From 85ed72a5a52344d202f671eb6892dc74656c29ea Mon Sep 17 00:00:00 2001 From: gmungoc Date: Tue, 18 Sep 2018 16:01:52 +0100 Subject: [PATCH] JAL-3063 JAXB binding classes generated by xjc from jalview.xsd --- src/jalview/xml/binding/jalview/AlcodonFrame.java | 326 ++ src/jalview/xml/binding/jalview/Annotation.java | 857 ++++ .../binding/jalview/AnnotationColourScheme.java | 254 + .../xml/binding/jalview/AnnotationElement.java | 203 + src/jalview/xml/binding/jalview/Feature.java | 363 ++ .../xml/binding/jalview/FeatureMatcher.java | 160 + .../xml/binding/jalview/FeatureMatcherSet.java | 192 + src/jalview/xml/binding/jalview/FilterBy.java | 61 + src/jalview/xml/binding/jalview/JalviewModel.java | 5090 ++++++++++++++++++++ .../xml/binding/jalview/JalviewModelType.java | 5090 ++++++++++++++++++++ .../xml/binding/jalview/JalviewUserColours.java | 612 +++ src/jalview/xml/binding/jalview/MapListType.java | 315 ++ src/jalview/xml/binding/jalview/Mapping.java | 113 + src/jalview/xml/binding/jalview/NoValueColour.java | 61 + src/jalview/xml/binding/jalview/ObjectFactory.java | 404 ++ src/jalview/xml/binding/jalview/Pdbentry.java | 247 + src/jalview/xml/binding/jalview/Sequence.java | 257 + src/jalview/xml/binding/jalview/SequenceSet.java | 318 ++ src/jalview/xml/binding/jalview/SequenceType.java | 153 + src/jalview/xml/binding/jalview/ThresholdType.java | 47 + src/jalview/xml/binding/jalview/VAMSAS.java | 109 + .../binding/jalview/WebServiceParameterSet.java | 194 + src/jalview/xml/binding/jalview/package-info.java | 9 + 23 files changed, 15435 insertions(+) create mode 100644 src/jalview/xml/binding/jalview/AlcodonFrame.java create mode 100644 src/jalview/xml/binding/jalview/Annotation.java create mode 100644 src/jalview/xml/binding/jalview/AnnotationColourScheme.java create mode 100644 src/jalview/xml/binding/jalview/AnnotationElement.java create mode 100644 src/jalview/xml/binding/jalview/Feature.java create mode 100644 src/jalview/xml/binding/jalview/FeatureMatcher.java create mode 100644 src/jalview/xml/binding/jalview/FeatureMatcherSet.java create mode 100644 src/jalview/xml/binding/jalview/FilterBy.java create mode 100644 src/jalview/xml/binding/jalview/JalviewModel.java create mode 100644 src/jalview/xml/binding/jalview/JalviewModelType.java create mode 100644 src/jalview/xml/binding/jalview/JalviewUserColours.java create mode 100644 src/jalview/xml/binding/jalview/MapListType.java create mode 100644 src/jalview/xml/binding/jalview/Mapping.java create mode 100644 src/jalview/xml/binding/jalview/NoValueColour.java create mode 100644 src/jalview/xml/binding/jalview/ObjectFactory.java create mode 100644 src/jalview/xml/binding/jalview/Pdbentry.java create mode 100644 src/jalview/xml/binding/jalview/Sequence.java create mode 100644 src/jalview/xml/binding/jalview/SequenceSet.java create mode 100644 src/jalview/xml/binding/jalview/SequenceType.java create mode 100644 src/jalview/xml/binding/jalview/ThresholdType.java create mode 100644 src/jalview/xml/binding/jalview/VAMSAS.java create mode 100644 src/jalview/xml/binding/jalview/WebServiceParameterSet.java create mode 100644 src/jalview/xml/binding/jalview/package-info.java diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java new file mode 100644 index 0000000..f4e7d84 --- /dev/null +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -0,0 +1,326 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.math.BigInteger; +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ *                 </sequence>
+ *                 <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = { + "alcodon", + "alcodMap" +}) +@XmlRootElement(name = "AlcodonFrame") +public class AlcodonFrame { + + protected List alcodon; + protected List alcodMap; + + /** + * Gets the value of the alcodon property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the alcodon property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAlcodon().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame.Alcodon } + * + * + */ + public List getAlcodon() { + if (alcodon == null) { + alcodon = new ArrayList(); + } + return this.alcodon; + } + + /** + * Gets the value of the alcodMap property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the alcodMap property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAlcodMap().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame.AlcodMap } + * + * + */ + public List getAlcodMap() { + if (alcodMap == null) { + alcodMap = new ArrayList(); + } + return this.alcodMap; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+     *       </sequence>
+     *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "mapping" + }) + public static class AlcodMap { + + @XmlElement(name = "Mapping", required = true) + protected Mapping mapping; + @XmlAttribute(name = "dnasq", required = true) + protected String dnasq; + + /** + * + * a Mapping entry and an associated protein sequence + * + * + * @return + * possible object is + * {@link Mapping } + * + */ + public Mapping getMapping() { + return mapping; + } + + /** + * Sets the value of the mapping property. + * + * @param value + * allowed object is + * {@link Mapping } + * + */ + public void setMapping(Mapping value) { + this.mapping = value; + } + + /** + * Gets the value of the dnasq property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDnasq() { + return dnasq; + } + + /** + * Sets the value of the dnasq property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDnasq(String value) { + this.dnasq = value; + } + + } + + + /** + * + * specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment. + * Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide). + * + * + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Alcodon { + + @XmlAttribute(name = "pos1") + protected BigInteger pos1; + @XmlAttribute(name = "pos2") + protected BigInteger pos2; + @XmlAttribute(name = "pos3") + protected BigInteger pos3; + + /** + * Gets the value of the pos1 property. + * + * @return + * possible object is + * {@link BigInteger } + * + */ + public BigInteger getPos1() { + return pos1; + } + + /** + * Sets the value of the pos1 property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setPos1(BigInteger value) { + this.pos1 = value; + } + + /** + * Gets the value of the pos2 property. + * + * @return + * possible object is + * {@link BigInteger } + * + */ + public BigInteger getPos2() { + return pos2; + } + + /** + * Sets the value of the pos2 property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setPos2(BigInteger value) { + this.pos2 = value; + } + + /** + * Gets the value of the pos3 property. + * + * @return + * possible object is + * {@link BigInteger } + * + */ + public BigInteger getPos3() { + return pos3; + } + + /** + * Sets the value of the pos3 property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setPos3(BigInteger value) { + this.pos3 = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java new file mode 100644 index 0000000..22f6674 --- /dev/null +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -0,0 +1,857 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="thresholdLine" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
