matcherSet;
959 @XmlAttribute(name = "type", required = true)
960 protected String type;
962 @XmlAttribute(name = "colour", required = true)
963 protected int colour;
965 @XmlAttribute(name = "display", required = true)
966 protected boolean display;
968 @XmlAttribute(name = "order")
969 protected Float order;
971 @XmlAttribute(name = "mincolour")
972 protected Integer mincolour;
974 @XmlAttribute(name = "noValueColour")
975 protected NoValueColour noValueColour;
977 @XmlAttribute(name = "threshold")
978 protected Float threshold;
980 @XmlAttribute(name = "threshstate")
981 protected Integer threshstate;
983 @XmlAttribute(name = "max")
986 @XmlAttribute(name = "min")
989 @XmlAttribute(name = "colourByLabel")
990 protected Boolean colourByLabel;
992 @XmlAttribute(name = "autoScale")
993 protected Boolean autoScale;
996 * Gets the value of the attributeName property.
999 * This accessor method returns a reference to the live list, not a
1000 * snapshot. Therefore any modification you make to the returned list will
1001 * be present inside the JAXB object. This is why there is not a
1002 * <CODE>set</CODE> method for the attributeName property.
1005 * For example, to add a new item, do as follows:
1008 * getAttributeName().add(newItem);
1013 * Objects of the following type(s) are allowed in the list {@link String
1018 public List<String> getAttributeName()
1020 if (attributeName == null)
1022 attributeName = new ArrayList<String>();
1024 return this.attributeName;
1028 * Gets the value of the matcherSet property.
1030 * @return possible object is {@link FeatureMatcherSet }
1033 public FeatureMatcherSet getMatcherSet()
1039 * Sets the value of the matcherSet property.
1042 * allowed object is {@link FeatureMatcherSet }
1045 public void setMatcherSet(FeatureMatcherSet value)
1047 this.matcherSet = value;
1051 * Gets the value of the type property.
1053 * @return possible object is {@link String }
1056 public String getType()
1062 * Sets the value of the type property.
1065 * allowed object is {@link String }
1068 public void setType(String value)
1074 * Gets the value of the colour property.
1077 public int getColour()
1083 * Sets the value of the colour property.
1086 public void setColour(int value)
1088 this.colour = value;
1092 * Gets the value of the display property.
1095 public boolean isDisplay()
1101 * Sets the value of the display property.
1104 public void setDisplay(boolean value)
1106 this.display = value;
1110 * Gets the value of the order property.
1112 * @return possible object is {@link Float }
1115 public Float getOrder()
1121 * Sets the value of the order property.
1124 * allowed object is {@link Float }
1127 public void setOrder(Float value)
1133 * Gets the value of the mincolour property.
1135 * @return possible object is {@link Integer }
1138 public Integer getMincolour()
1144 * Sets the value of the mincolour property.
1147 * allowed object is {@link Integer }
1150 public void setMincolour(Integer value)
1152 this.mincolour = value;
1156 * Gets the value of the noValueColour property.
1158 * @return possible object is {@link NoValueColour }
1161 public NoValueColour getNoValueColour()
1163 if (noValueColour == null)
1165 return NoValueColour.MIN;
1169 return noValueColour;
1174 * Sets the value of the noValueColour property.
1177 * allowed object is {@link NoValueColour }
1180 public void setNoValueColour(NoValueColour value)
1182 this.noValueColour = value;
1186 * Gets the value of the threshold property.
1188 * @return possible object is {@link Float }
1191 public Float getThreshold()
1197 * Sets the value of the threshold property.
1200 * allowed object is {@link Float }
1203 public void setThreshold(Float value)
1205 this.threshold = value;
1209 * Gets the value of the threshstate property.
1211 * @return possible object is {@link Integer }
1214 public Integer getThreshstate()
1220 * Sets the value of the threshstate property.
1223 * allowed object is {@link Integer }
1226 public void setThreshstate(Integer value)
1228 this.threshstate = value;
1232 * Gets the value of the max property.
1234 * @return possible object is {@link Float }
1237 public Float getMax()
1243 * Sets the value of the max property.
1246 * allowed object is {@link Float }
1249 public void setMax(Float value)
1255 * Gets the value of the min property.
1257 * @return possible object is {@link Float }
1260 public Float getMin()
1266 * Sets the value of the min property.
1269 * allowed object is {@link Float }
1272 public void setMin(Float value)
1278 * Gets the value of the colourByLabel property.
1280 * @return possible object is {@link Boolean }
1283 public Boolean isColourByLabel()
1285 return colourByLabel;
1289 * Sets the value of the colourByLabel property.
1292 * allowed object is {@link Boolean }
1295 public void setColourByLabel(Boolean value)
1297 this.colourByLabel = value;
1301 * Gets the value of the autoScale property.
1303 * @return possible object is {@link Boolean }
1306 public Boolean isAutoScale()
1312 * Sets the value of the autoScale property.
1315 * allowed object is {@link Boolean }
1318 public void setAutoScale(Boolean value)
1320 this.autoScale = value;
1329 * Java class for anonymous complex type.
1332 * The following schema fragment specifies the expected content contained
1333 * within this class.
1337 * <complexContent>
1338 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1340 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1341 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1343 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1344 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1345 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1346 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1347 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1348 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1349 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1350 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1351 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1352 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1353 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1354 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1355 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1356 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1357 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1358 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1359 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1360 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1361 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1363 * </complexContent>
1369 @XmlAccessorType(XmlAccessType.FIELD)
1370 @XmlType(name = "", propOrder = { "seq", "annotationColours" })
1371 public static class JGroup
1374 @XmlElement(namespace = "www.jalview.org", required = true)
1375 protected List<String> seq;
1377 @XmlElement(namespace = "www.jalview.org")
1378 protected AnnotationColourScheme annotationColours;
1380 @XmlAttribute(name = "start")
1381 protected Integer start;
1383 @XmlAttribute(name = "end")
1384 protected Integer end;
1386 @XmlAttribute(name = "name")
1387 protected String name;
1389 @XmlAttribute(name = "colour")
1390 protected String colour;
1392 @XmlAttribute(name = "consThreshold")
1393 protected Integer consThreshold;
1395 @XmlAttribute(name = "pidThreshold")
1396 protected Integer pidThreshold;
1398 @XmlAttribute(name = "outlineColour")
1399 protected Integer outlineColour;
1401 @XmlAttribute(name = "displayBoxes")
1402 protected Boolean displayBoxes;
1404 @XmlAttribute(name = "displayText")
1405 protected Boolean displayText;
1407 @XmlAttribute(name = "colourText")
1408 protected Boolean colourText;
1410 @XmlAttribute(name = "textCol1")
1411 protected Integer textCol1;
1413 @XmlAttribute(name = "textCol2")
1414 protected Integer textCol2;
1416 @XmlAttribute(name = "textColThreshold")
1417 protected Integer textColThreshold;
1419 @XmlAttribute(name = "showUnconserved")
1420 protected Boolean showUnconserved;
1422 @XmlAttribute(name = "ignoreGapsinConsensus")
1423 protected Boolean ignoreGapsinConsensus;
1425 @XmlAttribute(name = "showConsensusHistogram")
1426 protected Boolean showConsensusHistogram;
1428 @XmlAttribute(name = "showSequenceLogo")
1429 protected Boolean showSequenceLogo;
1431 @XmlAttribute(name = "normaliseSequenceLogo")
1432 protected Boolean normaliseSequenceLogo;
1434 @XmlAttribute(name = "id")
1435 protected String id;
1438 * Gets the value of the seq property.
1441 * This accessor method returns a reference to the live list, not a
1442 * snapshot. Therefore any modification you make to the returned list will
1443 * be present inside the JAXB object. This is why there is not a
1444 * <CODE>set</CODE> method for the seq property.
1447 * For example, to add a new item, do as follows:
1450 * getSeq().add(newItem);
1455 * Objects of the following type(s) are allowed in the list {@link String }
1459 public List<String> getSeq()
1463 seq = new ArrayList<String>();
1469 * Gets the value of the annotationColours property.
1471 * @return possible object is {@link AnnotationColourScheme }
1474 public AnnotationColourScheme getAnnotationColours()
1476 return annotationColours;
1480 * Sets the value of the annotationColours property.
1483 * allowed object is {@link AnnotationColourScheme }
1486 public void setAnnotationColours(AnnotationColourScheme value)
1488 this.annotationColours = value;
1492 * Gets the value of the start property.
1494 * @return possible object is {@link Integer }
1497 public Integer getStart()
1503 * Sets the value of the start property.
1506 * allowed object is {@link Integer }
1509 public void setStart(Integer value)
1515 * Gets the value of the end property.
1517 * @return possible object is {@link Integer }
1520 public Integer getEnd()
1526 * Sets the value of the end property.
1529 * allowed object is {@link Integer }
1532 public void setEnd(Integer value)
1538 * Gets the value of the name property.
1540 * @return possible object is {@link String }
1543 public String getName()
1549 * Sets the value of the name property.
1552 * allowed object is {@link String }
1555 public void setName(String value)
1561 * Gets the value of the colour property.
1563 * @return possible object is {@link String }
1566 public String getColour()
1572 * Sets the value of the colour property.
1575 * allowed object is {@link String }
1578 public void setColour(String value)
1580 this.colour = value;
1584 * Gets the value of the consThreshold property.
1586 * @return possible object is {@link Integer }
1589 public Integer getConsThreshold()
1591 return consThreshold;
1595 * Sets the value of the consThreshold property.
1598 * allowed object is {@link Integer }
1601 public void setConsThreshold(Integer value)
1603 this.consThreshold = value;
1607 * Gets the value of the pidThreshold property.
1609 * @return possible object is {@link Integer }
1612 public Integer getPidThreshold()
1614 return pidThreshold;
1618 * Sets the value of the pidThreshold property.
1621 * allowed object is {@link Integer }
1624 public void setPidThreshold(Integer value)
1626 this.pidThreshold = value;
1630 * Gets the value of the outlineColour property.
1632 * @return possible object is {@link Integer }
1635 public Integer getOutlineColour()
1637 return outlineColour;
1641 * Sets the value of the outlineColour property.
1644 * allowed object is {@link Integer }
1647 public void setOutlineColour(Integer value)
1649 this.outlineColour = value;
1653 * Gets the value of the displayBoxes property.
1655 * @return possible object is {@link Boolean }
1658 public Boolean isDisplayBoxes()
1660 return displayBoxes;
1664 * Sets the value of the displayBoxes property.
1667 * allowed object is {@link Boolean }
1670 public void setDisplayBoxes(Boolean value)
1672 this.displayBoxes = value;
1676 * Gets the value of the displayText property.
1678 * @return possible object is {@link Boolean }
1681 public Boolean isDisplayText()
1687 * Sets the value of the displayText property.
