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: 2018.09.18 at 01:33:02 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 JalviewModelType complex type.
29 * The following schema fragment specifies the expected content contained within
33 * <complexType name="JalviewModelType">
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>
170 * <attGroup ref="{www.jalview.org}swingwindow"/>
171 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
172 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
173 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
174 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
175 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
176 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
177 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
178 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
179 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
180 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
181 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
182 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
183 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
184 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
185 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
186 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
187 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
188 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
189 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
190 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
191 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
192 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
193 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
194 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
195 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
196 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
197 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
198 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
199 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
200 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
201 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
202 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
203 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
204 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
205 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
206 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
207 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
208 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
209 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
210 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
211 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
213 * </complexContent>
216 * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
218 * <complexContent>
219 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
221 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
223 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
225 * </complexContent>
228 * <element name="tree" maxOccurs="unbounded" minOccurs="0">
230 * <complexContent>
231 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
232 * <sequence minOccurs="0">
233 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
234 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
236 * <attGroup ref="{www.jalview.org}swingwindow"/>
237 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
238 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
239 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
240 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
241 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
242 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
243 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
244 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
245 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
246 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
248 * </complexContent>
251 * <element name="FeatureSettings" minOccurs="0">
253 * <complexContent>
254 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
256 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
258 * <complexContent>
259 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
261 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
262 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
264 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
265 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
266 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
267 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
268 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
269 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
270 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
271 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
272 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
273 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
274 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
275 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
277 * </complexContent>
280 * <element name="group" maxOccurs="unbounded" minOccurs="0">
282 * <complexContent>
283 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
284 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
285 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
287 * </complexContent>
292 * </complexContent>
298 * </complexContent>
304 @XmlAccessorType(XmlAccessType.FIELD)
306 name = "JalviewModelType",
307 namespace = "www.jalview.org",
309 { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
310 "userColours", "tree", "featureSettings" })
311 public class JalviewModelType
314 @XmlElement(required = true)
315 @XmlSchemaType(name = "dateTime")
316 protected XMLGregorianCalendar creationDate;
318 @XmlElement(required = true)
319 protected String version;
321 @XmlElement(required = true)
322 protected VAMSAS vamsasModel;
324 @XmlElement(name = "JSeq")
325 protected List<JalviewModelType.JSeq> jSeq;
327 @XmlElement(name = "JGroup")
328 protected List<JalviewModelType.JGroup> jGroup;
330 @XmlElement(name = "Viewport")
331 protected List<JalviewModelType.Viewport> viewport;
333 @XmlElement(name = "UserColours")
334 protected List<JalviewModelType.UserColours> userColours;
336 protected List<JalviewModelType.Tree> tree;
338 @XmlElement(name = "FeatureSettings")
339 protected JalviewModelType.FeatureSettings featureSettings;
342 * Gets the value of the creationDate property.
344 * @return possible object is {@link XMLGregorianCalendar }
347 public XMLGregorianCalendar getCreationDate()
353 * Sets the value of the creationDate property.
356 * allowed object is {@link XMLGregorianCalendar }
359 public void setCreationDate(XMLGregorianCalendar value)
361 this.creationDate = value;
365 * Gets the value of the version property.
367 * @return possible object is {@link String }
370 public String getVersion()
376 * Sets the value of the version property.
379 * allowed object is {@link String }
382 public void setVersion(String value)
384 this.version = value;
388 * Gets the value of the vamsasModel property.
390 * @return possible object is {@link VAMSAS }
393 public VAMSAS getVamsasModel()
399 * Sets the value of the vamsasModel property.
402 * allowed object is {@link VAMSAS }
405 public void setVamsasModel(VAMSAS value)
407 this.vamsasModel = value;
411 * Gets the value of the jSeq property.
414 * This accessor method returns a reference to the live list, not a snapshot.
415 * Therefore any modification you make to the returned list will be present
416 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
417 * for the jSeq property.
420 * For example, to add a new item, do as follows:
423 * getJSeq().add(newItem);
428 * Objects of the following type(s) are allowed in the list
429 * {@link JalviewModelType.JSeq }
433 public List<JalviewModelType.JSeq> getJSeq()
437 jSeq = new ArrayList<JalviewModelType.JSeq>();
443 * Gets the value of the jGroup property.
446 * This accessor method returns a reference to the live list, not a snapshot.
447 * Therefore any modification you make to the returned list will be present
448 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
449 * for the jGroup property.
452 * For example, to add a new item, do as follows:
455 * getJGroup().add(newItem);
460 * Objects of the following type(s) are allowed in the list
461 * {@link JalviewModelType.JGroup }
465 public List<JalviewModelType.JGroup> getJGroup()
469 jGroup = new ArrayList<JalviewModelType.JGroup>();
475 * Gets the value of the viewport property.
478 * This accessor method returns a reference to the live list, not a snapshot.
479 * Therefore any modification you make to the returned list will be present
480 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
481 * for the viewport property.
484 * For example, to add a new item, do as follows:
487 * getViewport().add(newItem);
492 * Objects of the following type(s) are allowed in the list
493 * {@link JalviewModelType.Viewport }
497 public List<JalviewModelType.Viewport> getViewport()
499 if (viewport == null)
501 viewport = new ArrayList<JalviewModelType.Viewport>();
503 return this.viewport;
507 * Gets the value of the userColours property.
510 * This accessor method returns a reference to the live list, not a snapshot.
511 * Therefore any modification you make to the returned list will be present
512 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
513 * for the userColours property.
516 * For example, to add a new item, do as follows:
519 * getUserColours().add(newItem);
524 * Objects of the following type(s) are allowed in the list
525 * {@link JalviewModelType.UserColours }
529 public List<JalviewModelType.UserColours> getUserColours()
531 if (userColours == null)
533 userColours = new ArrayList<JalviewModelType.UserColours>();
535 return this.userColours;
539 * Gets the value of the tree property.
542 * This accessor method returns a reference to the live list, not a snapshot.
543 * Therefore any modification you make to the returned list will be present
544 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
545 * for the tree property.
548 * For example, to add a new item, do as follows:
551 * getTree().add(newItem);
556 * Objects of the following type(s) are allowed in the list
557 * {@link JalviewModelType.Tree }
561 public List<JalviewModelType.Tree> getTree()
565 tree = new ArrayList<JalviewModelType.Tree>();
571 * Gets the value of the featureSettings property.
573 * @return possible object is {@link JalviewModelType.FeatureSettings }
576 public JalviewModelType.FeatureSettings getFeatureSettings()
578 return featureSettings;
582 * Sets the value of the featureSettings property.
585 * allowed object is {@link JalviewModelType.FeatureSettings }
588 public void setFeatureSettings(JalviewModelType.FeatureSettings value)
590 this.featureSettings = value;
595 * Java class for anonymous complex type.
598 * The following schema fragment specifies the expected content contained
603 * <complexContent>
604 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
606 * <element name="setting" maxOccurs="unbounded" minOccurs="0">
608 * <complexContent>
609 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
611 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
612 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
614 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
615 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
616 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
617 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
618 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
619 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
620 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
621 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
622 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
623 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
624 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
625 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
627 * </complexContent>
630 * <element name="group" maxOccurs="unbounded" minOccurs="0">
632 * <complexContent>
633 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
634 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
635 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
637 * </complexContent>
642 * </complexContent>
648 @XmlAccessorType(XmlAccessType.FIELD)
649 @XmlType(name = "", propOrder = { "setting", "group" })
650 public static class FeatureSettings
653 @XmlElement(namespace = "www.jalview.org")
654 protected List<JalviewModelType.FeatureSettings.Setting> setting;
656 @XmlElement(namespace = "www.jalview.org")
657 protected List<JalviewModelType.FeatureSettings.Group> group;
660 * Gets the value of the setting property.
663 * This accessor method returns a reference to the live list, not a
664 * snapshot. Therefore any modification you make to the returned list will
665 * be present inside the JAXB object. This is why there is not a
666 * <CODE>set</CODE> method for the setting property.
669 * For example, to add a new item, do as follows:
672 * getSetting().add(newItem);
677 * Objects of the following type(s) are allowed in the list
678 * {@link JalviewModelType.FeatureSettings.Setting }
682 public List<JalviewModelType.FeatureSettings.Setting> getSetting()
686 setting = new ArrayList<JalviewModelType.FeatureSettings.Setting>();
692 * Gets the value of the group property.
695 * This accessor method returns a reference to the live list, not a
696 * snapshot. Therefore any modification you make to the returned list will
697 * be present inside the JAXB object. This is why there is not a
698 * <CODE>set</CODE> method for the group property.
701 * For example, to add a new item, do as follows:
704 * getGroup().add(newItem);
709 * Objects of the following type(s) are allowed in the list
710 * {@link JalviewModelType.FeatureSettings.Group }
714 public List<JalviewModelType.FeatureSettings.Group> getGroup()
718 group = new ArrayList<JalviewModelType.FeatureSettings.Group>();
725 * Java class for anonymous complex type.
728 * The following schema fragment specifies the expected content contained
733 * <complexContent>
734 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
735 * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
736 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
738 * </complexContent>
744 @XmlAccessorType(XmlAccessType.FIELD)
746 public static class Group
749 @XmlAttribute(name = "name", required = true)
750 protected String name;
752 @XmlAttribute(name = "display", required = true)
753 protected boolean display;
756 * Gets the value of the name property.
758 * @return possible object is {@link String }
761 public String getName()
767 * Sets the value of the name property.