+ *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       <attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *       <attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = { + "annotationElement", + "label", + "description", + "thresholdLine", + "property" +}) +@XmlRootElement(name = "Annotation") +public class Annotation { + + protected List annotationElement; + @XmlElement(required = true) + protected String label; + protected String description; + protected Annotation.ThresholdLine thresholdLine; + protected List property; + @XmlAttribute(name = "graph", required = true) + protected boolean graph; + @XmlAttribute(name = "graphType") + protected Integer graphType; + @XmlAttribute(name = "sequenceRef") + protected String sequenceRef; + @XmlAttribute(name = "groupRef") + protected String groupRef; + @XmlAttribute(name = "graphColour") + protected Integer graphColour; + @XmlAttribute(name = "graphGroup") + protected Integer graphGroup; + @XmlAttribute(name = "graphHeight") + protected Integer graphHeight; + @XmlAttribute(name = "id") + protected String id; + @XmlAttribute(name = "scoreOnly") + protected Boolean scoreOnly; + @XmlAttribute(name = "score") + protected Double score; + @XmlAttribute(name = "visible") + protected Boolean visible; + @XmlAttribute(name = "centreColLabels") + protected Boolean centreColLabels; + @XmlAttribute(name = "scaleColLabels") + protected Boolean scaleColLabels; + @XmlAttribute(name = "showAllColLabels") + protected Boolean showAllColLabels; + @XmlAttribute(name = "autoCalculated") + protected Boolean autoCalculated; + @XmlAttribute(name = "belowAlignment") + protected Boolean belowAlignment; + @XmlAttribute(name = "calcId") + protected String calcId; + + /** + * Gets the value of the annotationElement property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the annotationElement property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAnnotationElement().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link AnnotationElement } + * + * + */ + public List getAnnotationElement() { + if (annotationElement == null) { + annotationElement = new ArrayList(); + } + return this.annotationElement; + } + + /** + * Gets the value of the label property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getLabel() { + return label; + } + + /** + * Sets the value of the label property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setLabel(String value) { + this.label = value; + } + + /** + * Gets the value of the description property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDescription() { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDescription(String value) { + this.description = value; + } + + /** + * Gets the value of the thresholdLine property. + * + * @return + * possible object is + * {@link Annotation.ThresholdLine } + * + */ + public Annotation.ThresholdLine getThresholdLine() { + return thresholdLine; + } + + /** + * Sets the value of the thresholdLine property. + * + * @param value + * allowed object is + * {@link Annotation.ThresholdLine } + * + */ + public void setThresholdLine(Annotation.ThresholdLine value) { + this.thresholdLine = value; + } + + /** + * Gets the value of the property property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the property property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getProperty().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Annotation.Property } + * + * + */ + public List getProperty() { + if (property == null) { + property = new ArrayList(); + } + return this.property; + } + + /** + * Gets the value of the graph property. + * + */ + public boolean isGraph() { + return graph; + } + + /** + * Sets the value of the graph property. + * + */ + public void setGraph(boolean value) { + this.graph = value; + } + + /** + * Gets the value of the graphType property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getGraphType() { + return graphType; + } + + /** + * Sets the value of the graphType property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGraphType(Integer value) { + this.graphType = value; + } + + /** + * Gets the value of the sequenceRef property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSequenceRef() { + return sequenceRef; + } + + /** + * Sets the value of the sequenceRef property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSequenceRef(String value) { + this.sequenceRef = value; + } + + /** + * Gets the value of the groupRef property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getGroupRef() { + return groupRef; + } + + /** + * Sets the value of the groupRef property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setGroupRef(String value) { + this.groupRef = value; + } + + /** + * Gets the value of the graphColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getGraphColour() { + return graphColour; + } + + /** + * Sets the value of the graphColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGraphColour(Integer value) { + this.graphColour = value; + } + + /** + * Gets the value of the graphGroup property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getGraphGroup() { + return graphGroup; + } + + /** + * Sets the value of the graphGroup property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGraphGroup(Integer value) { + this.graphGroup = value; + } + + /** + * Gets the value of the graphHeight property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getGraphHeight() { + return graphHeight; + } + + /** + * Sets the value of the graphHeight property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGraphHeight(Integer value) { + this.graphHeight = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the scoreOnly property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isScoreOnly() { + if (scoreOnly == null) { + return false; + } else { + return scoreOnly; + } + } + + /** + * Sets the value of the scoreOnly property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setScoreOnly(Boolean value) { + this.scoreOnly = value; + } + + /** + * Gets the value of the score property. + * + * @return + * possible object is + * {@link Double } + * + */ + public Double getScore() { + return score; + } + + /** + * Sets the value of the score property. + * + * @param value + * allowed object is + * {@link Double } + * + */ + public void setScore(Double value) { + this.score = value; + } + + /** + * Gets the value of the visible property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isVisible() { + return visible; + } + + /** + * Sets the value of the visible property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setVisible(Boolean value) { + this.visible = value; + } + + /** + * Gets the value of the centreColLabels property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isCentreColLabels() { + return centreColLabels; + } + + /** + * Sets the value of the centreColLabels property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setCentreColLabels(Boolean value) { + this.centreColLabels = value; + } + + /** + * Gets the value of the scaleColLabels property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isScaleColLabels() { + return scaleColLabels; + } + + /** + * Sets the value of the scaleColLabels property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setScaleColLabels(Boolean value) { + this.scaleColLabels = value; + } + + /** + * Gets the value of the showAllColLabels property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowAllColLabels() { + return showAllColLabels; + } + + /** + * Sets the value of the showAllColLabels property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowAllColLabels(Boolean value) { + this.showAllColLabels = value; + } + + /** + * Gets the value of the autoCalculated property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isAutoCalculated() { + if (autoCalculated == null) { + return false; + } else { + return autoCalculated; + } + } + + /** + * Sets the value of the autoCalculated property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setAutoCalculated(Boolean value) { + this.autoCalculated = value; + } + + /** + * Gets the value of the belowAlignment property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isBelowAlignment() { + if (belowAlignment == null) { + return true; + } else { + return belowAlignment; + } + } + + /** + * Sets the value of the belowAlignment property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setBelowAlignment(Boolean value) { + this.belowAlignment = value; + } + + /** + * Gets the value of the calcId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getCalcId() { + return calcId; + } + + /** + * Sets the value of the calcId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setCalcId(String