1690 * allowed object is {@link Boolean }
1693 public void setDisplayText(Boolean value)
1695 this.displayText = value;
1699 * Gets the value of the colourText property.
1701 * @return possible object is {@link Boolean }
1704 public Boolean isColourText()
1710 * Sets the value of the colourText property.
1713 * allowed object is {@link Boolean }
1716 public void setColourText(Boolean value)
1718 this.colourText = value;
1722 * Gets the value of the textCol1 property.
1724 * @return possible object is {@link Integer }
1727 public Integer getTextCol1()
1733 * Sets the value of the textCol1 property.
1736 * allowed object is {@link Integer }
1739 public void setTextCol1(Integer value)
1741 this.textCol1 = value;
1745 * Gets the value of the textCol2 property.
1747 * @return possible object is {@link Integer }
1750 public Integer getTextCol2()
1756 * Sets the value of the textCol2 property.
1759 * allowed object is {@link Integer }
1762 public void setTextCol2(Integer value)
1764 this.textCol2 = value;
1768 * Gets the value of the textColThreshold property.
1770 * @return possible object is {@link Integer }
1773 public Integer getTextColThreshold()
1775 return textColThreshold;
1779 * Sets the value of the textColThreshold property.
1782 * allowed object is {@link Integer }
1785 public void setTextColThreshold(Integer value)
1787 this.textColThreshold = value;
1791 * Gets the value of the showUnconserved property.
1793 * @return possible object is {@link Boolean }
1796 public Boolean isShowUnconserved()
1798 return showUnconserved;
1802 * Sets the value of the showUnconserved property.
1805 * allowed object is {@link Boolean }
1808 public void setShowUnconserved(Boolean value)
1810 this.showUnconserved = value;
1814 * Gets the value of the ignoreGapsinConsensus property.
1816 * @return possible object is {@link Boolean }
1819 public boolean isIgnoreGapsinConsensus()
1821 if (ignoreGapsinConsensus == null)
1827 return ignoreGapsinConsensus;
1832 * Sets the value of the ignoreGapsinConsensus property.
1835 * allowed object is {@link Boolean }
1838 public void setIgnoreGapsinConsensus(Boolean value)
1840 this.ignoreGapsinConsensus = value;
1844 * Gets the value of the showConsensusHistogram property.
1846 * @return possible object is {@link Boolean }
1849 public boolean isShowConsensusHistogram()
1851 if (showConsensusHistogram == null)
1857 return showConsensusHistogram;
1862 * Sets the value of the showConsensusHistogram property.
1865 * allowed object is {@link Boolean }
1868 public void setShowConsensusHistogram(Boolean value)
1870 this.showConsensusHistogram = value;
1874 * Gets the value of the showSequenceLogo property.
1876 * @return possible object is {@link Boolean }
1879 public boolean isShowSequenceLogo()
1881 if (showSequenceLogo == null)
1887 return showSequenceLogo;
1892 * Sets the value of the showSequenceLogo property.
1895 * allowed object is {@link Boolean }
1898 public void setShowSequenceLogo(Boolean value)
1900 this.showSequenceLogo = value;
1904 * Gets the value of the normaliseSequenceLogo property.
1906 * @return possible object is {@link Boolean }
1909 public boolean isNormaliseSequenceLogo()
1911 if (normaliseSequenceLogo == null)
1917 return normaliseSequenceLogo;
1922 * Sets the value of the normaliseSequenceLogo property.
1925 * allowed object is {@link Boolean }
1928 public void setNormaliseSequenceLogo(Boolean value)
1930 this.normaliseSequenceLogo = value;
1934 * Gets the value of the id property.
1936 * @return possible object is {@link String }
1939 public String getId()
1945 * Sets the value of the id property.
1948 * allowed object is {@link String }
1951 public void setId(String value)
1960 * Java class for anonymous complex type.
1963 * The following schema fragment specifies the expected content contained
1964 * within this class.
1968 * <complexContent>
1969 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1971 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1972 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1974 * <complexContent>
1975 * <extension base="{www.jalview.org}pdbentry">
1977 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1979 * <simpleContent>
1980 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1981 * <attGroup ref="{www.jalview.org}swingwindow"/>
1982 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1983 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1984 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1985 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1986 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1987 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1989 * </simpleContent>
1994 * </complexContent>
1997 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1998 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
2000 * <complexContent>
2001 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2003 * <element name="secondaryStructure" maxOccurs="unbounded">
2005 * <complexContent>
2006 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2007 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2008 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2009 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2010 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2012 * </complexContent>
2016 * <attGroup ref="{www.jalview.org}swingwindow"/>
2017 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2018 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2019 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2020 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2022 * </complexContent>
2026 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
2027 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
2028 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
2029 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2030 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2031 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2033 * </complexContent>
2039 @XmlAccessorType(XmlAccessType.FIELD)
2043 { "features", "pdbids", "hiddenSequences", "rnaViewer" })
2044 public static class JSeq
2047 @XmlElement(namespace = "www.jalview.org")
2048 protected List<Feature> features;
2050 @XmlElement(namespace = "www.jalview.org")
2051 protected List<JalviewModel.JSeq.Pdbids> pdbids;
2053 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
2054 protected List<Integer> hiddenSequences;
2056 @XmlElement(namespace = "www.jalview.org")
2057 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
2059 @XmlAttribute(name = "colour")
2060 protected Integer colour;
2062 @XmlAttribute(name = "start", required = true)
2063 protected int start;
2065 @XmlAttribute(name = "end", required = true)
2068 @XmlAttribute(name = "id", required = true)
2069 protected String id;
2071 @XmlAttribute(name = "hidden")
2072 protected Boolean hidden;
2074 @XmlAttribute(name = "viewreference")
2075 protected Boolean viewreference;
2078 * Gets the value of the features property.
2081 * This accessor method returns a reference to the live list, not a
2082 * snapshot. Therefore any modification you make to the returned list will
2083 * be present inside the JAXB object. This is why there is not a
2084 * <CODE>set</CODE> method for the features property.
2087 * For example, to add a new item, do as follows:
2090 * getFeatures().add(newItem);
2095 * Objects of the following type(s) are allowed in the list {@link Feature }
2099 public List<Feature> getFeatures()
2101 if (features == null)
2103 features = new ArrayList<Feature>();
2105 return this.features;
2109 * Gets the value of the pdbids property.
2112 * This accessor method returns a reference to the live list, not a
2113 * snapshot. Therefore any modification you make to the returned list will
2114 * be present inside the JAXB object. This is why there is not a
2115 * <CODE>set</CODE> method for the pdbids property.
2118 * For example, to add a new item, do as follows:
2121 * getPdbids().add(newItem);
2126 * Objects of the following type(s) are allowed in the list
2127 * {@link JalviewModel.JSeq.Pdbids }
2131 public List<JalviewModel.JSeq.Pdbids> getPdbids()
2135 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2141 * Gets the value of the hiddenSequences property.
2144 * This accessor method returns a reference to the live list, not a
2145 * snapshot. Therefore any modification you make to the returned list will
2146 * be present inside the JAXB object. This is why there is not a
2147 * <CODE>set</CODE> method for the hiddenSequences property.
2150 * For example, to add a new item, do as follows:
2153 * getHiddenSequences().add(newItem);
2158 * Objects of the following type(s) are allowed in the list {@link Integer }
2162 public List<Integer> getHiddenSequences()
2164 if (hiddenSequences == null)
2166 hiddenSequences = new ArrayList<Integer>();
2168 return this.hiddenSequences;
2172 * Gets the value of the rnaViewer property.
2175 * This accessor method returns a reference to the live list, not a
2176 * snapshot. Therefore any modification you make to the returned list will
2177 * be present inside the JAXB object. This is why there is not a
2178 * <CODE>set</CODE> method for the rnaViewer property.
2181 * For example, to add a new item, do as follows:
2184 * getRnaViewer().add(newItem);
2189 * Objects of the following type(s) are allowed in the list
2190 * {@link JalviewModel.JSeq.RnaViewer }
2194 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
2196 if (rnaViewer == null)
2198 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2200 return this.rnaViewer;
2204 * Gets the value of the colour property.
2206 * @return possible object is {@link Integer }
2209 public Integer getColour()
2215 * Sets the value of the colour property.
2218 * allowed object is {@link Integer }
2221 public void setColour(Integer value)
2223 this.colour = value;
2227 * Gets the value of the start property.
2230 public int getStart()
2236 * Sets the value of the start property.
2239 public void setStart(int value)
2245 * Gets the value of the end property.
2254 * Sets the value of the end property.
2257 public void setEnd(int value)
2263 * Gets the value of the id property.
2265 * @return possible object is {@link String }
2268 public String getId()
2274 * Sets the value of the id property.
2277 * allowed object is {@link String }
2280 public void setId(String value)
2286 * Gets the value of the hidden property.
2288 * @return possible object is {@link Boolean }
2291 public Boolean isHidden()
2297 * Sets the value of the hidden property.
2300 * allowed object is {@link Boolean }
2303 public void setHidden(Boolean value)
2305 this.hidden = value;
2309 * Gets the value of the viewreference property.
2311 * @return possible object is {@link Boolean }
2314 public Boolean isViewreference()
2316 return viewreference;
2320 * Sets the value of the viewreference property.
2323 * allowed object is {@link Boolean }
2326 public void setViewreference(Boolean value)
2328 this.viewreference = value;
2333 * Java class for anonymous complex type.
2336 * The following schema fragment specifies the expected content contained
2337 * within this class.
2341 * <complexContent>
2342 * <extension base="{www.jalview.org}pdbentry">
2344 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2346 * <simpleContent>
2347 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2348 * <attGroup ref="{www.jalview.org}swingwindow"/>
2349 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2350 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2351 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2352 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2353 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2354 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2356 * </simpleContent>
2361 * </complexContent>
2367 @XmlAccessorType(XmlAccessType.FIELD)
2368 @XmlType(name = "", propOrder = { "structureState" })
2369 public static class Pdbids extends Pdbentry
2372 @XmlElement(namespace = "www.jalview.org")
2373 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2376 * Gets the value of the structureState property.
2379 * This accessor method returns a reference to the live list, not a
2380 * snapshot. Therefore any modification you make to the returned list will
2381 * be present inside the JAXB object. This is why there is not a
2382 * <CODE>set</CODE> method for the structureState property.
2385 * For example, to add a new item, do as follows:
2388 * getStructureState().add(newItem);
2393 * Objects of the following type(s) are allowed in the list
2394 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2398 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
2400 if (structureState == null)
2402 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2404 return this.structureState;
2409 * Java class for anonymous complex type.
2412 * The following schema fragment specifies the expected content contained
2413 * within this class.