770 * allowed object is {@link String }
773 public void setName(String value)
779 * Gets the value of the display property.
782 public boolean isDisplay()
788 * Sets the value of the display property.
791 public void setDisplay(boolean value)
793 this.display = value;
800 * Java class for anonymous complex type.
803 * The following schema fragment specifies the expected content contained
808 * <complexContent>
809 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
811 * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
812 * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
814 * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
815 * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
816 * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
817 * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
818 * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
819 * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
820 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
821 * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
822 * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
823 * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
824 * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
825 * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
827 * </complexContent>
833 @XmlAccessorType(XmlAccessType.FIELD)
834 @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
835 public static class Setting
838 @XmlElement(namespace = "www.jalview.org")
839 protected List<String> attributeName;
841 @XmlElement(namespace = "www.jalview.org")
842 protected FeatureMatcherSet matcherSet;
844 @XmlAttribute(name = "type", required = true)
845 protected String type;
847 @XmlAttribute(name = "colour", required = true)
848 protected int colour;
850 @XmlAttribute(name = "display", required = true)
851 protected boolean display;
853 @XmlAttribute(name = "order")
854 protected Float order;
856 @XmlAttribute(name = "mincolour")
857 protected Integer mincolour;
859 @XmlAttribute(name = "noValueColour")
860 protected NoValueColour noValueColour;
862 @XmlAttribute(name = "threshold")
863 protected Float threshold;
865 @XmlAttribute(name = "threshstate")
866 protected Integer threshstate;
868 @XmlAttribute(name = "max")
871 @XmlAttribute(name = "min")
874 @XmlAttribute(name = "colourByLabel")
875 protected Boolean colourByLabel;
877 @XmlAttribute(name = "autoScale")
878 protected Boolean autoScale;
881 * Gets the value of the attributeName property.
884 * This accessor method returns a reference to the live list, not a
885 * snapshot. Therefore any modification you make to the returned list will
886 * be present inside the JAXB object. This is why there is not a
887 * <CODE>set</CODE> method for the attributeName property.
890 * For example, to add a new item, do as follows:
893 * getAttributeName().add(newItem);
898 * Objects of the following type(s) are allowed in the list {@link String
903 public List<String> getAttributeName()
905 if (attributeName == null)
907 attributeName = new ArrayList<String>();
909 return this.attributeName;
913 * Gets the value of the matcherSet property.
915 * @return possible object is {@link FeatureMatcherSet }
918 public FeatureMatcherSet getMatcherSet()
924 * Sets the value of the matcherSet property.
927 * allowed object is {@link FeatureMatcherSet }
930 public void setMatcherSet(FeatureMatcherSet value)
932 this.matcherSet = value;
936 * Gets the value of the type property.
938 * @return possible object is {@link String }
941 public String getType()
947 * Sets the value of the type property.
950 * allowed object is {@link String }
953 public void setType(String value)
959 * Gets the value of the colour property.
962 public int getColour()
968 * Sets the value of the colour property.
971 public void setColour(int value)
977 * Gets the value of the display property.
980 public boolean isDisplay()
986 * Sets the value of the display property.
989 public void setDisplay(boolean value)
991 this.display = value;
995 * Gets the value of the order property.
997 * @return possible object is {@link Float }
1000 public Float getOrder()
1006 * Sets the value of the order property.
1009 * allowed object is {@link Float }
1012 public void setOrder(Float value)
1018 * Gets the value of the mincolour property.
1020 * @return possible object is {@link Integer }
1023 public Integer getMincolour()
1029 * Sets the value of the mincolour property.
1032 * allowed object is {@link Integer }
1035 public void setMincolour(Integer value)
1037 this.mincolour = value;
1041 * Gets the value of the noValueColour property.
1043 * @return possible object is {@link NoValueColour }
1046 public NoValueColour getNoValueColour()
1048 if (noValueColour == null)
1050 return NoValueColour.MIN;
1054 return noValueColour;
1059 * Sets the value of the noValueColour property.
1062 * allowed object is {@link NoValueColour }
1065 public void setNoValueColour(NoValueColour value)
1067 this.noValueColour = value;
1071 * Gets the value of the threshold property.
1073 * @return possible object is {@link Float }
1076 public Float getThreshold()
1082 * Sets the value of the threshold property.
1085 * allowed object is {@link Float }
1088 public void setThreshold(Float value)
1090 this.threshold = value;
1094 * Gets the value of the threshstate property.
1096 * @return possible object is {@link Integer }
1099 public Integer getThreshstate()
1105 * Sets the value of the threshstate property.
1108 * allowed object is {@link Integer }
1111 public void setThreshstate(Integer value)
1113 this.threshstate = value;
1117 * Gets the value of the max property.
1119 * @return possible object is {@link Float }
1122 public Float getMax()
1128 * Sets the value of the max property.
1131 * allowed object is {@link Float }
1134 public void setMax(Float value)
1140 * Gets the value of the min property.
1142 * @return possible object is {@link Float }
1145 public Float getMin()
1151 * Sets the value of the min property.
1154 * allowed object is {@link Float }
1157 public void setMin(Float value)
1163 * Gets the value of the colourByLabel property.
1165 * @return possible object is {@link Boolean }
1168 public Boolean isColourByLabel()
1170 return colourByLabel;
1174 * Sets the value of the colourByLabel property.
1177 * allowed object is {@link Boolean }
1180 public void setColourByLabel(Boolean value)
1182 this.colourByLabel = value;
1186 * Gets the value of the autoScale property.
1188 * @return possible object is {@link Boolean }
1191 public Boolean isAutoScale()
1197 * Sets the value of the autoScale property.
1200 * allowed object is {@link Boolean }
1203 public void setAutoScale(Boolean value)
1205 this.autoScale = value;
1214 * Java class for anonymous complex type.
1217 * The following schema fragment specifies the expected content contained
1218 * within this class.
1222 * <complexContent>
1223 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1225 * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
1226 * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
1228 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
1229 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
1230 * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
1231 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
1232 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1233 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1234 * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
1235 * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1236 * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1237 * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1238 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
1239 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
1240 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
1241 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1242 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1243 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1244 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1245 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1246 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
1248 * </complexContent>
1254 @XmlAccessorType(XmlAccessType.FIELD)
1255 @XmlType(name = "", propOrder = { "seq", "annotationColours" })
1256 public static class JGroup
1259 @XmlElement(namespace = "www.jalview.org", required = true)
1260 protected List<String> seq;
1262 @XmlElement(namespace = "www.jalview.org")
1263 protected AnnotationColourScheme annotationColours;
1265 @XmlAttribute(name = "start")
1266 protected Integer start;
1268 @XmlAttribute(name = "end")
1269 protected Integer end;
1271 @XmlAttribute(name = "name")
1272 protected String name;
1274 @XmlAttribute(name = "colour")
1275 protected String colour;
1277 @XmlAttribute(name = "consThreshold")
1278 protected Integer consThreshold;
1280 @XmlAttribute(name = "pidThreshold")
1281 protected Integer pidThreshold;
1283 @XmlAttribute(name = "outlineColour")
1284 protected Integer outlineColour;
1286 @XmlAttribute(name = "displayBoxes")
1287 protected Boolean displayBoxes;
1289 @XmlAttribute(name = "displayText")
1290 protected Boolean displayText;
1292 @XmlAttribute(name = "colourText")
1293 protected Boolean colourText;
1295 @XmlAttribute(name = "textCol1")
1296 protected Integer textCol1;
1298 @XmlAttribute(name = "textCol2")
1299 protected Integer textCol2;
1301 @XmlAttribute(name = "textColThreshold")
1302 protected Integer textColThreshold;
1304 @XmlAttribute(name = "showUnconserved")
1305 protected Boolean showUnconserved;
1307 @XmlAttribute(name = "ignoreGapsinConsensus")
1308 protected Boolean ignoreGapsinConsensus;
1310 @XmlAttribute(name = "showConsensusHistogram")
1311 protected Boolean showConsensusHistogram;
1313 @XmlAttribute(name = "showSequenceLogo")
1314 protected Boolean showSequenceLogo;
1316 @XmlAttribute(name = "normaliseSequenceLogo")
1317 protected Boolean normaliseSequenceLogo;
1319 @XmlAttribute(name = "id")
1320 protected String id;
1323 * Gets the value of the seq property.
1326 * This accessor method returns a reference to the live list, not a
1327 * snapshot. Therefore any modification you make to the returned list will
1328 * be present inside the JAXB object. This is why there is not a
1329 * <CODE>set</CODE> method for the seq property.
1332 * For example, to add a new item, do as follows:
1335 * getSeq().add(newItem);
1340 * Objects of the following type(s) are allowed in the list {@link String }
1344 public List<String> getSeq()
1348 seq = new ArrayList<String>();
1354 * Gets the value of the annotationColours property.
1356 * @return possible object is {@link AnnotationColourScheme }
1359 public AnnotationColourScheme getAnnotationColours()
1361 return annotationColours;
1365 * Sets the value of the annotationColours property.
1368 * allowed object is {@link AnnotationColourScheme }
1371 public void setAnnotationColours(AnnotationColourScheme value)
1373 this.annotationColours = value;
1377 * Gets the value of the start property.
1379 * @return possible object is {@link Integer }
1382 public Integer getStart()
1388 * Sets the value of the start property.
1391 * allowed object is {@link Integer }
1394 public void setStart(Integer value)
1400 * Gets the value of the end property.
1402 * @return possible object is {@link Integer }
1405 public Integer getEnd()
1411 * Sets the value of the end property.