value) { + this.calcId = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Property { + + @XmlAttribute(name = "name") + protected String name; + @XmlAttribute(name = "value") + protected String value; + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class ThresholdLine { + + @XmlAttribute(name = "label") + protected String label; + @XmlAttribute(name = "value") + protected Float value; + @XmlAttribute(name = "colour") + protected Integer colour; + + /** + * Gets the value of the label property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getLabel() { + return label; + } + + /** + * Sets the value of the label property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setLabel(String value) { + this.label = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setValue(Float value) { + this.value = value; + } + + /** + * Gets the value of the colour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setColour(Integer value) { + this.colour = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java new file mode 100644 index 0000000..bcf3302 --- /dev/null +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@ -0,0 +1,254 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for AnnotationColourScheme complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="AnnotationColourScheme">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *       <attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       <attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org") +public class AnnotationColourScheme { + + @XmlAttribute(name = "aboveThreshold") + protected Integer aboveThreshold; + @XmlAttribute(name = "annotation") + protected String annotation; + @XmlAttribute(name = "minColour") + protected Integer minColour; + @XmlAttribute(name = "maxColour") + protected Integer maxColour; + @XmlAttribute(name = "colourScheme") + protected String colourScheme; + @XmlAttribute(name = "threshold") + protected Float threshold; + @XmlAttribute(name = "perSequence") + protected Boolean perSequence; + @XmlAttribute(name = "predefinedColours") + protected Boolean predefinedColours; + + /** + * Gets the value of the aboveThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getAboveThreshold() { + return aboveThreshold; + } + + /** + * Sets the value of the aboveThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setAboveThreshold(Integer value) { + this.aboveThreshold = value; + } + + /** + * Gets the value of the annotation property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getAnnotation() { + return annotation; + } + + /** + * Sets the value of the annotation property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setAnnotation(String value) { + this.annotation = value; + } + + /** + * Gets the value of the minColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getMinColour() { + return minColour; + } + + /** + * Sets the value of the minColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setMinColour(Integer value) { + this.minColour = value; + } + + /** + * Gets the value of the maxColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getMaxColour() { + return maxColour; + } + + /** + * Sets the value of the maxColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setMaxColour(Integer value) { + this.maxColour = value; + } + + /** + * Gets the value of the colourScheme property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getColourScheme() { + return colourScheme; + } + + /** + * Sets the value of the colourScheme property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setColourScheme(String value) { + this.colourScheme = value; + } + + /** + * Gets the value of the threshold property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getThreshold() { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setThreshold(Float value) { + this.threshold = value; + } + + /** + * Gets the value of the perSequence property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isPerSequence() { + return perSequence; + } + + /** + * Sets the value of the perSequence property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setPerSequence(Boolean value) { + this.perSequence = value; + } + + /** + * Gets the value of the predefinedColours property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isPredefinedColours() { + return predefinedColours; + } + + /** + * Sets the value of the predefinedColours property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setPredefinedColours(Boolean value) { + this.predefinedColours = value; + } + +} diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java new file mode 100644 index 0000000..dcee889 --- /dev/null +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@ -0,0 +1,203 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="secondaryStructure" minOccurs="0">
+ *           <simpleType>
+ *             <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               <length value="1"/>
+ *             </restriction>
+ *           </simpleType>
+ *         </element>
+ *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = { + "displayCharacter", + "description", + "secondaryStructure", + "value" +}) +@XmlRootElement(name = "annotationElement") +public class AnnotationElement { + + protected String displayCharacter; + protected String description; + protected String secondaryStructure; + protected Float value; + @XmlAttribute(name = "position", required = true) + protected int position; + @XmlAttribute(name = "colour") + protected Integer colour; + + /** + * Gets the value of the displayCharacter property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDisplayCharacter() { + return displayCharacter; + } + + /** + * Sets the value of the displayCharacter property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDisplayCharacter(String value) { + this.displayCharacter = value; + } + + /** + * Gets the value of the description property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDescription() { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDescription(String value) { + this.description = value; + } + + /** + * Gets the value of the secondaryStructure property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSecondaryStructure() { + return secondaryStructure; + } + + /** + * Sets the value of the secondaryStructure property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSecondaryStructure(String value) { + this.secondaryStructure = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setValue(Float value) { + this.value = value; + } + + /** + * Gets the value of the position property. + * + */ + public int getPosition() { + return position; + } + + /** + * Sets the value of the position property. + * + */ + public void setPosition(int value) { + this.position = value; + } + + /** + * Gets the value of the colour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setColour(Integer value) { + this.colour = value; + } + +} diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java new file mode 100644 index 0000000..1040636 --- /dev/null +++ b/src/jalview/xml/binding/jalview/Feature.java @@ -0,0 +1,363 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for feature complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="feature">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="otherData" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = { + "otherData" +}) +public class Feature { + + protected List otherData; + @XmlAttribute(name = "begin", required = true) + protected int begin; + @XmlAttribute(name = "end", required = true) + protected int end; + @XmlAttribute(name = "type", required = true) + protected String type; + @XmlAttribute(name = "description") + protected String description; + @XmlAttribute(name = "status") + protected String status; + @XmlAttribute(name = "featureGroup") + protected String featureGroup; + @XmlAttribute(name = "score") + protected Float score; + + /** + * Gets the value of the otherData property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the otherData property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getOtherData().