2417 * <simpleContent>
2418 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2419 * <attGroup ref="{www.jalview.org}swingwindow"/>
2420 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2421 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2422 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2423 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2424 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2425 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2427 * </simpleContent>
2433 @XmlAccessorType(XmlAccessType.FIELD)
2434 @XmlType(name = "", propOrder = { "value" })
2435 public static class StructureState
2439 protected String value;
2441 @XmlAttribute(name = "visible")
2442 protected Boolean visible;
2444 @XmlAttribute(name = "viewId")
2445 protected String viewId;
2447 @XmlAttribute(name = "alignwithAlignPanel")
2448 protected Boolean alignwithAlignPanel;
2450 @XmlAttribute(name = "colourwithAlignPanel")
2451 protected Boolean colourwithAlignPanel;
2453 @XmlAttribute(name = "colourByJmol")
2454 protected Boolean colourByJmol;
2456 @XmlAttribute(name = "type")
2457 protected String type;
2459 @XmlAttribute(name = "width")
2460 protected Integer width;
2462 @XmlAttribute(name = "height")
2463 protected Integer height;
2465 @XmlAttribute(name = "xpos")
2466 protected Integer xpos;
2468 @XmlAttribute(name = "ypos")
2469 protected Integer ypos;
2472 * Gets the value of the value property.
2474 * @return possible object is {@link String }
2477 public String getValue()
2483 * Sets the value of the value property.
2486 * allowed object is {@link String }
2489 public void setValue(String value)
2495 * Gets the value of the visible property.
2497 * @return possible object is {@link Boolean }
2500 public Boolean isVisible()
2506 * Sets the value of the visible property.
2509 * allowed object is {@link Boolean }
2512 public void setVisible(Boolean value)
2514 this.visible = value;
2518 * Gets the value of the viewId property.
2520 * @return possible object is {@link String }
2523 public String getViewId()
2529 * Sets the value of the viewId property.
2532 * allowed object is {@link String }
2535 public void setViewId(String value)
2537 this.viewId = value;
2541 * Gets the value of the alignwithAlignPanel property.
2543 * @return possible object is {@link Boolean }
2546 public boolean isAlignwithAlignPanel()
2548 if (alignwithAlignPanel == null)
2554 return alignwithAlignPanel;
2559 * Sets the value of the alignwithAlignPanel property.
2562 * allowed object is {@link Boolean }
2565 public void setAlignwithAlignPanel(Boolean value)
2567 this.alignwithAlignPanel = value;
2571 * Gets the value of the colourwithAlignPanel property.
2573 * @return possible object is {@link Boolean }
2576 public boolean isColourwithAlignPanel()
2578 if (colourwithAlignPanel == null)
2584 return colourwithAlignPanel;
2589 * Sets the value of the colourwithAlignPanel property.
2592 * allowed object is {@link Boolean }
2595 public void setColourwithAlignPanel(Boolean value)
2597 this.colourwithAlignPanel = value;
2601 * Gets the value of the colourByJmol property.
2603 * @return possible object is {@link Boolean }
2606 public boolean isColourByJmol()
2608 if (colourByJmol == null)
2614 return colourByJmol;
2619 * Sets the value of the colourByJmol property.
2622 * allowed object is {@link Boolean }
2625 public void setColourByJmol(Boolean value)
2627 this.colourByJmol = value;
2631 * Gets the value of the type property.
2633 * @return possible object is {@link String }
2636 public String getType()
2642 * Sets the value of the type property.
2645 * allowed object is {@link String }
2648 public void setType(String value)
2654 * Gets the value of the width property.
2656 * @return possible object is {@link Integer }
2659 public Integer getWidth()
2665 * Sets the value of the width property.
2668 * allowed object is {@link Integer }
2671 public void setWidth(Integer value)
2677 * Gets the value of the height property.
2679 * @return possible object is {@link Integer }
2682 public Integer getHeight()
2688 * Sets the value of the height property.
2691 * allowed object is {@link Integer }
2694 public void setHeight(Integer value)
2696 this.height = value;
2700 * Gets the value of the xpos property.
2702 * @return possible object is {@link Integer }
2705 public Integer getXpos()
2711 * Sets the value of the xpos property.
2714 * allowed object is {@link Integer }
2717 public void setXpos(Integer value)
2723 * Gets the value of the ypos property.
2725 * @return possible object is {@link Integer }
2728 public Integer getYpos()
2734 * Sets the value of the ypos property.
2737 * allowed object is {@link Integer }
2740 public void setYpos(Integer value)
2751 * Java class for anonymous complex type.
2754 * The following schema fragment specifies the expected content contained
2755 * within this class.
2759 * <complexContent>
2760 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2762 * <element name="secondaryStructure" maxOccurs="unbounded">
2764 * <complexContent>
2765 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2766 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2767 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2768 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2769 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2771 * </complexContent>
2775 * <attGroup ref="{www.jalview.org}swingwindow"/>
2776 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2777 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2778 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2779 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2781 * </complexContent>
2787 @XmlAccessorType(XmlAccessType.FIELD)
2788 @XmlType(name = "", propOrder = { "secondaryStructure" })
2789 public static class RnaViewer
2792 @XmlElement(namespace = "www.jalview.org", required = true)
2793 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2795 @XmlAttribute(name = "title")
2796 protected String title;
2798 @XmlAttribute(name = "viewId")
2799 protected String viewId;
2801 @XmlAttribute(name = "dividerLocation")
2802 protected Integer dividerLocation;
2804 @XmlAttribute(name = "selectedRna")
2805 protected Integer selectedRna;
2807 @XmlAttribute(name = "width")
2808 protected Integer width;
2810 @XmlAttribute(name = "height")
2811 protected Integer height;
2813 @XmlAttribute(name = "xpos")
2814 protected Integer xpos;
2816 @XmlAttribute(name = "ypos")
2817 protected Integer ypos;
2820 * Gets the value of the secondaryStructure property.
2823 * This accessor method returns a reference to the live list, not a
2824 * snapshot. Therefore any modification you make to the returned list will
2825 * be present inside the JAXB object. This is why there is not a
2826 * <CODE>set</CODE> method for the secondaryStructure property.
2829 * For example, to add a new item, do as follows:
2832 * getSecondaryStructure().add(newItem);
2837 * Objects of the following type(s) are allowed in the list
2838 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2842 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
2844 if (secondaryStructure == null)
2846 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2848 return this.secondaryStructure;
2852 * Gets the value of the title property.
2854 * @return possible object is {@link String }
2857 public String getTitle()
2863 * Sets the value of the title property.
2866 * allowed object is {@link String }
2869 public void setTitle(String value)
2875 * Gets the value of the viewId property.
2877 * @return possible object is {@link String }
2880 public String getViewId()
2886 * Sets the value of the viewId property.
2889 * allowed object is {@link String }
2892 public void setViewId(String value)
2894 this.viewId = value;
2898 * Gets the value of the dividerLocation property.
2900 * @return possible object is {@link Integer }
2903 public Integer getDividerLocation()
2905 return dividerLocation;
2909 * Sets the value of the dividerLocation property.
2912 * allowed object is {@link Integer }
2915 public void setDividerLocation(Integer value)
2917 this.dividerLocation = value;
2921 * Gets the value of the selectedRna property.
2923 * @return possible object is {@link Integer }
2926 public Integer getSelectedRna()
2932 * Sets the value of the selectedRna property.
2935 * allowed object is {@link Integer }
2938 public void setSelectedRna(Integer value)
2940 this.selectedRna = value;
2944 * Gets the value of the width property.
2946 * @return possible object is {@link Integer }
2949 public Integer getWidth()
2955 * Sets the value of the width property.
2958 * allowed object is {@link Integer }
2961 public void setWidth(Integer value)
2967 * Gets the value of the height property.
2969 * @return possible object is {@link Integer }
2972 public Integer getHeight()
2978 * Sets the value of the height property.
2981 * allowed object is {@link Integer }
2984 public void setHeight(Integer value)
2986 this.height = value;
2990 * Gets the value of the xpos property.
2992 * @return possible object is {@link Integer }
2995 public Integer getXpos()
3001 * Sets the value of the xpos property.
3004 * allowed object is {@link Integer }
3007 public void setXpos(Integer value)
3013 * Gets the value of the ypos property.
3015 * @return possible object is {@link Integer }
3018 public Integer getYpos()
3024 * Sets the value of the ypos property.
3027 * allowed object is {@link Integer }
3030 public void setYpos(Integer value)
3037 * Java class for anonymous complex type.
3040 * The following schema fragment specifies the expected content contained
3041 * within this class.
3045 * <complexContent>
3046 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3047 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3048 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
3049 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3050 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
3052 * </complexContent>
3058 @XmlAccessorType(XmlAccessType.FIELD)
3060 public static class SecondaryStructure
3063 @XmlAttribute(name = "title")
3064 protected String title;
3066 @XmlAttribute(name = "annotationId", required = true)
3067 protected String annotationId;
3069 @XmlAttribute(name = "gapped")
3070 protected Boolean gapped;
3072 @XmlAttribute(name = "viewerState")
3073 protected String viewerState;
3076 * Gets the value of the title property.
3078 * @return possible object is {@link String }
3081 public String getTitle()
3087 * Sets the value of the title property.
3090 * allowed object is {@link String }
3093 public void setTitle(String value)
3099 * Gets the value of the annotationId property.
3101 * @return possible object is {@link String }
3104 public String getAnnotationId()
3106 return annotationId;
3110 * Sets the value of the annotationId property.
3113 * allowed object is {@link String }
3116 public void setAnnotationId(String value)
3118 this.annotationId = value;
3122 * Gets the value of the gapped property.
3124 * @return possible object is {@link Boolean }
3127 public Boolean isGapped()
3133 * Sets the value of the gapped property.
3136 * allowed object is {@link Boolean }
3139 public void setGapped(Boolean value)
3141 this.gapped = value;
3145 * Gets the value of the viewerState property.
3147 * @return possible object is {@link String }
3150 public String getViewerState()
3156 * Sets the value of the viewerState property.
3159 * allowed object is {@link String }
3162 public void setViewerState(String value)
3164 this.viewerState = value;
3175 * Java class for anonymous complex type.
3178 * The following schema fragment specifies the expected content contained
3179 * within this class.