1414 * allowed object is {@link Integer }
1417 public void setEnd(Integer value)
1423 * Gets the value of the name property.
1425 * @return possible object is {@link String }
1428 public String getName()
1434 * Sets the value of the name property.
1437 * allowed object is {@link String }
1440 public void setName(String value)
1446 * Gets the value of the colour property.
1448 * @return possible object is {@link String }
1451 public String getColour()
1457 * Sets the value of the colour property.
1460 * allowed object is {@link String }
1463 public void setColour(String value)
1465 this.colour = value;
1469 * Gets the value of the consThreshold property.
1471 * @return possible object is {@link Integer }
1474 public Integer getConsThreshold()
1476 return consThreshold;
1480 * Sets the value of the consThreshold property.
1483 * allowed object is {@link Integer }
1486 public void setConsThreshold(Integer value)
1488 this.consThreshold = value;
1492 * Gets the value of the pidThreshold property.
1494 * @return possible object is {@link Integer }
1497 public Integer getPidThreshold()
1499 return pidThreshold;
1503 * Sets the value of the pidThreshold property.
1506 * allowed object is {@link Integer }
1509 public void setPidThreshold(Integer value)
1511 this.pidThreshold = value;
1515 * Gets the value of the outlineColour property.
1517 * @return possible object is {@link Integer }
1520 public Integer getOutlineColour()
1522 return outlineColour;
1526 * Sets the value of the outlineColour property.
1529 * allowed object is {@link Integer }
1532 public void setOutlineColour(Integer value)
1534 this.outlineColour = value;
1538 * Gets the value of the displayBoxes property.
1540 * @return possible object is {@link Boolean }
1543 public Boolean isDisplayBoxes()
1545 return displayBoxes;
1549 * Sets the value of the displayBoxes property.
1552 * allowed object is {@link Boolean }
1555 public void setDisplayBoxes(Boolean value)
1557 this.displayBoxes = value;
1561 * Gets the value of the displayText property.
1563 * @return possible object is {@link Boolean }
1566 public Boolean isDisplayText()
1572 * Sets the value of the displayText property.
1575 * allowed object is {@link Boolean }
1578 public void setDisplayText(Boolean value)
1580 this.displayText = value;
1584 * Gets the value of the colourText property.
1586 * @return possible object is {@link Boolean }
1589 public Boolean isColourText()
1595 * Sets the value of the colourText property.
1598 * allowed object is {@link Boolean }
1601 public void setColourText(Boolean value)
1603 this.colourText = value;
1607 * Gets the value of the textCol1 property.
1609 * @return possible object is {@link Integer }
1612 public Integer getTextCol1()
1618 * Sets the value of the textCol1 property.
1621 * allowed object is {@link Integer }
1624 public void setTextCol1(Integer value)
1626 this.textCol1 = value;
1630 * Gets the value of the textCol2 property.
1632 * @return possible object is {@link Integer }
1635 public Integer getTextCol2()
1641 * Sets the value of the textCol2 property.
1644 * allowed object is {@link Integer }
1647 public void setTextCol2(Integer value)
1649 this.textCol2 = value;
1653 * Gets the value of the textColThreshold property.
1655 * @return possible object is {@link Integer }
1658 public Integer getTextColThreshold()
1660 return textColThreshold;
1664 * Sets the value of the textColThreshold property.
1667 * allowed object is {@link Integer }
1670 public void setTextColThreshold(Integer value)
1672 this.textColThreshold = value;
1676 * Gets the value of the showUnconserved property.
1678 * @return possible object is {@link Boolean }
1681 public Boolean isShowUnconserved()
1683 return showUnconserved;
1687 * Sets the value of the showUnconserved property.
1690 * allowed object is {@link Boolean }
1693 public void setShowUnconserved(Boolean value)
1695 this.showUnconserved = value;
1699 * Gets the value of the ignoreGapsinConsensus property.
1701 * @return possible object is {@link Boolean }
1704 public boolean isIgnoreGapsinConsensus()
1706 if (ignoreGapsinConsensus == null)
1712 return ignoreGapsinConsensus;
1717 * Sets the value of the ignoreGapsinConsensus property.
1720 * allowed object is {@link Boolean }
1723 public void setIgnoreGapsinConsensus(Boolean value)
1725 this.ignoreGapsinConsensus = value;
1729 * Gets the value of the showConsensusHistogram property.
1731 * @return possible object is {@link Boolean }
1734 public boolean isShowConsensusHistogram()
1736 if (showConsensusHistogram == null)
1742 return showConsensusHistogram;
1747 * Sets the value of the showConsensusHistogram property.
1750 * allowed object is {@link Boolean }
1753 public void setShowConsensusHistogram(Boolean value)
1755 this.showConsensusHistogram = value;
1759 * Gets the value of the showSequenceLogo property.
1761 * @return possible object is {@link Boolean }
1764 public boolean isShowSequenceLogo()
1766 if (showSequenceLogo == null)
1772 return showSequenceLogo;
1777 * Sets the value of the showSequenceLogo property.
1780 * allowed object is {@link Boolean }
1783 public void setShowSequenceLogo(Boolean value)
1785 this.showSequenceLogo = value;
1789 * Gets the value of the normaliseSequenceLogo property.
1791 * @return possible object is {@link Boolean }
1794 public boolean isNormaliseSequenceLogo()
1796 if (normaliseSequenceLogo == null)
1802 return normaliseSequenceLogo;
1807 * Sets the value of the normaliseSequenceLogo property.
1810 * allowed object is {@link Boolean }
1813 public void setNormaliseSequenceLogo(Boolean value)
1815 this.normaliseSequenceLogo = value;
1819 * Gets the value of the id property.
1821 * @return possible object is {@link String }
1824 public String getId()
1830 * Sets the value of the id property.
1833 * allowed object is {@link String }
1836 public void setId(String value)
1845 * Java class for anonymous complex type.
1848 * The following schema fragment specifies the expected content contained
1849 * within this class.
1853 * <complexContent>
1854 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1856 * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
1857 * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
1859 * <complexContent>
1860 * <extension base="{www.jalview.org}pdbentry">
1862 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
1864 * <simpleContent>
1865 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
1866 * <attGroup ref="{www.jalview.org}swingwindow"/>
1867 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1868 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1869 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1870 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
1871 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
1872 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
1874 * </simpleContent>
1879 * </complexContent>
1882 * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
1883 * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
1885 * <complexContent>
1886 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1888 * <element name="secondaryStructure" maxOccurs="unbounded">
1890 * <complexContent>
1891 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
1892 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1893 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1894 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1895 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
1897 * </complexContent>
1901 * <attGroup ref="{www.jalview.org}swingwindow"/>
1902 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
1903 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
1904 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
1905 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
1907 * </complexContent>
1911 * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
1912 * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1913 * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
1914 * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
1915 * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1916 * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
1918 * </complexContent>
1924 @XmlAccessorType(XmlAccessType.FIELD)
1928 { "features", "pdbids", "hiddenSequences", "rnaViewer" })
1929 public static class JSeq
1932 @XmlElement(namespace = "www.jalview.org")
1933 protected List<Feature> features;
1935 @XmlElement(namespace = "www.jalview.org")
1936 protected List<JalviewModelType.JSeq.Pdbids> pdbids;
1938 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1939 protected List<Integer> hiddenSequences;
1941 @XmlElement(namespace = "www.jalview.org")
1942 protected List<JalviewModelType.JSeq.RnaViewer> rnaViewer;
1944 @XmlAttribute(name = "colour")
1945 protected Integer colour;
1947 @XmlAttribute(name = "start", required = true)
1948 protected int start;
1950 @XmlAttribute(name = "end", required = true)
1953 @XmlAttribute(name = "id", required = true)
1954 protected String id;
1956 @XmlAttribute(name = "hidden")
1957 protected Boolean hidden;
1959 @XmlAttribute(name = "viewreference")
1960 protected Boolean viewreference;
1963 * Gets the value of the features property.
1966 * This accessor method returns a reference to the live list, not a
1967 * snapshot. Therefore any modification you make to the returned list will
1968 * be present inside the JAXB object. This is why there is not a
1969 * <CODE>set</CODE> method for the features property.
1972 * For example, to add a new item, do as follows:
1975 * getFeatures().add(newItem);
1980 * Objects of the following type(s) are allowed in the list {@link Feature }
1984 public List<Feature> getFeatures()
1986 if (features == null)
1988 features = new ArrayList<Feature>();
1990 return this.features;
1994 * Gets the value of the pdbids property.
1997 * This accessor method returns a reference to the live list, not a
1998 * snapshot. Therefore any modification you make to the returned list will
1999 * be present inside the JAXB object. This is why there is not a
2000 * <CODE>set</CODE> method for the pdbids property.
2003 * For example, to add a new item, do as follows:
2006 * getPdbids().add(newItem);
2011 * Objects of the following type(s) are allowed in the list
2012 * {@link JalviewModelType.JSeq.Pdbids }
2016 public List<JalviewModelType.JSeq.Pdbids> getPdbids()
2020 pdbids = new ArrayList<JalviewModelType.JSeq.Pdbids>();
2026 * Gets the value of the hiddenSequences property.
2029 * This accessor method returns a reference to the live list, not a
2030 * snapshot. Therefore any modification you make to the returned list will
2031 * be present inside the JAXB object. This is why there is not a
2032 * <CODE>set</CODE> method for the hiddenSequences property.