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Feature.OtherData } + * + * + */ + public List getOtherData() { + if (otherData == null) { + otherData = new ArrayList(); + } + return this.otherData; + } + + /** + * Gets the value of the begin property. + * + */ + public int getBegin() { + return begin; + } + + /** + * Sets the value of the begin property. + * + */ + public void setBegin(int value) { + this.begin = value; + } + + /** + * Gets the value of the end property. + * + */ + public int getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + */ + public void setEnd(int value) { + this.end = value; + } + + /** + * Gets the value of the type property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getType() { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setType(String value) { + this.type = value; + } + + /** + * Gets the value of the description property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDescription() { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDescription(String value) { + this.description = value; + } + + /** + * Gets the value of the status property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getStatus() { + return status; + } + + /** + * Sets the value of the status property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setStatus(String value) { + this.status = value; + } + + /** + * Gets the value of the featureGroup property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFeatureGroup() { + return featureGroup; + } + + /** + * Sets the value of the featureGroup property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFeatureGroup(String value) { + this.featureGroup = value; + } + + /** + * Gets the value of the score property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getScore() { + return score; + } + + /** + * Sets the value of the score property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setScore(Float value) { + this.score = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class OtherData { + + @XmlAttribute(name = "key", required = true) + protected String key; + @XmlAttribute(name = "key2") + protected String key2; + @XmlAttribute(name = "value", required = true) + protected String value; + + /** + * Gets the value of the key property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getKey() { + return key; + } + + /** + * Sets the value of the key property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setKey(String value) { + this.key = value; + } + + /** + * Gets the value of the key2 property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getKey2() { + return key2; + } + + /** + * Sets the value of the key2 property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setKey2(String value) { + this.key2 = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java new file mode 100644 index 0000000..3f3d812 --- /dev/null +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@ -0,0 +1,160 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for FeatureMatcher complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="FeatureMatcher">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *         <element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       </sequence>
+ *       <attribute name="by" type="{www.jalview.org/colours}FilterBy" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = { + "attributeName", + "condition", + "value" +}) +public class FeatureMatcher { + + @XmlElement(namespace = "") + protected List attributeName; + @XmlElement(namespace = "", required = true) + protected String condition; + @XmlElement(namespace = "", required = true) + protected String value; + @XmlAttribute(name = "by") + protected FilterBy by; + + /** + * Gets the value of the attributeName property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the attributeName property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAttributeName().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getAttributeName() { + if (attributeName == null) { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * Gets the value of the condition property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getCondition() { + return condition; + } + + /** + * Sets the value of the condition property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setCondition(String value) { + this.condition = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + /** + * Gets the value of the by property. + * + * @return + * possible object is + * {@link FilterBy } + * + */ + public FilterBy getBy() { + return by; + } + + /** + * Sets the value of the by property. + * + * @param value + * allowed object is + * {@link FilterBy } + * + */ + public void setBy(FilterBy value) { + this.by = value; + } + +} diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java new file mode 100644 index 0000000..f33d379 --- /dev/null +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@ -0,0 +1,192 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlType; + + +/** + * A feature match condition, which may be simple or compound + * + *

Java class for FeatureMatcherSet complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="FeatureMatcherSet">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <choice>
+ *         <element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
+ *         <element name="compoundMatcher">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ *                 </sequence>
+ *                 <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </choice>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = { + "matchCondition", + "compoundMatcher" +}) +public class FeatureMatcherSet { + + @XmlElement(namespace = "") + protected FeatureMatcher matchCondition; + @XmlElement(namespace = "") + protected FeatureMatcherSet.CompoundMatcher compoundMatcher; + + /** + * Gets the value of the matchCondition property. + * + * @return + * possible object is + * {@link FeatureMatcher } + * + */ + public FeatureMatcher getMatchCondition() { + return matchCondition; + } + + /** + * Sets the value of the matchCondition property. + * + * @param value + * allowed object is + * {@link FeatureMatcher } + * + */ + public void setMatchCondition(FeatureMatcher value) { + this.matchCondition = value; + } + + /** + * Gets the value of the compoundMatcher property. + * + * @return + * possible object is + * {@link FeatureMatcherSet.CompoundMatcher } + * + */ + public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() { + return compoundMatcher; + } + + /** + * Sets the value of the compoundMatcher property. + * + * @param value + * allowed object is + * {@link FeatureMatcherSet.CompoundMatcher } + * + */ + public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) { + this.compoundMatcher = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+     *       </sequence>
+     *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "matcherSet" + }) + public static class CompoundMatcher { + + @XmlElement(namespace = "", required = true) + protected List matcherSet; + @XmlAttribute(name = "and", required = true) + protected boolean and; + + /** + * Gets the value of the matcherSet property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the matcherSet property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getMatcherSet().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link FeatureMatcherSet } + * + * + */ + public List getMatcherSet() { + if (matcherSet == null) { + matcherSet = new ArrayList(); + } + return this.matcherSet; + } + + /** + * Gets the value of the and property. + * + */ + public boolean isAnd() { + return and; + } + + /** + * Sets the value of the and property. + * + */ + public void setAnd(boolean value) { + this.and = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java new file mode 100644 index 0000000..7877175 --- /dev/null +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@ -0,0 +1,61 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.annotation.XmlEnum; +import javax.xml.bind.annotation.XmlEnumValue; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for FilterBy. + * + *