3183 * <complexContent>
3184 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3186 * <element name="sequencePoint" maxOccurs="unbounded">
3188 * <complexContent>
3189 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3190 * <attGroup ref="{www.jalview.org}position"/>
3191 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
3193 * </complexContent>
3196 * <element name="axis" maxOccurs="3" minOccurs="3">
3198 * <complexContent>
3199 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3200 * <attGroup ref="{www.jalview.org}position"/>
3202 * </complexContent>
3205 * <element name="seqPointMin">
3207 * <complexContent>
3208 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3209 * <attGroup ref="{www.jalview.org}position"/>
3211 * </complexContent>
3214 * <element name="seqPointMax">
3216 * <complexContent>
3217 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3218 * <attGroup ref="{www.jalview.org}position"/>
3220 * </complexContent>
3223 * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
3225 * <attGroup ref="{www.jalview.org}SimilarityParams"/>
3226 * <attGroup ref="{www.jalview.org}swingwindow"/>
3227 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3228 * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
3229 * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3230 * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3231 * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
3232 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
3233 * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
3234 * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3235 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3237 * </complexContent>
3243 @XmlAccessorType(XmlAccessType.FIELD)
3247 { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
3248 public static class PcaViewer
3251 @XmlElement(namespace = "www.jalview.org", required = true)
3252 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3254 @XmlElement(namespace = "www.jalview.org", required = true)
3255 protected List<JalviewModel.PcaViewer.Axis> axis;
3257 @XmlElement(namespace = "www.jalview.org", required = true)
3258 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3260 @XmlElement(namespace = "www.jalview.org", required = true)
3261 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3263 @XmlElement(namespace = "www.jalview.org", required = true)
3264 protected PcaDataType pcaData;
3266 @XmlAttribute(name = "title")
3267 protected String title;
3269 @XmlAttribute(name = "scoreModelName")
3270 protected String scoreModelName;
3272 @XmlAttribute(name = "xDim")
3273 protected Integer xDim;
3275 @XmlAttribute(name = "yDim")
3276 protected Integer yDim;
3278 @XmlAttribute(name = "zDim")
3279 protected Integer zDim;
3281 @XmlAttribute(name = "bgColour")
3282 protected Integer bgColour;
3284 @XmlAttribute(name = "scaleFactor")
3285 protected Float scaleFactor;
3287 @XmlAttribute(name = "showLabels")
3288 protected Boolean showLabels;
3290 @XmlAttribute(name = "linkToAllViews")
3291 protected Boolean linkToAllViews;
3293 @XmlAttribute(name = "includeGaps")
3294 protected Boolean includeGaps;
3296 @XmlAttribute(name = "matchGaps")
3297 protected Boolean matchGaps;
3299 @XmlAttribute(name = "includeGappedColumns")
3300 protected Boolean includeGappedColumns;
3302 @XmlAttribute(name = "denominateByShortestLength")
3303 protected Boolean denominateByShortestLength;
3305 @XmlAttribute(name = "width")
3306 protected Integer width;
3308 @XmlAttribute(name = "height")
3309 protected Integer height;
3311 @XmlAttribute(name = "xpos")
3312 protected Integer xpos;
3314 @XmlAttribute(name = "ypos")
3315 protected Integer ypos;
3318 * Gets the value of the sequencePoint property.
3321 * This accessor method returns a reference to the live list, not a
3322 * snapshot. Therefore any modification you make to the returned list will
3323 * be present inside the JAXB object. This is why there is not a
3324 * <CODE>set</CODE> method for the sequencePoint property.
3327 * For example, to add a new item, do as follows:
3330 * getSequencePoint().add(newItem);
3335 * Objects of the following type(s) are allowed in the list
3336 * {@link JalviewModel.PcaViewer.SequencePoint }
3340 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
3342 if (sequencePoint == null)
3344 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3346 return this.sequencePoint;
3350 * Gets the value of the axis property.
3353 * This accessor method returns a reference to the live list, not a
3354 * snapshot. Therefore any modification you make to the returned list will
3355 * be present inside the JAXB object. This is why there is not a
3356 * <CODE>set</CODE> method for the axis property.
3359 * For example, to add a new item, do as follows:
3362 * getAxis().add(newItem);
3367 * Objects of the following type(s) are allowed in the list
3368 * {@link JalviewModel.PcaViewer.Axis }
3372 public List<JalviewModel.PcaViewer.Axis> getAxis()
3376 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3382 * Gets the value of the seqPointMin property.
3384 * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
3387 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
3393 * Sets the value of the seqPointMin property.
3396 * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
3399 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
3401 this.seqPointMin = value;
3405 * Gets the value of the seqPointMax property.
3407 * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
3410 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
3416 * Sets the value of the seqPointMax property.
3419 * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
3422 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
3424 this.seqPointMax = value;
3428 * Gets the value of the pcaData property.
3430 * @return possible object is {@link PcaDataType }
3433 public PcaDataType getPcaData()
3439 * Sets the value of the pcaData property.
3442 * allowed object is {@link PcaDataType }
3445 public void setPcaData(PcaDataType value)
3447 this.pcaData = value;
3451 * Gets the value of the title property.
3453 * @return possible object is {@link String }
3456 public String getTitle()
3462 * Sets the value of the title property.
3465 * allowed object is {@link String }
3468 public void setTitle(String value)
3474 * Gets the value of the scoreModelName property.
3476 * @return possible object is {@link String }
3479 public String getScoreModelName()
3481 return scoreModelName;
3485 * Sets the value of the scoreModelName property.
3488 * allowed object is {@link String }
3491 public void setScoreModelName(String value)
3493 this.scoreModelName = value;
3497 * Gets the value of the xDim property.
3499 * @return possible object is {@link Integer }
3502 public Integer getXDim()
3508 * Sets the value of the xDim property.
3511 * allowed object is {@link Integer }
3514 public void setXDim(Integer value)
3520 * Gets the value of the yDim property.
3522 * @return possible object is {@link Integer }
3525 public Integer getYDim()
3531 * Sets the value of the yDim property.
3534 * allowed object is {@link Integer }
3537 public void setYDim(Integer value)
3543 * Gets the value of the zDim property.
3545 * @return possible object is {@link Integer }
3548 public Integer getZDim()
3554 * Sets the value of the zDim property.
3557 * allowed object is {@link Integer }
3560 public void setZDim(Integer value)
3566 * Gets the value of the bgColour property.
3568 * @return possible object is {@link Integer }
3571 public Integer getBgColour()
3577 * Sets the value of the bgColour property.
3580 * allowed object is {@link Integer }
3583 public void setBgColour(Integer value)
3585 this.bgColour = value;
3589 * Gets the value of the scaleFactor property.
3591 * @return possible object is {@link Float }
3594 public Float getScaleFactor()
3600 * Sets the value of the scaleFactor property.
3603 * allowed object is {@link Float }
3606 public void setScaleFactor(Float value)
3608 this.scaleFactor = value;
3612 * Gets the value of the showLabels property.
3614 * @return possible object is {@link Boolean }
3617 public Boolean isShowLabels()
3623 * Sets the value of the showLabels property.
3626 * allowed object is {@link Boolean }
3629 public void setShowLabels(Boolean value)
3631 this.showLabels = value;
3635 * Gets the value of the linkToAllViews property.
3637 * @return possible object is {@link Boolean }
3640 public Boolean isLinkToAllViews()
3642 return linkToAllViews;
3646 * Sets the value of the linkToAllViews property.
3649 * allowed object is {@link Boolean }
3652 public void setLinkToAllViews(Boolean value)
3654 this.linkToAllViews = value;
3658 * Gets the value of the includeGaps property.
3660 * @return possible object is {@link Boolean }
3663 public Boolean isIncludeGaps()
3669 * Sets the value of the includeGaps property.
3672 * allowed object is {@link Boolean }
3675 public void setIncludeGaps(Boolean value)
3677 this.includeGaps = value;
3681 * Gets the value of the matchGaps property.
3683 * @return possible object is {@link Boolean }
3686 public Boolean isMatchGaps()
3692 * Sets the value of the matchGaps property.
3695 * allowed object is {@link Boolean }
3698 public void setMatchGaps(Boolean value)
3700 this.matchGaps = value;
3704 * Gets the value of the includeGappedColumns property.
3706 * @return possible object is {@link Boolean }
3709 public Boolean isIncludeGappedColumns()
3711 return includeGappedColumns;
3715 * Sets the value of the includeGappedColumns property.
3718 * allowed object is {@link Boolean }
3721 public void setIncludeGappedColumns(Boolean value)
3723 this.includeGappedColumns = value;
3727 * Gets the value of the denominateByShortestLength property.
3729 * @return possible object is {@link Boolean }
3732 public Boolean isDenominateByShortestLength()
3734 return denominateByShortestLength;
3738 * Sets the value of the denominateByShortestLength property.
3741 * allowed object is {@link Boolean }
3744 public void setDenominateByShortestLength(Boolean value)
3746 this.denominateByShortestLength = value;
3750 * Gets the value of the width property.
3752 * @return possible object is {@link Integer }
3755 public Integer getWidth()
3761 * Sets the value of the width property.
3764 * allowed object is {@link Integer }
3767 public void setWidth(Integer value)
3773 * Gets the value of the height property.
3775 * @return possible object is {@link Integer }
3778 public Integer getHeight()
3784 * Sets the value of the height property.
3787 * allowed object is {@link Integer }
3790 public void setHeight(Integer value)
3792 this.height = value;
3796 * Gets the value of the xpos property.
3798 * @return possible object is {@link Integer }
3801 public Integer getXpos()
3807 * Sets the value of the xpos property.
3810 * allowed object is {@link Integer }
3813 public void setXpos(Integer value)
3819 * Gets the value of the ypos property.
3821 * @return possible object is {@link Integer }
3824 public Integer getYpos()
3830 * Sets the value of the ypos property.
3833 * allowed object is {@link Integer }
3836 public void setYpos(Integer value)
3843 * Java class for anonymous complex type.
3846 * The following schema fragment specifies the expected content contained
3847 * within this class.
3851 * <complexContent>
3852 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3853 * <attGroup ref="{www.jalview.org}position"/>
3855 * </complexContent>
3861 @XmlAccessorType(XmlAccessType.FIELD)
3863 public static class Axis
3866 @XmlAttribute(name = "xPos")
3867 protected Float xPos;
3869 @XmlAttribute(name = "yPos")
3870 protected Float yPos;
3872 @XmlAttribute(name = "zPos")
3873 protected Float zPos;
3876 * Gets the value of the xPos property.
3878 * @return possible object is {@link Float }
3881 public Float getXPos()
3887 * Sets the value of the xPos property.
3890 * allowed object is {@link Float }
3893 public void setXPos(Float value)
3899 * Gets the value of the yPos property.
3901 * @return possible object is {@link Float }
3904 public Float getYPos()
3910 * Sets the value of the yPos property.
3913 * allowed object is {@link Float }
3916 public void setYPos(Float value)
3922 * Gets the value of the zPos property.
3924 * @return possible object is {@link Float }
3927 public Float getZPos()
3933 * Sets the value of the zPos property.
3936 * allowed object is {@link Float }
3939 public void setZPos(Float value)
3948 * Java class for anonymous complex type.
3951 * The following schema fragment specifies the expected content contained
3952 * within this class.
3956 * <complexContent>
3957 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3958 * <attGroup ref="{www.jalview.org}position"/>
3960 * </complexContent>
3966 @XmlAccessorType(XmlAccessType.FIELD)
3968 public static class SeqPointMax
3971 @XmlAttribute(name = "xPos")
3972 protected Float xPos;
3974 @XmlAttribute(name = "yPos")
3975 protected Float yPos;
3977 @XmlAttribute(name = "zPos")
3978 protected Float zPos;
3981 * Gets the value of the xPos property.