2035 * For example, to add a new item, do as follows:
2038 * getHiddenSequences().add(newItem);
2043 * Objects of the following type(s) are allowed in the list {@link Integer }
2047 public List<Integer> getHiddenSequences()
2049 if (hiddenSequences == null)
2051 hiddenSequences = new ArrayList<Integer>();
2053 return this.hiddenSequences;
2057 * Gets the value of the rnaViewer property.
2060 * This accessor method returns a reference to the live list, not a
2061 * snapshot. Therefore any modification you make to the returned list will
2062 * be present inside the JAXB object. This is why there is not a
2063 * <CODE>set</CODE> method for the rnaViewer property.
2066 * For example, to add a new item, do as follows:
2069 * getRnaViewer().add(newItem);
2074 * Objects of the following type(s) are allowed in the list
2075 * {@link JalviewModelType.JSeq.RnaViewer }
2079 public List<JalviewModelType.JSeq.RnaViewer> getRnaViewer()
2081 if (rnaViewer == null)
2083 rnaViewer = new ArrayList<JalviewModelType.JSeq.RnaViewer>();
2085 return this.rnaViewer;
2089 * Gets the value of the colour property.
2091 * @return possible object is {@link Integer }
2094 public Integer getColour()
2100 * Sets the value of the colour property.
2103 * allowed object is {@link Integer }
2106 public void setColour(Integer value)
2108 this.colour = value;
2112 * Gets the value of the start property.
2115 public int getStart()
2121 * Sets the value of the start property.
2124 public void setStart(int value)
2130 * Gets the value of the end property.
2139 * Sets the value of the end property.
2142 public void setEnd(int value)
2148 * Gets the value of the id property.
2150 * @return possible object is {@link String }
2153 public String getId()
2159 * Sets the value of the id property.
2162 * allowed object is {@link String }
2165 public void setId(String value)
2171 * Gets the value of the hidden property.
2173 * @return possible object is {@link Boolean }
2176 public Boolean isHidden()
2182 * Sets the value of the hidden property.
2185 * allowed object is {@link Boolean }
2188 public void setHidden(Boolean value)
2190 this.hidden = value;
2194 * Gets the value of the viewreference property.
2196 * @return possible object is {@link Boolean }
2199 public Boolean isViewreference()
2201 return viewreference;
2205 * Sets the value of the viewreference property.
2208 * allowed object is {@link Boolean }
2211 public void setViewreference(Boolean value)
2213 this.viewreference = value;
2218 * Java class for anonymous complex type.
2221 * The following schema fragment specifies the expected content contained
2222 * within this class.
2226 * <complexContent>
2227 * <extension base="{www.jalview.org}pdbentry">
2229 * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
2231 * <simpleContent>
2232 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2233 * <attGroup ref="{www.jalview.org}swingwindow"/>
2234 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2235 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2236 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2237 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2238 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2239 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2241 * </simpleContent>
2246 * </complexContent>
2252 @XmlAccessorType(XmlAccessType.FIELD)
2253 @XmlType(name = "", propOrder = { "structureState" })
2254 public static class Pdbids extends Pdbentry
2257 @XmlElement(namespace = "www.jalview.org")
2258 protected List<JalviewModelType.JSeq.Pdbids.StructureState> structureState;
2261 * Gets the value of the structureState property.
2264 * This accessor method returns a reference to the live list, not a
2265 * snapshot. Therefore any modification you make to the returned list will
2266 * be present inside the JAXB object. This is why there is not a
2267 * <CODE>set</CODE> method for the structureState property.
2270 * For example, to add a new item, do as follows:
2273 * getStructureState().add(newItem);
2278 * Objects of the following type(s) are allowed in the list
2279 * {@link JalviewModelType.JSeq.Pdbids.StructureState }
2283 public List<JalviewModelType.JSeq.Pdbids.StructureState> getStructureState()
2285 if (structureState == null)
2287 structureState = new ArrayList<JalviewModelType.JSeq.Pdbids.StructureState>();
2289 return this.structureState;
2294 * Java class for anonymous complex type.
2297 * The following schema fragment specifies the expected content contained
2298 * within this class.
2302 * <simpleContent>
2303 * <extension base="<http://www.w3.org/2001/XMLSchema>string">
2304 * <attGroup ref="{www.jalview.org}swingwindow"/>
2305 * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2306 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2307 * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2308 * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
2309 * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
2310 * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
2312 * </simpleContent>
2318 @XmlAccessorType(XmlAccessType.FIELD)
2319 @XmlType(name = "", propOrder = { "value" })
2320 public static class StructureState
2324 protected String value;
2326 @XmlAttribute(name = "visible")
2327 protected Boolean visible;
2329 @XmlAttribute(name = "viewId")
2330 protected String viewId;
2332 @XmlAttribute(name = "alignwithAlignPanel")
2333 protected Boolean alignwithAlignPanel;
2335 @XmlAttribute(name = "colourwithAlignPanel")
2336 protected Boolean colourwithAlignPanel;
2338 @XmlAttribute(name = "colourByJmol")
2339 protected Boolean colourByJmol;
2341 @XmlAttribute(name = "type")
2342 protected String type;
2344 @XmlAttribute(name = "width")
2345 protected Integer width;
2347 @XmlAttribute(name = "height")
2348 protected Integer height;
2350 @XmlAttribute(name = "xpos")
2351 protected Integer xpos;
2353 @XmlAttribute(name = "ypos")
2354 protected Integer ypos;
2357 * Gets the value of the value property.
2359 * @return possible object is {@link String }
2362 public String getValue()
2368 * Sets the value of the value property.
2371 * allowed object is {@link String }
2374 public void setValue(String value)
2380 * Gets the value of the visible property.
2382 * @return possible object is {@link Boolean }
2385 public Boolean isVisible()
2391 * Sets the value of the visible property.
2394 * allowed object is {@link Boolean }
2397 public void setVisible(Boolean value)
2399 this.visible = value;
2403 * Gets the value of the viewId property.
2405 * @return possible object is {@link String }
2408 public String getViewId()
2414 * Sets the value of the viewId property.
2417 * allowed object is {@link String }
2420 public void setViewId(String value)
2422 this.viewId = value;
2426 * Gets the value of the alignwithAlignPanel property.
2428 * @return possible object is {@link Boolean }
2431 public boolean isAlignwithAlignPanel()
2433 if (alignwithAlignPanel == null)
2439 return alignwithAlignPanel;
2444 * Sets the value of the alignwithAlignPanel property.
2447 * allowed object is {@link Boolean }
2450 public void setAlignwithAlignPanel(Boolean value)
2452 this.alignwithAlignPanel = value;
2456 * Gets the value of the colourwithAlignPanel property.
2458 * @return possible object is {@link Boolean }
2461 public boolean isColourwithAlignPanel()
2463 if (colourwithAlignPanel == null)
2469 return colourwithAlignPanel;
2474 * Sets the value of the colourwithAlignPanel property.
2477 * allowed object is {@link Boolean }
2480 public void setColourwithAlignPanel(Boolean value)
2482 this.colourwithAlignPanel = value;
2486 * Gets the value of the colourByJmol property.
2488 * @return possible object is {@link Boolean }
2491 public boolean isColourByJmol()
2493 if (colourByJmol == null)
2499 return colourByJmol;
2504 * Sets the value of the colourByJmol property.
2507 * allowed object is {@link Boolean }
2510 public void setColourByJmol(Boolean value)
2512 this.colourByJmol = value;
2516 * Gets the value of the type property.
2518 * @return possible object is {@link String }
2521 public String getType()
2527 * Sets the value of the type property.
2530 * allowed object is {@link String }
2533 public void setType(String value)
2539 * Gets the value of the width property.
2541 * @return possible object is {@link Integer }
2544 public Integer getWidth()
2550 * Sets the value of the width property.
2553 * allowed object is {@link Integer }
2556 public void setWidth(Integer value)
2562 * Gets the value of the height property.
2564 * @return possible object is {@link Integer }
2567 public Integer getHeight()
2573 * Sets the value of the height property.
2576 * allowed object is {@link Integer }
2579 public void setHeight(Integer value)
2581 this.height = value;
2585 * Gets the value of the xpos property.
2587 * @return possible object is {@link Integer }
2590 public Integer getXpos()
2596 * Sets the value of the xpos property.
2599 * allowed object is {@link Integer }
2602 public void setXpos(Integer value)
2608 * Gets the value of the ypos property.
2610 * @return possible object is {@link Integer }
2613 public Integer getYpos()
2619 * Sets the value of the ypos property.
2622 * allowed object is {@link Integer }
2625 public void setYpos(Integer value)
2636 * Java class for anonymous complex type.
2639 * The following schema fragment specifies the expected content contained
2640 * within this class.
2644 * <complexContent>
2645 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2647 * <element name="secondaryStructure" maxOccurs="unbounded">
2649 * <complexContent>
2650 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2651 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2652 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2653 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2654 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2656 * </complexContent>
2660 * <attGroup ref="{www.jalview.org}swingwindow"/>
2661 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2662 * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
2663 * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
2664 * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
2666 * </complexContent>
2672 @XmlAccessorType(XmlAccessType.FIELD)
2673 @XmlType(name = "", propOrder = { "secondaryStructure" })
2674 public static class RnaViewer
2677 @XmlElement(namespace = "www.jalview.org", required = true)
2678 protected List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2680 @XmlAttribute(name = "title")
2681 protected String title;
2683 @XmlAttribute(name = "viewId")
2684 protected String viewId;
2686 @XmlAttribute(name = "dividerLocation")
2687 protected Integer dividerLocation;
2689 @XmlAttribute(name = "selectedRna")
2690 protected Integer selectedRna;
2692 @XmlAttribute(name = "width")
2693 protected Integer width;
2695 @XmlAttribute(name = "height")
2696 protected Integer height;
2698 @XmlAttribute(name = "xpos")
2699 protected Integer xpos;
2701 @XmlAttribute(name = "ypos")
2702 protected Integer ypos;
2705 * Gets the value of the secondaryStructure property.