The following schema fragment specifies the expected content contained within this class. + *

+ * 

+ * <simpleType name="FilterBy">
+ *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     <enumeration value="byLabel"/>
+ *     <enumeration value="byScore"/>
+ *     <enumeration value="byAttribute"/>
+ *   </restriction>
+ * </simpleType>
+ *
+ * + */ +@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours") +@XmlEnum +public enum FilterBy { + + @XmlEnumValue("byLabel") + BY_LABEL("byLabel"), + @XmlEnumValue("byScore") + BY_SCORE("byScore"), + @XmlEnumValue("byAttribute") + BY_ATTRIBUTE("byAttribute"); + private final String value; + + FilterBy(String v) { + value = v; + } + + public String value() { + return value; + } + + public static FilterBy fromValue(String v) { + for (FilterBy c: FilterBy.values()) { + if (c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } + +} diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java new file mode 100644 index 0000000..9cc7d80 --- /dev/null +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -0,0 +1,5090 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlID; +import javax.xml.bind.annotation.XmlSchemaType; +import javax.xml.bind.annotation.XmlType; +import javax.xml.bind.annotation.XmlValue; +import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; +import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +import javax.xml.datatype.XMLGregorianCalendar; + + +/** + *

Java class for JalviewModel complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="JalviewModel">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ *         <sequence>
+ *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org}pdbentry">
+ *                             <sequence>
+ *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ *                                 <complexType>
+ *                                   <simpleContent>
+ *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </extension>
+ *                                   </simpleContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="secondaryStructure" maxOccurs="unbounded">
+ *                                 <complexType>
+ *                                   <complexContent>
+ *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </restriction>
+ *                                   </complexContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                             <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                   </sequence>
+ *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ *                   </sequence>
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence minOccurs="0">
+ *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="FeatureSettings" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ *                             </sequence>
+ *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *         </sequence>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = { + "creationDate", + "version", + "vamsasModel", + "jSeq", + "jGroup", + "viewport", + "userColours", + "tree", + "featureSettings" +}) +public class JalviewModel { + + @XmlElement(required = true) + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar creationDate; + @XmlElement(required = true) + protected String version; + @XmlElement(required = true) + protected VAMSAS vamsasModel; + @XmlElement(name = "JSeq") + protected List jSeq; + @XmlElement(name = "JGroup") + protected List jGroup; + @XmlElement(name = "Viewport") + protected List viewport; + @XmlElement(name = "UserColours") + protected List userColours; + protected List tree; + @XmlElement(name = "FeatureSettings") + protected JalviewModel.FeatureSettings featureSettings; + + /** + * Gets the value of the creationDate property. + * + * @return + * possible object is + * {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getCreationDate() { + return creationDate; + } + + /** + * Sets the value of the creationDate property. + * + * @param value + * allowed object is + * {@link XMLGregorianCalendar } + * + */ + public void setCreationDate(XMLGregorianCalendar value) { + this.creationDate = value; + } + + /** + * Gets the value of the version property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getVersion() { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setVersion(String value) { + this.version = value; + } + + /** + * Gets the value of the vamsasModel property. + * + * @return + * possible object is + * {@link VAMSAS } + * + */ + public VAMSAS getVamsasModel() { + return vamsasModel; + } + + /** + * Sets the value of the vamsasModel property. + * + * @param value + * allowed object is + * {@link VAMSAS } + * + */ + public void setVamsasModel(VAMSAS value) { + this.vamsasModel = value; + } + + /** + * Gets the value of the jSeq property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the jSeq property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getJSeq().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq } + * + * + */ + public List getJSeq() { + if (jSeq == null) { + jSeq = new ArrayList(); + } + return this.jSeq; + } + + /** + * Gets the value of the jGroup property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the jGroup property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getJGroup().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JGroup } + * + * + */ + public List getJGroup() { + if (jGroup == null) { + jGroup = new ArrayList(); + } + return this.jGroup; + } + + /** + * Gets the value of the viewport property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the viewport property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getViewport().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport } + * + * + */ + public List getViewport() { + if (viewport == null) { + viewport = new ArrayList(); + } + return this.viewport; + } + + /** + * Gets the value of the userColours property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the userColours property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getUserColours().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.UserColours } + * + * + */ + public List getUserColours() { + if (userColours == null) { + userColours = new ArrayList(); + } + return this.userColours; + } + + /** + * Gets the value of the tree property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the tree property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getTree().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Tree } + * + * + */ + public List getTree() { + if (tree == null) { + tree = new ArrayList(); + } + return this.tree; + } + + /** + * Gets the value of the featureSettings property. + * + * @return + * possible object is + * {@link JalviewModel.FeatureSettings } + * + */ + public JalviewModel.FeatureSettings getFeatureSettings() { + return featureSettings; + } + + /** + * Sets the value of the featureSettings property. + * + * @param value + * allowed object is + * {@link JalviewModel.FeatureSettings } + * + */ + public void setFeatureSettings(JalviewModel.FeatureSettings value) { + this.featureSettings = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *                 </sequence>