3983 * @return possible object is {@link Float }
3986 public Float getXPos()
3992 * Sets the value of the xPos property.
3995 * allowed object is {@link Float }
3998 public void setXPos(Float value)
4004 * Gets the value of the yPos property.
4006 * @return possible object is {@link Float }
4009 public Float getYPos()
4015 * Sets the value of the yPos property.
4018 * allowed object is {@link Float }
4021 public void setYPos(Float value)
4027 * Gets the value of the zPos property.
4029 * @return possible object is {@link Float }
4032 public Float getZPos()
4038 * Sets the value of the zPos property.
4041 * allowed object is {@link Float }
4044 public void setZPos(Float value)
4053 * Java class for anonymous complex type.
4056 * The following schema fragment specifies the expected content contained
4057 * within this class.
4061 * <complexContent>
4062 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4063 * <attGroup ref="{www.jalview.org}position"/>
4065 * </complexContent>
4071 @XmlAccessorType(XmlAccessType.FIELD)
4073 public static class SeqPointMin
4076 @XmlAttribute(name = "xPos")
4077 protected Float xPos;
4079 @XmlAttribute(name = "yPos")
4080 protected Float yPos;
4082 @XmlAttribute(name = "zPos")
4083 protected Float zPos;
4086 * Gets the value of the xPos property.
4088 * @return possible object is {@link Float }
4091 public Float getXPos()
4097 * Sets the value of the xPos property.
4100 * allowed object is {@link Float }
4103 public void setXPos(Float value)
4109 * Gets the value of the yPos property.
4111 * @return possible object is {@link Float }
4114 public Float getYPos()
4120 * Sets the value of the yPos property.
4123 * allowed object is {@link Float }
4126 public void setYPos(Float value)
4132 * Gets the value of the zPos property.
4134 * @return possible object is {@link Float }
4137 public Float getZPos()
4143 * Sets the value of the zPos property.
4146 * allowed object is {@link Float }
4149 public void setZPos(Float value)
4158 * Java class for anonymous complex type.
4161 * The following schema fragment specifies the expected content contained
4162 * within this class.
4166 * <complexContent>
4167 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4168 * <attGroup ref="{www.jalview.org}position"/>
4169 * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
4171 * </complexContent>
4177 @XmlAccessorType(XmlAccessType.FIELD)
4179 public static class SequencePoint
4182 @XmlAttribute(name = "sequenceRef")
4183 protected String sequenceRef;
4185 @XmlAttribute(name = "xPos")
4186 protected Float xPos;
4188 @XmlAttribute(name = "yPos")
4189 protected Float yPos;
4191 @XmlAttribute(name = "zPos")
4192 protected Float zPos;
4195 * Gets the value of the sequenceRef property.
4197 * @return possible object is {@link String }
4200 public String getSequenceRef()
4206 * Sets the value of the sequenceRef property.
4209 * allowed object is {@link String }
4212 public void setSequenceRef(String value)
4214 this.sequenceRef = value;
4218 * Gets the value of the xPos property.
4220 * @return possible object is {@link Float }
4223 public Float getXPos()
4229 * Sets the value of the xPos property.
4232 * allowed object is {@link Float }
4235 public void setXPos(Float value)
4241 * Gets the value of the yPos property.
4243 * @return possible object is {@link Float }
4246 public Float getYPos()
4252 * Sets the value of the yPos property.
4255 * allowed object is {@link Float }
4258 public void setYPos(Float value)
4264 * Gets the value of the zPos property.
4266 * @return possible object is {@link Float }
4269 public Float getZPos()
4275 * Sets the value of the zPos property.
4278 * allowed object is {@link Float }
4281 public void setZPos(Float value)
4292 * Java class for anonymous complex type.
4295 * The following schema fragment specifies the expected content contained
4296 * within this class.
4300 * <complexContent>
4301 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4302 * <sequence minOccurs="0">
4303 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
4304 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
4306 * <attGroup ref="{www.jalview.org}swingwindow"/>
4307 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
4308 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
4309 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
4310 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
4311 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4312 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4313 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4314 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4315 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4316 * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4317 * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
4318 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
4319 * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4321 * </complexContent>
4327 @XmlAccessorType(XmlAccessType.FIELD)
4328 @XmlType(name = "", propOrder = { "title", "newick" })
4329 public static class Tree
4332 @XmlElement(namespace = "www.jalview.org")
4333 protected String title;
4335 @XmlElement(namespace = "www.jalview.org")
4336 protected String newick;
4338 @XmlAttribute(name = "fontName")
4339 protected String fontName;
4341 @XmlAttribute(name = "fontSize")
4342 protected Integer fontSize;
4344 @XmlAttribute(name = "fontStyle")
4345 protected Integer fontStyle;
4347 @XmlAttribute(name = "threshold")
4348 protected Float threshold;
4350 @XmlAttribute(name = "showBootstrap")
4351 protected Boolean showBootstrap;
4353 @XmlAttribute(name = "showDistances")
4354 protected Boolean showDistances;
4356 @XmlAttribute(name = "markUnlinked")
4357 protected Boolean markUnlinked;
4359 @XmlAttribute(name = "fitToWindow")
4360 protected Boolean fitToWindow;
4362 @XmlAttribute(name = "currentTree")
4363 protected Boolean currentTree;
4365 @XmlAttribute(name = "columnWise")
4366 protected Boolean columnWise;
4368 @XmlAttribute(name = "columnReference")
4369 protected String columnReference;
4371 @XmlAttribute(name = "id")
4372 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4374 @XmlSchemaType(name = "ID")
4375 protected String id;
4377 @XmlAttribute(name = "linkToAllViews")
4378 protected Boolean linkToAllViews;
4380 @XmlAttribute(name = "width")
4381 protected Integer width;
4383 @XmlAttribute(name = "height")
4384 protected Integer height;
4386 @XmlAttribute(name = "xpos")
4387 protected Integer xpos;
4389 @XmlAttribute(name = "ypos")
4390 protected Integer ypos;
4393 * Gets the value of the title property.
4395 * @return possible object is {@link String }
4398 public String getTitle()
4404 * Sets the value of the title property.
4407 * allowed object is {@link String }
4410 public void setTitle(String value)
4416 * Gets the value of the newick property.
4418 * @return possible object is {@link String }
4421 public String getNewick()
4427 * Sets the value of the newick property.
4430 * allowed object is {@link String }
4433 public void setNewick(String value)
4435 this.newick = value;
4439 * Gets the value of the fontName property.
4441 * @return possible object is {@link String }
4444 public String getFontName()
4450 * Sets the value of the fontName property.
4453 * allowed object is {@link String }
4456 public void setFontName(String value)
4458 this.fontName = value;
4462 * Gets the value of the fontSize property.
4464 * @return possible object is {@link Integer }
4467 public Integer getFontSize()
4473 * Sets the value of the fontSize property.
4476 * allowed object is {@link Integer }
4479 public void setFontSize(Integer value)
4481 this.fontSize = value;
4485 * Gets the value of the fontStyle property.
4487 * @return possible object is {@link Integer }
4490 public Integer getFontStyle()
4496 * Sets the value of the fontStyle property.
4499 * allowed object is {@link Integer }
4502 public void setFontStyle(Integer value)
4504 this.fontStyle = value;
4508 * Gets the value of the threshold property.
4510 * @return possible object is {@link Float }
4513 public Float getThreshold()
4519 * Sets the value of the threshold property.
4522 * allowed object is {@link Float }
4525 public void setThreshold(Float value)
4527 this.threshold = value;
4531 * Gets the value of the showBootstrap property.
4533 * @return possible object is {@link Boolean }
4536 public Boolean isShowBootstrap()
4538 return showBootstrap;
4542 * Sets the value of the showBootstrap property.
4545 * allowed object is {@link Boolean }
4548 public void setShowBootstrap(Boolean value)
4550 this.showBootstrap = value;
4554 * Gets the value of the showDistances property.
4556 * @return possible object is {@link Boolean }
4559 public Boolean isShowDistances()
4561 return showDistances;
4565 * Sets the value of the showDistances property.
4568 * allowed object is {@link Boolean }
4571 public void setShowDistances(Boolean value)
4573 this.showDistances = value;
4577 * Gets the value of the markUnlinked property.
4579 * @return possible object is {@link Boolean }
4582 public Boolean isMarkUnlinked()
4584 return markUnlinked;
4588 * Sets the value of the markUnlinked property.
4591 * allowed object is {@link Boolean }
4594 public void setMarkUnlinked(Boolean value)
4596 this.markUnlinked = value;
4600 * Gets the value of the fitToWindow property.
4602 * @return possible object is {@link Boolean }
4605 public Boolean isFitToWindow()
4611 * Sets the value of the fitToWindow property.
4614 * allowed object is {@link Boolean }
4617 public void setFitToWindow(Boolean value)
4619 this.fitToWindow = value;
4623 * Gets the value of the currentTree property.
4625 * @return possible object is {@link Boolean }
4628 public Boolean isCurrentTree()
4634 * Sets the value of the currentTree property.
4637 * allowed object is {@link Boolean }
4640 public void setCurrentTree(Boolean value)
4642 this.currentTree = value;
4646 * Gets the value of the columnWise property.
4648 * @return possible object is {@link Boolean }
4651 public boolean isColumnWise()
4653 if (columnWise == null)
4664 * Sets the value of the columnWise property.
4667 * allowed object is {@link Boolean }
4670 public void setColumnWise(Boolean value)
4672 this.columnWise = value;
4676 * Gets the value of the columnReference property.
4678 * @return possible object is {@link String }
4681 public String getColumnReference()
4683 return columnReference;
4687 * Sets the value of the columnReference property.
4690 * allowed object is {@link String }
4693 public void setColumnReference(String value)
4695 this.columnReference = value;
4699 * Gets the value of the id property.
4701 * @return possible object is {@link String }
4704 public String getId()
4710 * Sets the value of the id property.
4713 * allowed object is {@link String }
4716 public void setId(String value)
4722 * Gets the value of the linkToAllViews property.
4724 * @return possible object is {@link Boolean }
4727 public boolean isLinkToAllViews()
4729 if (linkToAllViews == null)
4735 return linkToAllViews;
4740 * Sets the value of the linkToAllViews property.
4743 * allowed object is {@link Boolean }
4746 public void setLinkToAllViews(Boolean value)
4748 this.linkToAllViews = value;
4752 * Gets the value of the width property.
4754 * @return possible object is {@link Integer }
4757 public Integer getWidth()
4763 * Sets the value of the width property.
4766 * allowed object is {@link Integer }
4769 public void setWidth(Integer value)
4775 * Gets the value of the height property.
4777 * @return possible object is {@link Integer }
4780 public Integer getHeight()
4786 * Sets the value of the height property.