2708 * This accessor method returns a reference to the live list, not a
2709 * snapshot. Therefore any modification you make to the returned list will
2710 * be present inside the JAXB object. This is why there is not a
2711 * <CODE>set</CODE> method for the secondaryStructure property.
2714 * For example, to add a new item, do as follows:
2717 * getSecondaryStructure().add(newItem);
2722 * Objects of the following type(s) are allowed in the list
2723 * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
2727 public List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
2729 if (secondaryStructure == null)
2731 secondaryStructure = new ArrayList<JalviewModelType.JSeq.RnaViewer.SecondaryStructure>();
2733 return this.secondaryStructure;
2737 * Gets the value of the title property.
2739 * @return possible object is {@link String }
2742 public String getTitle()
2748 * Sets the value of the title property.
2751 * allowed object is {@link String }
2754 public void setTitle(String value)
2760 * Gets the value of the viewId property.
2762 * @return possible object is {@link String }
2765 public String getViewId()
2771 * Sets the value of the viewId property.
2774 * allowed object is {@link String }
2777 public void setViewId(String value)
2779 this.viewId = value;
2783 * Gets the value of the dividerLocation property.
2785 * @return possible object is {@link Integer }
2788 public Integer getDividerLocation()
2790 return dividerLocation;
2794 * Sets the value of the dividerLocation property.
2797 * allowed object is {@link Integer }
2800 public void setDividerLocation(Integer value)
2802 this.dividerLocation = value;
2806 * Gets the value of the selectedRna property.
2808 * @return possible object is {@link Integer }
2811 public Integer getSelectedRna()
2817 * Sets the value of the selectedRna property.
2820 * allowed object is {@link Integer }
2823 public void setSelectedRna(Integer value)
2825 this.selectedRna = value;
2829 * Gets the value of the width property.
2831 * @return possible object is {@link Integer }
2834 public Integer getWidth()
2840 * Sets the value of the width property.
2843 * allowed object is {@link Integer }
2846 public void setWidth(Integer value)
2852 * Gets the value of the height property.
2854 * @return possible object is {@link Integer }
2857 public Integer getHeight()
2863 * Sets the value of the height property.
2866 * allowed object is {@link Integer }
2869 public void setHeight(Integer value)
2871 this.height = value;
2875 * Gets the value of the xpos property.
2877 * @return possible object is {@link Integer }
2880 public Integer getXpos()
2886 * Sets the value of the xpos property.
2889 * allowed object is {@link Integer }
2892 public void setXpos(Integer value)
2898 * Gets the value of the ypos property.
2900 * @return possible object is {@link Integer }
2903 public Integer getYpos()
2909 * Sets the value of the ypos property.
2912 * allowed object is {@link Integer }
2915 public void setYpos(Integer value)
2922 * Java class for anonymous complex type.
2925 * The following schema fragment specifies the expected content contained
2926 * within this class.
2930 * <complexContent>
2931 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
2932 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
2933 * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
2934 * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
2935 * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
2937 * </complexContent>
2943 @XmlAccessorType(XmlAccessType.FIELD)
2945 public static class SecondaryStructure
2948 @XmlAttribute(name = "title")
2949 protected String title;
2951 @XmlAttribute(name = "annotationId", required = true)
2952 protected String annotationId;
2954 @XmlAttribute(name = "gapped")
2955 protected Boolean gapped;
2957 @XmlAttribute(name = "viewerState")
2958 protected String viewerState;
2961 * Gets the value of the title property.
2963 * @return possible object is {@link String }
2966 public String getTitle()
2972 * Sets the value of the title property.
2975 * allowed object is {@link String }
2978 public void setTitle(String value)
2984 * Gets the value of the annotationId property.
2986 * @return possible object is {@link String }
2989 public String getAnnotationId()
2991 return annotationId;
2995 * Sets the value of the annotationId property.
2998 * allowed object is {@link String }
3001 public void setAnnotationId(String value)
3003 this.annotationId = value;
3007 * Gets the value of the gapped property.
3009 * @return possible object is {@link Boolean }
3012 public Boolean isGapped()
3018 * Sets the value of the gapped property.
3021 * allowed object is {@link Boolean }
3024 public void setGapped(Boolean value)
3026 this.gapped = value;
3030 * Gets the value of the viewerState property.
3032 * @return possible object is {@link String }
3035 public String getViewerState()
3041 * Sets the value of the viewerState property.
3044 * allowed object is {@link String }
3047 public void setViewerState(String value)
3049 this.viewerState = value;
3060 * Java class for anonymous complex type.
3063 * The following schema fragment specifies the expected content contained
3064 * within this class.
3068 * <complexContent>
3069 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3070 * <sequence minOccurs="0">
3071 * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
3072 * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
3074 * <attGroup ref="{www.jalview.org}swingwindow"/>
3075 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
3076 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
3077 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
3078 * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
3079 * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3080 * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3081 * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3082 * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3083 * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3084 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
3086 * </complexContent>
3092 @XmlAccessorType(XmlAccessType.FIELD)
3093 @XmlType(name = "", propOrder = { "title", "newick" })
3094 public static class Tree
3097 @XmlElement(namespace = "www.jalview.org")
3098 protected String title;
3100 @XmlElement(namespace = "www.jalview.org")
3101 protected String newick;
3103 @XmlAttribute(name = "fontName")
3104 protected String fontName;
3106 @XmlAttribute(name = "fontSize")
3107 protected Integer fontSize;
3109 @XmlAttribute(name = "fontStyle")
3110 protected Integer fontStyle;
3112 @XmlAttribute(name = "threshold")
3113 protected Float threshold;
3115 @XmlAttribute(name = "showBootstrap")
3116 protected Boolean showBootstrap;
3118 @XmlAttribute(name = "showDistances")
3119 protected Boolean showDistances;
3121 @XmlAttribute(name = "markUnlinked")
3122 protected Boolean markUnlinked;
3124 @XmlAttribute(name = "fitToWindow")
3125 protected Boolean fitToWindow;
3127 @XmlAttribute(name = "currentTree")
3128 protected Boolean currentTree;
3130 @XmlAttribute(name = "id")
3131 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
3133 @XmlSchemaType(name = "ID")
3134 protected String id;
3136 @XmlAttribute(name = "width")
3137 protected Integer width;
3139 @XmlAttribute(name = "height")
3140 protected Integer height;
3142 @XmlAttribute(name = "xpos")
3143 protected Integer xpos;
3145 @XmlAttribute(name = "ypos")
3146 protected Integer ypos;
3149 * Gets the value of the title property.
3151 * @return possible object is {@link String }
3154 public String getTitle()
3160 * Sets the value of the title property.
3163 * allowed object is {@link String }
3166 public void setTitle(String value)
3172 * Gets the value of the newick property.
3174 * @return possible object is {@link String }
3177 public String getNewick()
3183 * Sets the value of the newick property.
3186 * allowed object is {@link String }
3189 public void setNewick(String value)
3191 this.newick = value;
3195 * Gets the value of the fontName property.
3197 * @return possible object is {@link String }
3200 public String getFontName()
3206 * Sets the value of the fontName property.
3209 * allowed object is {@link String }
3212 public void setFontName(String value)
3214 this.fontName = value;
3218 * Gets the value of the fontSize property.
3220 * @return possible object is {@link Integer }
3223 public Integer getFontSize()
3229 * Sets the value of the fontSize property.
3232 * allowed object is {@link Integer }
3235 public void setFontSize(Integer value)
3237 this.fontSize = value;
3241 * Gets the value of the fontStyle property.
3243 * @return possible object is {@link Integer }
3246 public Integer getFontStyle()
3252 * Sets the value of the fontStyle property.
3255 * allowed object is {@link Integer }
3258 public void setFontStyle(Integer value)
3260 this.fontStyle = value;
3264 * Gets the value of the threshold property.
3266 * @return possible object is {@link Float }
3269 public Float getThreshold()
3275 * Sets the value of the threshold property.
3278 * allowed object is {@link Float }
3281 public void setThreshold(Float value)
3283 this.threshold = value;
3287 * Gets the value of the showBootstrap property.
3289 * @return possible object is {@link Boolean }
3292 public Boolean isShowBootstrap()
3294 return showBootstrap;
3298 * Sets the value of the showBootstrap property.
3301 * allowed object is {@link Boolean }
3304 public void setShowBootstrap(Boolean value)
3306 this.showBootstrap = value;
3310 * Gets the value of the showDistances property.
3312 * @return possible object is {@link Boolean }
3315 public Boolean isShowDistances()
3317 return showDistances;
3321 * Sets the value of the showDistances property.
3324 * allowed object is {@link Boolean }
3327 public void setShowDistances(Boolean value)
3329 this.showDistances = value;
3333 * Gets the value of the markUnlinked property.
3335 * @return possible object is {@link Boolean }
3338 public Boolean isMarkUnlinked()
3340 return markUnlinked;
3344 * Sets the value of the markUnlinked property.