+     *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="group" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "setting", + "group" + }) + public static class FeatureSettings { + + @XmlElement(namespace = "www.jalview.org") + protected List setting; + @XmlElement(namespace = "www.jalview.org") + protected List group; + + /** + * Gets the value of the setting property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the setting property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getSetting().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.FeatureSettings.Setting } + * + * + */ + public List getSetting() { + if (setting == null) { + setting = new ArrayList(); + } + return this.setting; + } + + /** + * Gets the value of the group property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the group property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getGroup().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.FeatureSettings.Group } + * + * + */ + public List getGroup() { + if (group == null) { + group = new ArrayList(); + } + return this.group; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Group { + + @XmlAttribute(name = "name", required = true) + protected String name; + @XmlAttribute(name = "display", required = true) + protected boolean display; + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) { + this.display = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+         *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+         *       </sequence>
+         *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+         *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "attributeName", + "matcherSet" + }) + public static class Setting { + + @XmlElement(namespace = "www.jalview.org") + protected List attributeName; + @XmlElement(namespace = "www.jalview.org") + protected FeatureMatcherSet matcherSet; + @XmlAttribute(name = "type", required = true) + protected String type; + @XmlAttribute(name = "colour", required = true) + protected int colour; + @XmlAttribute(name = "display", required = true) + protected boolean display; + @XmlAttribute(name = "order") + protected Float order; + @XmlAttribute(name = "mincolour") + protected Integer mincolour; + @XmlAttribute(name = "noValueColour") + protected NoValueColour noValueColour; + @XmlAttribute(name = "threshold") + protected Float threshold; + @XmlAttribute(name = "threshstate") + protected Integer threshstate; + @XmlAttribute(name = "max") + protected Float max; + @XmlAttribute(name = "min") + protected Float min; + @XmlAttribute(name = "colourByLabel") + protected Boolean colourByLabel; + @XmlAttribute(name = "autoScale") + protected Boolean autoScale; + + /** + * Gets the value of the attributeName property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the attributeName property. + * + *

+ * For example, to add a new item, do as follows: + * 

+             *    getAttributeName().add(newItem);
+             *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getAttributeName() { + if (attributeName == null) { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * Gets the value of the matcherSet property. + * + * @return + * possible object is + * {@link FeatureMatcherSet } + * + */ + public FeatureMatcherSet getMatcherSet() { + return matcherSet; + } + + /** + * Sets the value of the matcherSet property. + * + * @param value + * allowed object is + * {@link FeatureMatcherSet } + * + */ + public void setMatcherSet(FeatureMatcherSet value) { + this.matcherSet = value; + } + + /** + * Gets the value of the type property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getType() { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setType(String value) { + this.type = value; + } + + /** + * Gets the value of the colour property. + * + */ + public int getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + */ + public void setColour(int value) { + this.colour = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) { + this.display = value; + } + + /** + * Gets the value of the order property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getOrder() { + return order; + } + + /** + * Sets the value of the order property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setOrder(Float value) { + this.order = value; + } + + /** + * Gets the value of the mincolour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getMincolour() { + return mincolour; + } + + /** + * Sets the value of the mincolour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setMincolour(Integer value) { + this.mincolour = value; + } + + /** + * Gets the value of the noValueColour property. + * + * @return + * possible object is + * {@link NoValueColour } + * + */ + public NoValueColour getNoValueColour() { + if (noValueColour == null) { + return NoValueColour.MIN; + } else { + return noValueColour; + } + } + + /** + * Sets the value of the noValueColour property. + * + * @param value + * allowed object is + * {@link NoValueColour } + * + */ + public void setNoValueColour(NoValueColour value) { + this.noValueColour = value; + } + + /** + * Gets the value of the threshold property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getThreshold() { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setThreshold(Float value) { + this.threshold = value; + } + + /** + * Gets the value of the threshstate property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getThreshstate() { + return threshstate; + } + + /** + * Sets the value of the threshstate property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setThreshstate(Integer value) { + this.threshstate = value; + } + + /** + * Gets the value of the max property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getMax() { + return max; + } + + /** + * Sets the value of the max property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setMax(Float value) { + this.max = value; + } + + /** + * Gets the value of the min property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getMin() { + return min; + } + + /** + * Sets the value of the min property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setMin(Float value) { + this.min = value; + } + + /** + * Gets the value of the colourByLabel property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isColourByLabel() { + return colourByLabel; + } + + /** + * Sets the value of the colourByLabel property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourByLabel(Boolean value) { + this.colourByLabel = value; + } + + /** + * Gets the value of the autoScale property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isAutoScale() { + return autoScale; + } + + /** + * Sets the value of the autoScale property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setAutoScale(Boolean value) { + this.autoScale = value; + } + + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "seq", + "annotationColours" + }) + public static class JGroup { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List seq; + @XmlElement(namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + @XmlAttribute(name = "start") + protected Integer start; + @XmlAttribute(name = "end") + protected Integer end; + @XmlAttribute(name = "name") + protected String name; + @XmlAttribute(name = "colour") + protected String colour; + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + @XmlAttribute(name = "outlineColour") + protected Integer outlineColour; + @XmlAttribute(name = "displayBoxes") + protected Boolean displayBoxes; + @XmlAttribute(name = "displayText") + protected Boolean displayText; + @XmlAttribute(name = "colourText") + protected Boolean colourText; + @XmlAttribute(name = "textCol1") + protected Integer textCol1; + @XmlAttribute(name = "textCol2") + protected Integer textCol2; + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + @XmlAttribute(name = "id") + protected String id; + + /** + * Gets the value of the seq property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the seq property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getSeq().