4789 * allowed object is {@link Integer }
4792 public void setHeight(Integer value)
4794 this.height = value;
4798 * Gets the value of the xpos property.
4800 * @return possible object is {@link Integer }
4803 public Integer getXpos()
4809 * Sets the value of the xpos property.
4812 * allowed object is {@link Integer }
4815 public void setXpos(Integer value)
4821 * Gets the value of the ypos property.
4823 * @return possible object is {@link Integer }
4826 public Integer getYpos()
4832 * Sets the value of the ypos property.
4835 * allowed object is {@link Integer }
4838 public void setYpos(Integer value)
4847 * Java class for anonymous complex type.
4850 * The following schema fragment specifies the expected content contained
4851 * within this class.
4855 * <complexContent>
4856 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4858 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
4860 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
4862 * </complexContent>
4868 @XmlAccessorType(XmlAccessType.FIELD)
4869 @XmlType(name = "", propOrder = { "userColourScheme" })
4870 public static class UserColours
4874 name = "UserColourScheme",
4875 namespace = "www.jalview.org",
4877 protected JalviewUserColours userColourScheme;
4879 @XmlAttribute(name = "id")
4880 protected String id;
4883 * Gets the value of the userColourScheme property.
4885 * @return possible object is {@link JalviewUserColours }
4888 public JalviewUserColours getUserColourScheme()
4890 return userColourScheme;
4894 * Sets the value of the userColourScheme property.
4897 * allowed object is {@link JalviewUserColours }
4900 public void setUserColourScheme(JalviewUserColours value)
4902 this.userColourScheme = value;
4906 * Gets the value of the id property.
4908 * @return possible object is {@link String }
4911 public String getId()
4917 * Sets the value of the id property.
4920 * allowed object is {@link String }
4923 public void setId(String value)
4932 * Java class for anonymous complex type.
4935 * The following schema fragment specifies the expected content contained
4936 * within this class.
4940 * <complexContent>
4941 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4943 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
4944 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
4946 * <complexContent>
4947 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4948 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
4949 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
4951 * </complexContent>
4954 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
4956 * <complexContent>
4957 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
4958 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
4959 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4960 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4962 * </complexContent>
4965 * <element name="overview" minOccurs="0">
4967 * <complexContent>
4968 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
4969 * <attGroup ref="{www.jalview.org}swingwindow"/>
4970 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4971 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4972 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4973 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
4974 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4976 * </complexContent>
4980 * <attGroup ref="{www.jalview.org}swingwindow"/>
4981 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4982 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4983 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
4984 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4985 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
4986 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
4987 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4988 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4989 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4990 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4991 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
4992 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4993 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4994 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4995 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4996 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4997 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
4998 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
4999 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
5000 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
5001 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5002 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5003 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5004 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
5005 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5006 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5007 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
5008 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
5009 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
5010 * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
5011 * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
5012 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
5013 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
5014 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
5015 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
5016 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
5017 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
5018 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
5019 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
5020 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
5021 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
5022 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
5023 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
5024 * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5025 * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5027 * </complexContent>
5033 @XmlAccessorType(XmlAccessType.FIELD)
5037 { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
5038 public static class Viewport
5041 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
5042 protected AnnotationColourScheme annotationColours;
5044 @XmlElement(namespace = "www.jalview.org")
5045 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
5047 @XmlElement(namespace = "www.jalview.org")
5048 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
5050 @XmlElement(namespace = "www.jalview.org")
5051 protected JalviewModel.Viewport.Overview overview;
5053 @XmlAttribute(name = "conservationSelected")
5054 protected Boolean conservationSelected;
5056 @XmlAttribute(name = "pidSelected")
5057 protected Boolean pidSelected;
5059 @XmlAttribute(name = "bgColour")
5060 protected String bgColour;
5062 @XmlAttribute(name = "consThreshold")
5063 protected Integer consThreshold;
5065 @XmlAttribute(name = "pidThreshold")
5066 protected Integer pidThreshold;
5068 @XmlAttribute(name = "title")
5069 protected String title;
5071 @XmlAttribute(name = "showFullId")
5072 protected Boolean showFullId;
5074 @XmlAttribute(name = "rightAlignIds")
5075 protected Boolean rightAlignIds;
5077 @XmlAttribute(name = "showText")
5078 protected Boolean showText;
5080 @XmlAttribute(name = "showColourText")
5081 protected Boolean showColourText;
5083 @XmlAttribute(name = "showUnconserved")
5084 protected Boolean showUnconserved;
5086 @XmlAttribute(name = "showBoxes")
5087 protected Boolean showBoxes;
5089 @XmlAttribute(name = "wrapAlignment")
5090 protected Boolean wrapAlignment;
5092 @XmlAttribute(name = "renderGaps")
5093 protected Boolean renderGaps;
5095 @XmlAttribute(name = "showSequenceFeatures")
5096 protected Boolean showSequenceFeatures;
5098 @XmlAttribute(name = "showNPfeatureTooltip")
5099 protected Boolean showNPfeatureTooltip;
5101 @XmlAttribute(name = "showDbRefTooltip")
5102 protected Boolean showDbRefTooltip;
5104 @XmlAttribute(name = "followHighlight")
5105 protected Boolean followHighlight;
5107 @XmlAttribute(name = "followSelection")
5108 protected Boolean followSelection;
5110 @XmlAttribute(name = "showAnnotation")
5111 protected Boolean showAnnotation;
5113 @XmlAttribute(name = "centreColumnLabels")
5114 protected Boolean centreColumnLabels;
5116 @XmlAttribute(name = "showGroupConservation")
5117 protected Boolean showGroupConservation;
5119 @XmlAttribute(name = "showGroupConsensus")
5120 protected Boolean showGroupConsensus;
5122 @XmlAttribute(name = "showConsensusHistogram")
5123 protected Boolean showConsensusHistogram;
5125 @XmlAttribute(name = "showSequenceLogo")
5126 protected Boolean showSequenceLogo;
5128 @XmlAttribute(name = "normaliseSequenceLogo")
5129 protected Boolean normaliseSequenceLogo;
5131 @XmlAttribute(name = "ignoreGapsinConsensus")
5132 protected Boolean ignoreGapsinConsensus;
5134 @XmlAttribute(name = "startRes")
5135 protected Integer startRes;
5137 @XmlAttribute(name = "startSeq")
5138 protected Integer startSeq;
5140 @XmlAttribute(name = "charWidth")
5141 protected Integer charWidth;
5143 @XmlAttribute(name = "charHeight")
5144 protected Integer charHeight;
5146 @XmlAttribute(name = "fontName")
5147 protected String fontName;
5149 @XmlAttribute(name = "fontSize")
5150 protected Integer fontSize;
5152 @XmlAttribute(name = "fontStyle")
5153 protected Integer fontStyle;
5155 @XmlAttribute(name = "scaleProteinAsCdna")
5156 protected Boolean scaleProteinAsCdna;
5158 @XmlAttribute(name = "viewName")
5159 protected String viewName;
5161 @XmlAttribute(name = "sequenceSetId")
5162 protected String sequenceSetId;
5164 @XmlAttribute(name = "gatheredViews")
5165 protected Boolean gatheredViews;
5167 @XmlAttribute(name = "textCol1")
5168 protected Integer textCol1;
5170 @XmlAttribute(name = "textCol2")
5171 protected Integer textCol2;
5173 @XmlAttribute(name = "textColThreshold")
5174 protected Integer textColThreshold;
5176 @XmlAttribute(name = "id")
5177 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5179 @XmlSchemaType(name = "ID")
5180 protected String id;
5182 @XmlAttribute(name = "complementId")
5183 protected String complementId;
5185 @XmlAttribute(name = "showComplementFeatures")
5186 protected Boolean showComplementFeatures;
5188 @XmlAttribute(name = "showComplementFeaturesOnTop")
5189 protected Boolean showComplementFeaturesOnTop;
5191 @XmlAttribute(name = "width")
5192 protected Integer width;
5194 @XmlAttribute(name = "height")
5195 protected Integer height;
5197 @XmlAttribute(name = "xpos")
5198 protected Integer xpos;
5200 @XmlAttribute(name = "ypos")
5201 protected Integer ypos;
5204 * Gets the value of the annotationColours property.
5206 * @return possible object is {@link AnnotationColourScheme }
5209 public AnnotationColourScheme getAnnotationColours()
5211 return annotationColours;
5215 * Sets the value of the annotationColours property.
5218 * allowed object is {@link AnnotationColourScheme }
5221 public void setAnnotationColours(AnnotationColourScheme value)
5223 this.annotationColours = value;
5227 * Gets the value of the hiddenColumns property.
5230 * This accessor method returns a reference to the live list, not a
5231 * snapshot. Therefore any modification you make to the returned list will
5232 * be present inside the JAXB object. This is why there is not a
5233 * <CODE>set</CODE> method for the hiddenColumns property.
5236 * For example, to add a new item, do as follows:
5239 * getHiddenColumns().add(newItem);
5244 * Objects of the following type(s) are allowed in the list
5245 * {@link JalviewModel.Viewport.HiddenColumns }
5249 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
5251 if (hiddenColumns == null)
5253 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5255 return this.hiddenColumns;
5259 * Gets the value of the calcIdParam property.
5262 * This accessor method returns a reference to the live list, not a
5263 * snapshot. Therefore any modification you make to the returned list will
5264 * be present inside the JAXB object. This is why there is not a
5265 * <CODE>set</CODE> method for the calcIdParam property.
5268 * For example, to add a new item, do as follows:
5271 * getCalcIdParam().add(newItem);
5276 * Objects of the following type(s) are allowed in the list
5277 * {@link JalviewModel.Viewport.CalcIdParam }
5281 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
5283 if (calcIdParam == null)
5285 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5287 return this.calcIdParam;
5291 * Gets the value of the overview property.
5293 * @return possible object is {@link JalviewModel.Viewport.Overview }
5296 public JalviewModel.Viewport.Overview getOverview()
5302 * Sets the value of the overview property.
5305 * allowed object is {@link JalviewModel.Viewport.Overview }
5308 public void setOverview(JalviewModel.Viewport.Overview value)
5310 this.overview = value;
5314 * Gets the value of the conservationSelected property.
5316 * @return possible object is {@link Boolean }
5319 public Boolean isConservationSelected()
5321 return conservationSelected;
5325 * Sets the value of the conservationSelected property.
5328 * allowed object is {@link Boolean }
5331 public void setConservationSelected(Boolean value)
5333 this.conservationSelected = value;
5337 * Gets the value of the pidSelected property.
5339 * @return possible object is {@link Boolean }
5342 public Boolean isPidSelected()
5348 * Sets the value of the pidSelected property.
5351 * allowed object is {@link Boolean }
5354 public void setPidSelected(Boolean value)
5356 this.pidSelected = value;
5360 * Gets the value of the bgColour property.