3347 * allowed object is {@link Boolean }
3350 public void setMarkUnlinked(Boolean value)
3352 this.markUnlinked = value;
3356 * Gets the value of the fitToWindow property.
3358 * @return possible object is {@link Boolean }
3361 public Boolean isFitToWindow()
3367 * Sets the value of the fitToWindow property.
3370 * allowed object is {@link Boolean }
3373 public void setFitToWindow(Boolean value)
3375 this.fitToWindow = value;
3379 * Gets the value of the currentTree property.
3381 * @return possible object is {@link Boolean }
3384 public Boolean isCurrentTree()
3390 * Sets the value of the currentTree property.
3393 * allowed object is {@link Boolean }
3396 public void setCurrentTree(Boolean value)
3398 this.currentTree = value;
3402 * Gets the value of the id property.
3404 * @return possible object is {@link String }
3407 public String getId()
3413 * Sets the value of the id property.
3416 * allowed object is {@link String }
3419 public void setId(String value)
3425 * Gets the value of the width property.
3427 * @return possible object is {@link Integer }
3430 public Integer getWidth()
3436 * Sets the value of the width property.
3439 * allowed object is {@link Integer }
3442 public void setWidth(Integer value)
3448 * Gets the value of the height property.
3450 * @return possible object is {@link Integer }
3453 public Integer getHeight()
3459 * Sets the value of the height property.
3462 * allowed object is {@link Integer }
3465 public void setHeight(Integer value)
3467 this.height = value;
3471 * Gets the value of the xpos property.
3473 * @return possible object is {@link Integer }
3476 public Integer getXpos()
3482 * Sets the value of the xpos property.
3485 * allowed object is {@link Integer }
3488 public void setXpos(Integer value)
3494 * Gets the value of the ypos property.
3496 * @return possible object is {@link Integer }
3499 public Integer getYpos()
3505 * Sets the value of the ypos property.
3508 * allowed object is {@link Integer }
3511 public void setYpos(Integer value)
3520 * Java class for anonymous complex type.
3523 * The following schema fragment specifies the expected content contained
3524 * within this class.
3528 * <complexContent>
3529 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3531 * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
3533 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
3535 * </complexContent>
3541 @XmlAccessorType(XmlAccessType.FIELD)
3542 @XmlType(name = "", propOrder = { "userColourScheme" })
3543 public static class UserColours
3547 name = "UserColourScheme",
3548 namespace = "www.jalview.org",
3550 protected JalviewUserColours userColourScheme;
3552 @XmlAttribute(name = "id")
3553 protected String id;
3556 * Gets the value of the userColourScheme property.
3558 * @return possible object is {@link JalviewUserColours }
3561 public JalviewUserColours getUserColourScheme()
3563 return userColourScheme;
3567 * Sets the value of the userColourScheme property.
3570 * allowed object is {@link JalviewUserColours }
3573 public void setUserColourScheme(JalviewUserColours value)
3575 this.userColourScheme = value;
3579 * Gets the value of the id property.
3581 * @return possible object is {@link String }
3584 public String getId()
3590 * Sets the value of the id property.
3593 * allowed object is {@link String }
3596 public void setId(String value)
3605 * Java class for anonymous complex type.
3608 * The following schema fragment specifies the expected content contained
3609 * within this class.
3613 * <complexContent>
3614 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3616 * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
3617 * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
3619 * <complexContent>
3620 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
3621 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
3622 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
3624 * </complexContent>
3627 * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
3629 * <complexContent>
3630 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
3631 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
3632 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3633 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3635 * </complexContent>
3639 * <attGroup ref="{www.jalview.org}swingwindow"/>
3640 * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3641 * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3642 * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
3643 * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
3644 * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
3645 * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
3646 * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3647 * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3648 * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3649 * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3650 * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3651 * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3652 * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3653 * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3654 * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3655 * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3656 * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3657 * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3658 * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3659 * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3660 * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3661 * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3662 * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3663 * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3664 * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3665 * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
3666 * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3667 * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
3668 * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
3669 * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
3670 * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
3671 * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
3672 * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
3673 * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
3674 * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
3675 * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
3676 * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
3677 * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
3678 * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
3679 * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
3680 * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
3682 * </complexContent>
3688 @XmlAccessorType(XmlAccessType.FIELD)
3692 { "annotationColours", "hiddenColumns", "calcIdParam" })
3693 public static class Viewport
3696 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
3697 protected AnnotationColourScheme annotationColours;
3699 @XmlElement(namespace = "www.jalview.org")
3700 protected List<JalviewModelType.Viewport.HiddenColumns> hiddenColumns;
3702 @XmlElement(namespace = "www.jalview.org")
3703 protected List<JalviewModelType.Viewport.CalcIdParam> calcIdParam;
3705 @XmlAttribute(name = "conservationSelected")
3706 protected Boolean conservationSelected;
3708 @XmlAttribute(name = "pidSelected")
3709 protected Boolean pidSelected;
3711 @XmlAttribute(name = "bgColour")
3712 protected String bgColour;
3714 @XmlAttribute(name = "consThreshold")
3715 protected Integer consThreshold;
3717 @XmlAttribute(name = "pidThreshold")
3718 protected Integer pidThreshold;
3720 @XmlAttribute(name = "title")
3721 protected String title;
3723 @XmlAttribute(name = "showFullId")
3724 protected Boolean showFullId;
3726 @XmlAttribute(name = "rightAlignIds")
3727 protected Boolean rightAlignIds;
3729 @XmlAttribute(name = "showText")
3730 protected Boolean showText;
3732 @XmlAttribute(name = "showColourText")
3733 protected Boolean showColourText;
3735 @XmlAttribute(name = "showUnconserved")
3736 protected Boolean showUnconserved;
3738 @XmlAttribute(name = "showBoxes")
3739 protected Boolean showBoxes;
3741 @XmlAttribute(name = "wrapAlignment")
3742 protected Boolean wrapAlignment;
3744 @XmlAttribute(name = "renderGaps")
3745 protected Boolean renderGaps;
3747 @XmlAttribute(name = "showSequenceFeatures")
3748 protected Boolean showSequenceFeatures;
3750 @XmlAttribute(name = "showNPfeatureTooltip")
3751 protected Boolean showNPfeatureTooltip;
3753 @XmlAttribute(name = "showDbRefTooltip")
3754 protected Boolean showDbRefTooltip;
3756 @XmlAttribute(name = "followHighlight")
3757 protected Boolean followHighlight;
3759 @XmlAttribute(name = "followSelection")
3760 protected Boolean followSelection;
3762 @XmlAttribute(name = "showAnnotation")
3763 protected Boolean showAnnotation;
3765 @XmlAttribute(name = "centreColumnLabels")
3766 protected Boolean centreColumnLabels;
3768 @XmlAttribute(name = "showGroupConservation")
3769 protected Boolean showGroupConservation;
3771 @XmlAttribute(name = "showGroupConsensus")
3772 protected Boolean showGroupConsensus;
3774 @XmlAttribute(name = "showConsensusHistogram")
3775 protected Boolean showConsensusHistogram;
3777 @XmlAttribute(name = "showSequenceLogo")
3778 protected Boolean showSequenceLogo;
3780 @XmlAttribute(name = "normaliseSequenceLogo")
3781 protected Boolean normaliseSequenceLogo;
3783 @XmlAttribute(name = "ignoreGapsinConsensus")
3784 protected Boolean ignoreGapsinConsensus;
3786 @XmlAttribute(name = "startRes")
3787 protected Integer startRes;
3789 @XmlAttribute(name = "startSeq")
3790 protected Integer startSeq;
3792 @XmlAttribute(name = "fontName")
3793 protected String fontName;
3795 @XmlAttribute(name = "fontSize")
3796 protected Integer fontSize;
3798 @XmlAttribute(name = "fontStyle")
3799 protected Integer fontStyle;
3801 @XmlAttribute(name = "scaleProteinAsCdna")
3802 protected Boolean scaleProteinAsCdna;
3804 @XmlAttribute(name = "viewName")
3805 protected String viewName;
3807 @XmlAttribute(name = "sequenceSetId")
3808 protected String sequenceSetId;
3810 @XmlAttribute(name = "gatheredViews")
3811 protected Boolean gatheredViews;
3813 @XmlAttribute(name = "textCol1")
3814 protected Integer textCol1;
3816 @XmlAttribute(name = "textCol2")
3817 protected Integer textCol2;
3819 @XmlAttribute(name = "textColThreshold")
3820 protected Integer textColThreshold;
3822 @XmlAttribute(name = "id")
3823 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
3825 @XmlSchemaType(name = "ID")
3826 protected String id;
3828 @XmlAttribute(name = "complementId")
3829 protected String complementId;
3831 @XmlAttribute(name = "width")
3832 protected Integer width;
3834 @XmlAttribute(name = "height")
3835 protected Integer height;
3837 @XmlAttribute(name = "xpos")
3838 protected Integer xpos;
3840 @XmlAttribute(name = "ypos")
3841 protected Integer ypos;
3844 * Gets the value of the annotationColours property.
3846 * @return possible object is {@link AnnotationColourScheme }
3849 public AnnotationColourScheme getAnnotationColours()
3851 return annotationColours;
3855 * Sets the value of the annotationColours property.
3858 * allowed object is {@link AnnotationColourScheme }
3861 public void setAnnotationColours(AnnotationColourScheme value)
3863 this.annotationColours = value;
3867 * Gets the value of the hiddenColumns property.