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getSeq() { + if (seq == null) { + seq = new ArrayList(); + } + return this.seq; + } + + /** + * Gets the value of the annotationColours property. + * + * @return + * possible object is + * {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() { + return annotationColours; + } + + /** + * Sets the value of the annotationColours property. + * + * @param value + * allowed object is + * {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) { + this.annotationColours = value; + } + + /** + * Gets the value of the start property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStart(Integer value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setEnd(Integer value) { + this.end = value; + } + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the colour property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setColour(String value) { + this.colour = value; + } + + /** + * Gets the value of the consThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getConsThreshold() { + return consThreshold; + } + + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setConsThreshold(Integer value) { + this.consThreshold = value; + } + + /** + * Gets the value of the pidThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getPidThreshold() { + return pidThreshold; + } + + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setPidThreshold(Integer value) { + this.pidThreshold = value; + } + + /** + * Gets the value of the outlineColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getOutlineColour() { + return outlineColour; + } + + /** + * Sets the value of the outlineColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setOutlineColour(Integer value) { + this.outlineColour = value; + } + + /** + * Gets the value of the displayBoxes property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isDisplayBoxes() { + return displayBoxes; + } + + /** + * Sets the value of the displayBoxes property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setDisplayBoxes(Boolean value) { + this.displayBoxes = value; + } + + /** + * Gets the value of the displayText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isDisplayText() { + return displayText; + } + + /** + * Sets the value of the displayText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setDisplayText(Boolean value) { + this.displayText = value; + } + + /** + * Gets the value of the colourText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isColourText() { + return colourText; + } + + /** + * Sets the value of the colourText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourText(Boolean value) { + this.colourText = value; + } + + /** + * Gets the value of the textCol1 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol1() { + return textCol1; + } + + /** + * Sets the value of the textCol1 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol1(Integer value) { + this.textCol1 = value; + } + + /** + * Gets the value of the textCol2 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol2() { + return textCol2; + } + + /** + * Sets the value of the textCol2 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol2(Integer value) { + this.textCol2 = value; + } + + /** + * Gets the value of the textColThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextColThreshold() { + return textColThreshold; + } + + /** + * Sets the value of the textColThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextColThreshold(Integer value) { + this.textColThreshold = value; + } + + /** + * Gets the value of the showUnconserved property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowUnconserved() { + return showUnconserved; + } + + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) { + this.showUnconserved = value; + } + + /** + * Gets the value of the ignoreGapsinConsensus property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() { + if (ignoreGapsinConsensus == null) { + return true; + } else { + return ignoreGapsinConsensus; + } + } + + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) { + this.ignoreGapsinConsensus = value; + } + + /** + * Gets the value of the showConsensusHistogram property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowConsensusHistogram() { + if (showConsensusHistogram == null) { + return true; + } else { + return showConsensusHistogram; + } + } + + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) { + this.showConsensusHistogram = value; + } + + /** + * Gets the value of the showSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowSequenceLogo() { + if (showSequenceLogo == null) { + return false; + } else { + return showSequenceLogo; + } + } + + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) { + this.showSequenceLogo = value; + } + + /** + * Gets the value of the normaliseSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() { + if (normaliseSequenceLogo == null) { + return false; + } else { + return normaliseSequenceLogo; + } + } + + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) { + this.normaliseSequenceLogo = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org}pdbentry">
+     *                 <sequence>
+     *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *                     <complexType>
+     *                       <simpleContent>
+     *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *                           <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </extension>
+     *                       </simpleContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="secondaryStructure" maxOccurs="unbounded">
+     *                     <complexType>
+     *                       <complexContent>
+     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </restriction>
+     *                       </complexContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "features", + "pdbids", + "hiddenSequences", + "rnaViewer" + }) + public static class JSeq { + + @XmlElement(namespace = "www.jalview.org") + protected List features; + @XmlElement(namespace = "www.jalview.org") + protected List pdbids; + @XmlElement(namespace = "www.jalview.org", type = Integer.class) + protected List hiddenSequences; + @XmlElement(namespace = "www.jalview.org") + protected List rnaViewer; + @XmlAttribute(name = "colour") + protected Integer colour; + @XmlAttribute(name = "start", required = true) + protected int start; + @XmlAttribute(name = "end", required = true) + protected int end; + @XmlAttribute(name = "id", required = true) + protected String id; + @XmlAttribute(name = "hidden") + protected Boolean hidden; + @XmlAttribute(name = "viewreference") + protected Boolean viewreference; + + /** + * Gets the value of the features property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the features property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getFeatures().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Feature } + * + * + */ + public List getFeatures() { + if (features == null) { + features = new ArrayList(); + } + return this.features; + } + + /** + * Gets the value of the pdbids property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the pdbids property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getPdbids().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.Pdbids } + * + * + */ + public List getPdbids() { + if (pdbids == null) { + pdbids = new ArrayList(); + } + return this.pdbids; + } + + /** + * Gets the value of the hiddenSequences property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the hiddenSequences property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getHiddenSequences().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Integer } + * + * + */ + public List getHiddenSequences() { + if (hiddenSequences == null) { + hiddenSequences = new ArrayList(); + } + return this.hiddenSequences; + } + + /** + * Gets the value of the rnaViewer property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the rnaViewer property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getRnaViewer().