5362 * @return possible object is {@link String }
5365 public String getBgColour()
5371 * Sets the value of the bgColour property.
5374 * allowed object is {@link String }
5377 public void setBgColour(String value)
5379 this.bgColour = value;
5383 * Gets the value of the consThreshold property.
5385 * @return possible object is {@link Integer }
5388 public Integer getConsThreshold()
5390 return consThreshold;
5394 * Sets the value of the consThreshold property.
5397 * allowed object is {@link Integer }
5400 public void setConsThreshold(Integer value)
5402 this.consThreshold = value;
5406 * Gets the value of the pidThreshold property.
5408 * @return possible object is {@link Integer }
5411 public Integer getPidThreshold()
5413 return pidThreshold;
5417 * Sets the value of the pidThreshold property.
5420 * allowed object is {@link Integer }
5423 public void setPidThreshold(Integer value)
5425 this.pidThreshold = value;
5429 * Gets the value of the title property.
5431 * @return possible object is {@link String }
5434 public String getTitle()
5440 * Sets the value of the title property.
5443 * allowed object is {@link String }
5446 public void setTitle(String value)
5452 * Gets the value of the showFullId property.
5454 * @return possible object is {@link Boolean }
5457 public Boolean isShowFullId()
5463 * Sets the value of the showFullId property.
5466 * allowed object is {@link Boolean }
5469 public void setShowFullId(Boolean value)
5471 this.showFullId = value;
5475 * Gets the value of the rightAlignIds property.
5477 * @return possible object is {@link Boolean }
5480 public Boolean isRightAlignIds()
5482 return rightAlignIds;
5486 * Sets the value of the rightAlignIds property.
5489 * allowed object is {@link Boolean }
5492 public void setRightAlignIds(Boolean value)
5494 this.rightAlignIds = value;
5498 * Gets the value of the showText property.
5500 * @return possible object is {@link Boolean }
5503 public Boolean isShowText()
5509 * Sets the value of the showText property.
5512 * allowed object is {@link Boolean }
5515 public void setShowText(Boolean value)
5517 this.showText = value;
5521 * Gets the value of the showColourText property.
5523 * @return possible object is {@link Boolean }
5526 public Boolean isShowColourText()
5528 return showColourText;
5532 * Sets the value of the showColourText property.
5535 * allowed object is {@link Boolean }
5538 public void setShowColourText(Boolean value)
5540 this.showColourText = value;
5544 * Gets the value of the showUnconserved property.
5546 * @return possible object is {@link Boolean }
5549 public boolean isShowUnconserved()
5551 if (showUnconserved == null)
5557 return showUnconserved;
5562 * Sets the value of the showUnconserved property.
5565 * allowed object is {@link Boolean }
5568 public void setShowUnconserved(Boolean value)
5570 this.showUnconserved = value;
5574 * Gets the value of the showBoxes property.
5576 * @return possible object is {@link Boolean }
5579 public Boolean isShowBoxes()
5585 * Sets the value of the showBoxes property.
5588 * allowed object is {@link Boolean }
5591 public void setShowBoxes(Boolean value)
5593 this.showBoxes = value;
5597 * Gets the value of the wrapAlignment property.
5599 * @return possible object is {@link Boolean }
5602 public Boolean isWrapAlignment()
5604 return wrapAlignment;
5608 * Sets the value of the wrapAlignment property.
5611 * allowed object is {@link Boolean }
5614 public void setWrapAlignment(Boolean value)
5616 this.wrapAlignment = value;
5620 * Gets the value of the renderGaps property.
5622 * @return possible object is {@link Boolean }
5625 public Boolean isRenderGaps()
5631 * Sets the value of the renderGaps property.
5634 * allowed object is {@link Boolean }
5637 public void setRenderGaps(Boolean value)
5639 this.renderGaps = value;
5643 * Gets the value of the showSequenceFeatures property.
5645 * @return possible object is {@link Boolean }
5648 public Boolean isShowSequenceFeatures()
5650 return showSequenceFeatures;
5654 * Sets the value of the showSequenceFeatures property.
5657 * allowed object is {@link Boolean }
5660 public void setShowSequenceFeatures(Boolean value)
5662 this.showSequenceFeatures = value;
5666 * Gets the value of the showNPfeatureTooltip property.
5668 * @return possible object is {@link Boolean }
5671 public Boolean isShowNPfeatureTooltip()
5673 return showNPfeatureTooltip;
5677 * Sets the value of the showNPfeatureTooltip property.
5680 * allowed object is {@link Boolean }
5683 public void setShowNPfeatureTooltip(Boolean value)
5685 this.showNPfeatureTooltip = value;
5689 * Gets the value of the showDbRefTooltip property.
5691 * @return possible object is {@link Boolean }
5694 public Boolean isShowDbRefTooltip()
5696 return showDbRefTooltip;
5700 * Sets the value of the showDbRefTooltip property.
5703 * allowed object is {@link Boolean }
5706 public void setShowDbRefTooltip(Boolean value)
5708 this.showDbRefTooltip = value;
5712 * Gets the value of the followHighlight property.
5714 * @return possible object is {@link Boolean }
5717 public boolean isFollowHighlight()
5719 if (followHighlight == null)
5725 return followHighlight;
5730 * Sets the value of the followHighlight property.
5733 * allowed object is {@link Boolean }
5736 public void setFollowHighlight(Boolean value)
5738 this.followHighlight = value;
5742 * Gets the value of the followSelection property.
5744 * @return possible object is {@link Boolean }
5747 public boolean isFollowSelection()
5749 if (followSelection == null)
5755 return followSelection;
5760 * Sets the value of the followSelection property.
5763 * allowed object is {@link Boolean }
5766 public void setFollowSelection(Boolean value)
5768 this.followSelection = value;
5772 * Gets the value of the showAnnotation property.
5774 * @return possible object is {@link Boolean }
5777 public Boolean isShowAnnotation()
5779 return showAnnotation;
5783 * Sets the value of the showAnnotation property.
5786 * allowed object is {@link Boolean }
5789 public void setShowAnnotation(Boolean value)
5791 this.showAnnotation = value;
5795 * Gets the value of the centreColumnLabels property.
5797 * @return possible object is {@link Boolean }
5800 public boolean isCentreColumnLabels()
5802 if (centreColumnLabels == null)
5808 return centreColumnLabels;
5813 * Sets the value of the centreColumnLabels property.
5816 * allowed object is {@link Boolean }
5819 public void setCentreColumnLabels(Boolean value)
5821 this.centreColumnLabels = value;
5825 * Gets the value of the showGroupConservation property.
5827 * @return possible object is {@link Boolean }
5830 public boolean isShowGroupConservation()
5832 if (showGroupConservation == null)
5838 return showGroupConservation;
5843 * Sets the value of the showGroupConservation property.
5846 * allowed object is {@link Boolean }
5849 public void setShowGroupConservation(Boolean value)
5851 this.showGroupConservation = value;
5855 * Gets the value of the showGroupConsensus property.
5857 * @return possible object is {@link Boolean }
5860 public boolean isShowGroupConsensus()
5862 if (showGroupConsensus == null)
5868 return showGroupConsensus;
5873 * Sets the value of the showGroupConsensus property.
5876 * allowed object is {@link Boolean }
5879 public void setShowGroupConsensus(Boolean value)
5881 this.showGroupConsensus = value;
5885 * Gets the value of the showConsensusHistogram property.
5887 * @return possible object is {@link Boolean }
5890 public boolean isShowConsensusHistogram()
5892 if (showConsensusHistogram == null)
5898 return showConsensusHistogram;
5903 * Sets the value of the showConsensusHistogram property.
5906 * allowed object is {@link Boolean }
5909 public void setShowConsensusHistogram(Boolean value)
5911 this.showConsensusHistogram = value;
5915 * Gets the value of the showSequenceLogo property.
5917 * @return possible object is {@link Boolean }
5920 public boolean isShowSequenceLogo()
5922 if (showSequenceLogo == null)
5928 return showSequenceLogo;
5933 * Sets the value of the showSequenceLogo property.
5936 * allowed object is {@link Boolean }
5939 public void setShowSequenceLogo(Boolean value)
5941 this.showSequenceLogo = value;
5945 * Gets the value of the normaliseSequenceLogo property.
5947 * @return possible object is {@link Boolean }
5950 public boolean isNormaliseSequenceLogo()
5952 if (normaliseSequenceLogo == null)
5958 return normaliseSequenceLogo;
5963 * Sets the value of the normaliseSequenceLogo property.
5966 * allowed object is {@link Boolean }
5969 public void setNormaliseSequenceLogo(Boolean value)
5971 this.normaliseSequenceLogo = value;
5975 * Gets the value of the ignoreGapsinConsensus property.
5977 * @return possible object is {@link Boolean }
5980 public boolean isIgnoreGapsinConsensus()
5982 if (ignoreGapsinConsensus == null)
5988 return ignoreGapsinConsensus;
5993 * Sets the value of the ignoreGapsinConsensus property.
5996 * allowed object is {@link Boolean }
5999 public void setIgnoreGapsinConsensus(Boolean value)
6001 this.ignoreGapsinConsensus = value;
6005 * Gets the value of the startRes property.
6007 * @return possible object is {@link Integer }
6010 public Integer getStartRes()
6016 * Sets the value of the startRes property.
6019 * allowed object is {@link Integer }
6022 public void setStartRes(Integer value)
6024 this.startRes = value;
6028 * Gets the value of the startSeq property.
6030 * @return possible object is {@link Integer }
6033 public Integer getStartSeq()
6039 * Sets the value of the startSeq property.
6042 * allowed object is {@link Integer }
6045 public void setStartSeq(Integer value)
6047 this.startSeq = value;
6051 * Gets the value of the charWidth property.
6053 * @return possible object is {@link Integer }
6056 public Integer getCharWidth()
6062 * Sets the value of the charWidth property.
6065 * allowed object is {@link Integer }
6068 public void setCharWidth(Integer value)
6070 this.charWidth = value;
6074 * Gets the value of the charHeight property.
6076 * @return possible object is {@link Integer }
6079 public Integer getCharHeight()
6085 * Sets the value of the charHeight property.
6088 * allowed object is {@link Integer }
6091 public void setCharHeight(Integer value)
6093 this.charHeight = value;
6097 * Gets the value of the fontName property.
6099 * @return possible object is {@link String }
6102 public String getFontName()
6108 * Sets the value of the fontName property.
6111 * allowed object is {@link String }
6114 public void setFontName(String value)
6116 this.fontName = value;
6120 * Gets the value of the fontSize property.
6122 * @return possible object is {@link Integer }
6125 public Integer getFontSize()
6131 * Sets the value of the fontSize property.
6134 * allowed object is {@link Integer }
6137 public void setFontSize(Integer value)
6139 this.fontSize = value;
6143 * Gets the value of the fontStyle property.
6145 * @return possible object is {@link Integer }
6148 public Integer getFontStyle()
6154 * Sets the value of the fontStyle property.