3870 * This accessor method returns a reference to the live list, not a
3871 * snapshot. Therefore any modification you make to the returned list will
3872 * be present inside the JAXB object. This is why there is not a
3873 * <CODE>set</CODE> method for the hiddenColumns property.
3876 * For example, to add a new item, do as follows:
3879 * getHiddenColumns().add(newItem);
3884 * Objects of the following type(s) are allowed in the list
3885 * {@link JalviewModelType.Viewport.HiddenColumns }
3889 public List<JalviewModelType.Viewport.HiddenColumns> getHiddenColumns()
3891 if (hiddenColumns == null)
3893 hiddenColumns = new ArrayList<JalviewModelType.Viewport.HiddenColumns>();
3895 return this.hiddenColumns;
3899 * Gets the value of the calcIdParam property.
3902 * This accessor method returns a reference to the live list, not a
3903 * snapshot. Therefore any modification you make to the returned list will
3904 * be present inside the JAXB object. This is why there is not a
3905 * <CODE>set</CODE> method for the calcIdParam property.
3908 * For example, to add a new item, do as follows:
3911 * getCalcIdParam().add(newItem);
3916 * Objects of the following type(s) are allowed in the list
3917 * {@link JalviewModelType.Viewport.CalcIdParam }
3921 public List<JalviewModelType.Viewport.CalcIdParam> getCalcIdParam()
3923 if (calcIdParam == null)
3925 calcIdParam = new ArrayList<JalviewModelType.Viewport.CalcIdParam>();
3927 return this.calcIdParam;
3931 * Gets the value of the conservationSelected property.
3933 * @return possible object is {@link Boolean }
3936 public Boolean isConservationSelected()
3938 return conservationSelected;
3942 * Sets the value of the conservationSelected property.
3945 * allowed object is {@link Boolean }
3948 public void setConservationSelected(Boolean value)
3950 this.conservationSelected = value;
3954 * Gets the value of the pidSelected property.
3956 * @return possible object is {@link Boolean }
3959 public Boolean isPidSelected()
3965 * Sets the value of the pidSelected property.
3968 * allowed object is {@link Boolean }
3971 public void setPidSelected(Boolean value)
3973 this.pidSelected = value;
3977 * Gets the value of the bgColour property.
3979 * @return possible object is {@link String }
3982 public String getBgColour()
3988 * Sets the value of the bgColour property.
3991 * allowed object is {@link String }
3994 public void setBgColour(String value)
3996 this.bgColour = value;
4000 * Gets the value of the consThreshold property.
4002 * @return possible object is {@link Integer }
4005 public Integer getConsThreshold()
4007 return consThreshold;
4011 * Sets the value of the consThreshold property.
4014 * allowed object is {@link Integer }
4017 public void setConsThreshold(Integer value)
4019 this.consThreshold = value;
4023 * Gets the value of the pidThreshold property.
4025 * @return possible object is {@link Integer }
4028 public Integer getPidThreshold()
4030 return pidThreshold;
4034 * Sets the value of the pidThreshold property.
4037 * allowed object is {@link Integer }
4040 public void setPidThreshold(Integer value)
4042 this.pidThreshold = value;
4046 * Gets the value of the title property.
4048 * @return possible object is {@link String }
4051 public String getTitle()
4057 * Sets the value of the title property.
4060 * allowed object is {@link String }
4063 public void setTitle(String value)
4069 * Gets the value of the showFullId property.
4071 * @return possible object is {@link Boolean }
4074 public Boolean isShowFullId()
4080 * Sets the value of the showFullId property.
4083 * allowed object is {@link Boolean }
4086 public void setShowFullId(Boolean value)
4088 this.showFullId = value;
4092 * Gets the value of the rightAlignIds property.
4094 * @return possible object is {@link Boolean }
4097 public Boolean isRightAlignIds()
4099 return rightAlignIds;
4103 * Sets the value of the rightAlignIds property.
4106 * allowed object is {@link Boolean }
4109 public void setRightAlignIds(Boolean value)
4111 this.rightAlignIds = value;
4115 * Gets the value of the showText property.
4117 * @return possible object is {@link Boolean }
4120 public Boolean isShowText()
4126 * Sets the value of the showText property.
4129 * allowed object is {@link Boolean }
4132 public void setShowText(Boolean value)
4134 this.showText = value;
4138 * Gets the value of the showColourText property.
4140 * @return possible object is {@link Boolean }
4143 public Boolean isShowColourText()
4145 return showColourText;
4149 * Sets the value of the showColourText property.
4152 * allowed object is {@link Boolean }
4155 public void setShowColourText(Boolean value)
4157 this.showColourText = value;
4161 * Gets the value of the showUnconserved property.
4163 * @return possible object is {@link Boolean }
4166 public boolean isShowUnconserved()
4168 if (showUnconserved == null)
4174 return showUnconserved;
4179 * Sets the value of the showUnconserved property.
4182 * allowed object is {@link Boolean }
4185 public void setShowUnconserved(Boolean value)
4187 this.showUnconserved = value;
4191 * Gets the value of the showBoxes property.
4193 * @return possible object is {@link Boolean }
4196 public Boolean isShowBoxes()
4202 * Sets the value of the showBoxes property.
4205 * allowed object is {@link Boolean }
4208 public void setShowBoxes(Boolean value)
4210 this.showBoxes = value;
4214 * Gets the value of the wrapAlignment property.
4216 * @return possible object is {@link Boolean }
4219 public Boolean isWrapAlignment()
4221 return wrapAlignment;
4225 * Sets the value of the wrapAlignment property.
4228 * allowed object is {@link Boolean }
4231 public void setWrapAlignment(Boolean value)
4233 this.wrapAlignment = value;
4237 * Gets the value of the renderGaps property.
4239 * @return possible object is {@link Boolean }
4242 public Boolean isRenderGaps()
4248 * Sets the value of the renderGaps property.
4251 * allowed object is {@link Boolean }
4254 public void setRenderGaps(Boolean value)
4256 this.renderGaps = value;
4260 * Gets the value of the showSequenceFeatures property.
4262 * @return possible object is {@link Boolean }
4265 public Boolean isShowSequenceFeatures()
4267 return showSequenceFeatures;
4271 * Sets the value of the showSequenceFeatures property.
4274 * allowed object is {@link Boolean }
4277 public void setShowSequenceFeatures(Boolean value)
4279 this.showSequenceFeatures = value;
4283 * Gets the value of the showNPfeatureTooltip property.
4285 * @return possible object is {@link Boolean }
4288 public Boolean isShowNPfeatureTooltip()
4290 return showNPfeatureTooltip;
4294 * Sets the value of the showNPfeatureTooltip property.
4297 * allowed object is {@link Boolean }
4300 public void setShowNPfeatureTooltip(Boolean value)
4302 this.showNPfeatureTooltip = value;
4306 * Gets the value of the showDbRefTooltip property.
4308 * @return possible object is {@link Boolean }
4311 public Boolean isShowDbRefTooltip()
4313 return showDbRefTooltip;
4317 * Sets the value of the showDbRefTooltip property.
4320 * allowed object is {@link Boolean }
4323 public void setShowDbRefTooltip(Boolean value)
4325 this.showDbRefTooltip = value;
4329 * Gets the value of the followHighlight property.
4331 * @return possible object is {@link Boolean }
4334 public boolean isFollowHighlight()
4336 if (followHighlight == null)
4342 return followHighlight;
4347 * Sets the value of the followHighlight property.
4350 * allowed object is {@link Boolean }
4353 public void setFollowHighlight(Boolean value)
4355 this.followHighlight = value;
4359 * Gets the value of the followSelection property.
4361 * @return possible object is {@link Boolean }
4364 public boolean isFollowSelection()
4366 if (followSelection == null)
4372 return followSelection;
4377 * Sets the value of the followSelection property.
4380 * allowed object is {@link Boolean }
4383 public void setFollowSelection(Boolean value)
4385 this.followSelection = value;
4389 * Gets the value of the showAnnotation property.
4391 * @return possible object is {@link Boolean }
4394 public Boolean isShowAnnotation()
4396 return showAnnotation;
4400 * Sets the value of the showAnnotation property.
4403 * allowed object is {@link Boolean }
4406 public void setShowAnnotation(Boolean value)
4408 this.showAnnotation = value;
4412 * Gets the value of the centreColumnLabels property.
4414 * @return possible object is {@link Boolean }
4417 public boolean isCentreColumnLabels()
4419 if (centreColumnLabels == null)
4425 return centreColumnLabels;
4430 * Sets the value of the centreColumnLabels property.
4433 * allowed object is {@link Boolean }
4436 public void setCentreColumnLabels(Boolean value)
4438 this.centreColumnLabels = value;
4442 * Gets the value of the showGroupConservation property.
4444 * @return possible object is {@link Boolean }
4447 public boolean isShowGroupConservation()
4449 if (showGroupConservation == null)
4455 return showGroupConservation;
4460 * Sets the value of the showGroupConservation property.
4463 * allowed object is {@link Boolean }
4466 public void setShowGroupConservation(Boolean value)
4468 this.showGroupConservation = value;
4472 * Gets the value of the showGroupConsensus property.
4474 * @return possible object is {@link Boolean }
4477 public boolean isShowGroupConsensus()
4479 if (showGroupConsensus == null)
4485 return showGroupConsensus;
4490 * Sets the value of the showGroupConsensus property.
4493 * allowed object is {@link Boolean }
4496 public void setShowGroupConsensus(Boolean value)
4498 this.showGroupConsensus = value;
4502 * Gets the value of the showConsensusHistogram property.