6157 * allowed object is {@link Integer }
6160 public void setFontStyle(Integer value)
6162 this.fontStyle = value;
6166 * Gets the value of the scaleProteinAsCdna property.
6168 * @return possible object is {@link Boolean }
6171 public boolean isScaleProteinAsCdna()
6173 if (scaleProteinAsCdna == null)
6179 return scaleProteinAsCdna;
6184 * Sets the value of the scaleProteinAsCdna property.
6187 * allowed object is {@link Boolean }
6190 public void setScaleProteinAsCdna(Boolean value)
6192 this.scaleProteinAsCdna = value;
6196 * Gets the value of the viewName property.
6198 * @return possible object is {@link String }
6201 public String getViewName()
6207 * Sets the value of the viewName property.
6210 * allowed object is {@link String }
6213 public void setViewName(String value)
6215 this.viewName = value;
6219 * Gets the value of the sequenceSetId property.
6221 * @return possible object is {@link String }
6224 public String getSequenceSetId()
6226 return sequenceSetId;
6230 * Sets the value of the sequenceSetId property.
6233 * allowed object is {@link String }
6236 public void setSequenceSetId(String value)
6238 this.sequenceSetId = value;
6242 * Gets the value of the gatheredViews property.
6244 * @return possible object is {@link Boolean }
6247 public Boolean isGatheredViews()
6249 return gatheredViews;
6253 * Sets the value of the gatheredViews property.
6256 * allowed object is {@link Boolean }
6259 public void setGatheredViews(Boolean value)
6261 this.gatheredViews = value;
6265 * Gets the value of the textCol1 property.
6267 * @return possible object is {@link Integer }
6270 public Integer getTextCol1()
6276 * Sets the value of the textCol1 property.
6279 * allowed object is {@link Integer }
6282 public void setTextCol1(Integer value)
6284 this.textCol1 = value;
6288 * Gets the value of the textCol2 property.
6290 * @return possible object is {@link Integer }
6293 public Integer getTextCol2()
6299 * Sets the value of the textCol2 property.
6302 * allowed object is {@link Integer }
6305 public void setTextCol2(Integer value)
6307 this.textCol2 = value;
6311 * Gets the value of the textColThreshold property.
6313 * @return possible object is {@link Integer }
6316 public Integer getTextColThreshold()
6318 return textColThreshold;
6322 * Sets the value of the textColThreshold property.
6325 * allowed object is {@link Integer }
6328 public void setTextColThreshold(Integer value)
6330 this.textColThreshold = value;
6334 * Gets the value of the id property.
6336 * @return possible object is {@link String }
6339 public String getId()
6345 * Sets the value of the id property.
6348 * allowed object is {@link String }
6351 public void setId(String value)
6357 * Gets the value of the complementId property.
6359 * @return possible object is {@link String }
6362 public String getComplementId()
6364 return complementId;
6368 * Sets the value of the complementId property.
6371 * allowed object is {@link String }
6374 public void setComplementId(String value)
6376 this.complementId = value;
6380 * Gets the value of the showComplementFeatures property.
6382 * @return possible object is {@link Boolean }
6385 public boolean isShowComplementFeatures()
6387 if (showComplementFeatures == null)
6393 return showComplementFeatures;
6398 * Sets the value of the showComplementFeatures property.
6401 * allowed object is {@link Boolean }
6404 public void setShowComplementFeatures(Boolean value)
6406 this.showComplementFeatures = value;
6410 * Gets the value of the showComplementFeaturesOnTop property.
6412 * @return possible object is {@link Boolean }
6415 public boolean isShowComplementFeaturesOnTop()
6417 if (showComplementFeaturesOnTop == null)
6423 return showComplementFeaturesOnTop;
6428 * Sets the value of the showComplementFeaturesOnTop property.
6431 * allowed object is {@link Boolean }
6434 public void setShowComplementFeaturesOnTop(Boolean value)
6436 this.showComplementFeaturesOnTop = value;
6440 * Gets the value of the width property.
6442 * @return possible object is {@link Integer }
6445 public Integer getWidth()
6451 * Sets the value of the width property.
6454 * allowed object is {@link Integer }
6457 public void setWidth(Integer value)
6463 * Gets the value of the height property.
6465 * @return possible object is {@link Integer }
6468 public Integer getHeight()
6474 * Sets the value of the height property.
6477 * allowed object is {@link Integer }
6480 public void setHeight(Integer value)
6482 this.height = value;
6486 * Gets the value of the xpos property.
6488 * @return possible object is {@link Integer }
6491 public Integer getXpos()
6497 * Sets the value of the xpos property.
6500 * allowed object is {@link Integer }
6503 public void setXpos(Integer value)
6509 * Gets the value of the ypos property.
6511 * @return possible object is {@link Integer }
6514 public Integer getYpos()
6520 * Sets the value of the ypos property.
6523 * allowed object is {@link Integer }
6526 public void setYpos(Integer value)
6533 * Java class for anonymous complex type.
6536 * The following schema fragment specifies the expected content contained
6537 * within this class.
6541 * <complexContent>
6542 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
6543 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
6544 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
6545 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6547 * </complexContent>
6553 @XmlAccessorType(XmlAccessType.FIELD)
6555 public static class CalcIdParam extends WebServiceParameterSet
6558 @XmlAttribute(name = "calcId", required = true)
6559 protected String calcId;
6561 @XmlAttribute(name = "needsUpdate")
6562 protected Boolean needsUpdate;
6564 @XmlAttribute(name = "autoUpdate", required = true)
6565 protected boolean autoUpdate;
6568 * Gets the value of the calcId property.
6570 * @return possible object is {@link String }
6573 public String getCalcId()
6579 * Sets the value of the calcId property.
6582 * allowed object is {@link String }
6585 public void setCalcId(String value)
6587 this.calcId = value;
6591 * Gets the value of the needsUpdate property.
6593 * @return possible object is {@link Boolean }
6596 public boolean isNeedsUpdate()
6598 if (needsUpdate == null)
6609 * Sets the value of the needsUpdate property.
6612 * allowed object is {@link Boolean }
6615 public void setNeedsUpdate(Boolean value)
6617 this.needsUpdate = value;
6621 * Gets the value of the autoUpdate property.
6624 public boolean isAutoUpdate()
6630 * Sets the value of the autoUpdate property.
6633 public void setAutoUpdate(boolean value)
6635 this.autoUpdate = value;
6642 * Java class for anonymous complex type.
6645 * The following schema fragment specifies the expected content contained
6646 * within this class.
6650 * <complexContent>
6651 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6652 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
6653 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
6655 * </complexContent>
6661 @XmlAccessorType(XmlAccessType.FIELD)
6663 public static class HiddenColumns
6666 @XmlAttribute(name = "start")
6667 protected Integer start;
6669 @XmlAttribute(name = "end")
6670 protected Integer end;
6673 * Gets the value of the start property.
6675 * @return possible object is {@link Integer }
6678 public Integer getStart()
6684 * Sets the value of the start property.
6687 * allowed object is {@link Integer }
6690 public void setStart(Integer value)
6696 * Gets the value of the end property.
6698 * @return possible object is {@link Integer }
6701 public Integer getEnd()
6707 * Sets the value of the end property.
6710 * allowed object is {@link Integer }
6713 public void setEnd(Integer value)
6722 * Java class for anonymous complex type.
6725 * The following schema fragment specifies the expected content contained
6726 * within this class.
6730 * <complexContent>
6731 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
6732 * <attGroup ref="{www.jalview.org}swingwindow"/>
6733 * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
6734 * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6735 * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6736 * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
6737 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
6739 * </complexContent>
6745 @XmlAccessorType(XmlAccessType.FIELD)
6747 public static class Overview
6750 @XmlAttribute(name = "showHidden")
6751 protected Boolean showHidden;
6753 @XmlAttribute(name = "residueColour")
6754 protected Integer residueColour;
6756 @XmlAttribute(name = "gapColour")
6757 protected Integer gapColour;
6759 @XmlAttribute(name = "hiddenColour")
6760 protected Integer hiddenColour;
6762 @XmlAttribute(name = "title")
6763 protected String title;
6765 @XmlAttribute(name = "width")
6766 protected Integer width;
6768 @XmlAttribute(name = "height")
6769 protected Integer height;
6771 @XmlAttribute(name = "xpos")
6772 protected Integer xpos;
6774 @XmlAttribute(name = "ypos")
6775 protected Integer ypos;
6778 * Gets the value of the showHidden property.
6780 * @return possible object is {@link Boolean }
6783 public Boolean isShowHidden()
6789 * Sets the value of the showHidden property.
6792 * allowed object is {@link Boolean }
6795 public void setShowHidden(Boolean value)
6797 this.showHidden = value;
6801 * Gets the value of the residueColour property.
6803 * @return possible object is {@link Integer }
6806 public Integer getResidueColour()
6808 return residueColour;
6812 * Sets the value of the residueColour property.
6815 * allowed object is {@link Integer }
6818 public void setResidueColour(Integer value)
6820 this.residueColour = value;
6824 * Gets the value of the gapColour property.
6826 * @return possible object is {@link Integer }
6829 public Integer getGapColour()
6835 * Sets the value of the gapColour property.
6838 * allowed object is {@link Integer }
6841 public void setGapColour(Integer value)
6843 this.gapColour = value;
6847 * Gets the value of the hiddenColour property.
6849 * @return possible object is {@link Integer }
6852 public Integer getHiddenColour()
6854 return hiddenColour;
6858 * Sets the value of the hiddenColour property.
6861 * allowed object is {@link Integer }
6864 public void setHiddenColour(Integer value)
6866 this.hiddenColour = value;
6870 * Gets the value of the title property.
6872 * @return possible object is {@link String }
6875 public String getTitle()
6881 * Sets the value of the title property.
6884 * allowed object is {@link String }
6887 public void setTitle(String value)
6893 * Gets the value of the width property.
6895 * @return possible object is {@link Integer }
6898 public Integer getWidth()
6904 * Sets the value of the width property.
6907 * allowed object is {@link Integer }
6910 public void setWidth(Integer value)
6916 * Gets the value of the height property.
6918 * @return possible object is {@link Integer }
6921 public Integer getHeight()
6927 * Sets the value of the height property.
6930 * allowed object is {@link Integer }
6933 public void setHeight(Integer value)
6935 this.height = value;
6939 * Gets the value of the xpos property.
6941 * @return possible object is {@link Integer }
6944 public Integer getXpos()
6950 * Sets the value of the xpos property.
6953 * allowed object is {@link Integer }
6956 public void setXpos(Integer value)
6962 * Gets the value of the ypos property.
6964 * @return possible object is {@link Integer }
6967 public Integer getYpos()
6973 * Sets the value of the ypos property.
6976 * allowed object is {@link Integer }
6979 public void setYpos(Integer value)