4504 * @return possible object is {@link Boolean }
4507 public boolean isShowConsensusHistogram()
4509 if (showConsensusHistogram == null)
4515 return showConsensusHistogram;
4520 * Sets the value of the showConsensusHistogram property.
4523 * allowed object is {@link Boolean }
4526 public void setShowConsensusHistogram(Boolean value)
4528 this.showConsensusHistogram = value;
4532 * Gets the value of the showSequenceLogo property.
4534 * @return possible object is {@link Boolean }
4537 public boolean isShowSequenceLogo()
4539 if (showSequenceLogo == null)
4545 return showSequenceLogo;
4550 * Sets the value of the showSequenceLogo property.
4553 * allowed object is {@link Boolean }
4556 public void setShowSequenceLogo(Boolean value)
4558 this.showSequenceLogo = value;
4562 * Gets the value of the normaliseSequenceLogo property.
4564 * @return possible object is {@link Boolean }
4567 public boolean isNormaliseSequenceLogo()
4569 if (normaliseSequenceLogo == null)
4575 return normaliseSequenceLogo;
4580 * Sets the value of the normaliseSequenceLogo property.
4583 * allowed object is {@link Boolean }
4586 public void setNormaliseSequenceLogo(Boolean value)
4588 this.normaliseSequenceLogo = value;
4592 * Gets the value of the ignoreGapsinConsensus property.
4594 * @return possible object is {@link Boolean }
4597 public boolean isIgnoreGapsinConsensus()
4599 if (ignoreGapsinConsensus == null)
4605 return ignoreGapsinConsensus;
4610 * Sets the value of the ignoreGapsinConsensus property.
4613 * allowed object is {@link Boolean }
4616 public void setIgnoreGapsinConsensus(Boolean value)
4618 this.ignoreGapsinConsensus = value;
4622 * Gets the value of the startRes property.
4624 * @return possible object is {@link Integer }
4627 public Integer getStartRes()
4633 * Sets the value of the startRes property.
4636 * allowed object is {@link Integer }
4639 public void setStartRes(Integer value)
4641 this.startRes = value;
4645 * Gets the value of the startSeq property.
4647 * @return possible object is {@link Integer }
4650 public Integer getStartSeq()
4656 * Sets the value of the startSeq property.
4659 * allowed object is {@link Integer }
4662 public void setStartSeq(Integer value)
4664 this.startSeq = value;
4668 * Gets the value of the fontName property.
4670 * @return possible object is {@link String }
4673 public String getFontName()
4679 * Sets the value of the fontName property.
4682 * allowed object is {@link String }
4685 public void setFontName(String value)
4687 this.fontName = value;
4691 * Gets the value of the fontSize property.
4693 * @return possible object is {@link Integer }
4696 public Integer getFontSize()
4702 * Sets the value of the fontSize property.
4705 * allowed object is {@link Integer }
4708 public void setFontSize(Integer value)
4710 this.fontSize = value;
4714 * Gets the value of the fontStyle property.
4716 * @return possible object is {@link Integer }
4719 public Integer getFontStyle()
4725 * Sets the value of the fontStyle property.
4728 * allowed object is {@link Integer }
4731 public void setFontStyle(Integer value)
4733 this.fontStyle = value;
4737 * Gets the value of the scaleProteinAsCdna property.
4739 * @return possible object is {@link Boolean }
4742 public boolean isScaleProteinAsCdna()
4744 if (scaleProteinAsCdna == null)
4750 return scaleProteinAsCdna;
4755 * Sets the value of the scaleProteinAsCdna property.
4758 * allowed object is {@link Boolean }
4761 public void setScaleProteinAsCdna(Boolean value)
4763 this.scaleProteinAsCdna = value;
4767 * Gets the value of the viewName property.
4769 * @return possible object is {@link String }
4772 public String getViewName()
4778 * Sets the value of the viewName property.
4781 * allowed object is {@link String }
4784 public void setViewName(String value)
4786 this.viewName = value;
4790 * Gets the value of the sequenceSetId property.
4792 * @return possible object is {@link String }
4795 public String getSequenceSetId()
4797 return sequenceSetId;
4801 * Sets the value of the sequenceSetId property.
4804 * allowed object is {@link String }
4807 public void setSequenceSetId(String value)
4809 this.sequenceSetId = value;
4813 * Gets the value of the gatheredViews property.
4815 * @return possible object is {@link Boolean }
4818 public Boolean isGatheredViews()
4820 return gatheredViews;
4824 * Sets the value of the gatheredViews property.
4827 * allowed object is {@link Boolean }
4830 public void setGatheredViews(Boolean value)
4832 this.gatheredViews = value;
4836 * Gets the value of the textCol1 property.
4838 * @return possible object is {@link Integer }
4841 public Integer getTextCol1()
4847 * Sets the value of the textCol1 property.
4850 * allowed object is {@link Integer }
4853 public void setTextCol1(Integer value)
4855 this.textCol1 = value;
4859 * Gets the value of the textCol2 property.
4861 * @return possible object is {@link Integer }
4864 public Integer getTextCol2()
4870 * Sets the value of the textCol2 property.
4873 * allowed object is {@link Integer }
4876 public void setTextCol2(Integer value)
4878 this.textCol2 = value;
4882 * Gets the value of the textColThreshold property.
4884 * @return possible object is {@link Integer }
4887 public Integer getTextColThreshold()
4889 return textColThreshold;
4893 * Sets the value of the textColThreshold property.
4896 * allowed object is {@link Integer }
4899 public void setTextColThreshold(Integer value)
4901 this.textColThreshold = value;
4905 * Gets the value of the id property.
4907 * @return possible object is {@link String }
4910 public String getId()
4916 * Sets the value of the id property.
4919 * allowed object is {@link String }
4922 public void setId(String value)
4928 * Gets the value of the complementId property.
4930 * @return possible object is {@link String }
4933 public String getComplementId()
4935 return complementId;
4939 * Sets the value of the complementId property.
4942 * allowed object is {@link String }
4945 public void setComplementId(String value)
4947 this.complementId = value;
4951 * Gets the value of the width property.
4953 * @return possible object is {@link Integer }
4956 public Integer getWidth()
4962 * Sets the value of the width property.
4965 * allowed object is {@link Integer }
4968 public void setWidth(Integer value)
4974 * Gets the value of the height property.
4976 * @return possible object is {@link Integer }
4979 public Integer getHeight()
4985 * Sets the value of the height property.
4988 * allowed object is {@link Integer }
4991 public void setHeight(Integer value)
4993 this.height = value;
4997 * Gets the value of the xpos property.
4999 * @return possible object is {@link Integer }
5002 public Integer getXpos()
5008 * Sets the value of the xpos property.
5011 * allowed object is {@link Integer }
5014 public void setXpos(Integer value)
5020 * Gets the value of the ypos property.
5022 * @return possible object is {@link Integer }
5025 public Integer getYpos()
5031 * Sets the value of the ypos property.
5034 * allowed object is {@link Integer }
5037 public void setYpos(Integer value)
5044 * Java class for anonymous complex type.
5047 * The following schema fragment specifies the expected content contained
5048 * within this class.
5052 * <complexContent>
5053 * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
5054 * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
5055 * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
5056 * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
5058 * </complexContent>
5064 @XmlAccessorType(XmlAccessType.FIELD)
5066 public static class CalcIdParam extends WebServiceParameterSet
5069 @XmlAttribute(name = "calcId", required = true)
5070 protected String calcId;
5072 @XmlAttribute(name = "needsUpdate")
5073 protected Boolean needsUpdate;
5075 @XmlAttribute(name = "autoUpdate", required = true)
5076 protected boolean autoUpdate;
5079 * Gets the value of the calcId property.
5081 * @return possible object is {@link String }
5084 public String getCalcId()
5090 * Sets the value of the calcId property.
5093 * allowed object is {@link String }
5096 public void setCalcId(String value)
5098 this.calcId = value;
5102 * Gets the value of the needsUpdate property.
5104 * @return possible object is {@link Boolean }
5107 public boolean isNeedsUpdate()
5109 if (needsUpdate == null)
5120 * Sets the value of the needsUpdate property.
5123 * allowed object is {@link Boolean }
5126 public void setNeedsUpdate(Boolean value)
5128 this.needsUpdate = value;
5132 * Gets the value of the autoUpdate property.
5135 public boolean isAutoUpdate()
5141 * Sets the value of the autoUpdate property.
5144 public void setAutoUpdate(boolean value)
5146 this.autoUpdate = value;
5153 * Java class for anonymous complex type.
5156 * The following schema fragment specifies the expected content contained
5157 * within this class.
5161 * <complexContent>
5162 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
5163 * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
5164 * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
5166 * </complexContent>
5172 @XmlAccessorType(XmlAccessType.FIELD)
5174 public static class HiddenColumns
5177 @XmlAttribute(name = "start")
5178 protected Integer start;
5180 @XmlAttribute(name = "end")
5181 protected Integer end;
5184 * Gets the value of the start property.
5186 * @return possible object is {@link Integer }
5189 public Integer getStart()
5195 * Sets the value of the start property.
5198 * allowed object is {@link Integer }
5201 public void setStart(Integer value)
5207 * Gets the value of the end property.
5209 * @return possible object is {@link Integer }
5212 public Integer getEnd()
5218 * Sets the value of the end property.
5221 * allowed object is {@link Integer }
5224 public void setEnd(Integer value)