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.RnaViewer } + * + * + */ + public List getRnaViewer() { + if (rnaViewer == null) { + rnaViewer = new ArrayList(); + } + return this.rnaViewer; + } + + /** + * Gets the value of the colour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setColour(Integer value) { + this.colour = value; + } + + /** + * Gets the value of the start property. + * + */ + public int getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + */ + public void setStart(int value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + */ + public int getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + */ + public void setEnd(int value) { + this.end = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the hidden property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isHidden() { + return hidden; + } + + /** + * Sets the value of the hidden property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setHidden(Boolean value) { + this.hidden = value; + } + + /** + * Gets the value of the viewreference property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isViewreference() { + return viewreference; + } + + /** + * Sets the value of the viewreference property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setViewreference(Boolean value) { + this.viewreference = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org}pdbentry">
+         *       <sequence>
+         *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+         *           <complexType>
+         *             <simpleContent>
+         *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
+         *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+         *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </extension>
+         *             </simpleContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "structureState" + }) + public static class Pdbids + extends Pdbentry + { + + @XmlElement(namespace = "www.jalview.org") + protected List structureState; + + /** + * Gets the value of the structureState property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the structureState property. + * + *

+ * For example, to add a new item, do as follows: + * 

+             *    getStructureState().add(newItem);
+             *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.Pdbids.StructureState } + * + * + */ + public List getStructureState() { + if (structureState == null) { + structureState = new ArrayList(); + } + return this.structureState; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+             * <complexType>
+             *   <simpleContent>
+             *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+             *       <attGroup ref="{www.jalview.org}swingwindow"/>
+             *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+             *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </extension>
+             *   </simpleContent>
+             * </complexType>
+             *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "value" + }) + public static class StructureState { + + @XmlValue + protected String value; + @XmlAttribute(name = "visible") + protected Boolean visible; + @XmlAttribute(name = "viewId") + protected String viewId; + @XmlAttribute(name = "alignwithAlignPanel") + protected Boolean alignwithAlignPanel; + @XmlAttribute(name = "colourwithAlignPanel") + protected Boolean colourwithAlignPanel; + @XmlAttribute(name = "colourByJmol") + protected Boolean colourByJmol; + @XmlAttribute(name = "type") + protected String type; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + /** + * Gets the value of the visible property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isVisible() { + return visible; + } + + /** + * Sets the value of the visible property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setVisible(Boolean value) { + this.visible = value; + } + + /** + * Gets the value of the viewId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewId() { + return viewId; + } + + /** + * Sets the value of the viewId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewId(String value) { + this.viewId = value; + } + + /** + * Gets the value of the alignwithAlignPanel property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isAlignwithAlignPanel() { + if (alignwithAlignPanel == null) { + return true; + } else { + return alignwithAlignPanel; + } + } + + /** + * Sets the value of the alignwithAlignPanel property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setAlignwithAlignPanel(Boolean value) { + this.alignwithAlignPanel = value; + } + + /** + * Gets the value of the colourwithAlignPanel property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isColourwithAlignPanel() { + if (colourwithAlignPanel == null) { + return false; + } else { + return colourwithAlignPanel; + } + } + + /** + * Sets the value of the colourwithAlignPanel property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourwithAlignPanel(Boolean value) { + this.colourwithAlignPanel = value; + } + + /** + * Gets the value of the colourByJmol property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isColourByJmol() { + if (colourByJmol == null) { + return true; + } else { + return colourByJmol; + } + } + + /** + * Sets the value of the colourByJmol property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourByJmol(Boolean value) { + this.colourByJmol = value; + } + + /** + * Gets the value of the type property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getType() { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setType(String value) { + this.type = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="secondaryStructure" maxOccurs="unbounded">
+         *           <complexType>
+         *             <complexContent>
+         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </restriction>
+         *             </complexContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "secondaryStructure" + }) + public static class RnaViewer { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List secondaryStructure; + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "viewId") + protected String viewId; + @XmlAttribute(name = "dividerLocation") + protected Integer dividerLocation; + @XmlAttribute(name = "selectedRna") + protected Integer selectedRna; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the secondaryStructure property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the secondaryStructure property. + * + *

+ * For example, to add a new item, do as follows: + * 

+             *    getSecondaryStructure().add(newItem);
+             *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } + * + * + */ + public List getSecondaryStructure() { + if (secondaryStructure == null) { + secondaryStructure = new ArrayList(); + } + return this.secondaryStructure; + } + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the viewId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewId() { + return viewId; + } + + /** + * Sets the value of the viewId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewId(String value) { + this.viewId = value; + } + + /** + * Gets the value of the dividerLocation property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getDividerLocation() { + return dividerLocation; + } + + /** + * Sets the value of the dividerLocation property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setDividerLocation(Integer value) { + this.dividerLocation = value; + } + + /** + * Gets the value of the selectedRna property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getSelectedRna() { + return selectedRna; + } + + /** + * Sets the value of the selectedRna property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setSelectedRna(Integer value) { + this.selectedRna = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+             * <complexType>
+             *   <complexContent>
+             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </restriction>
+             *   </complexContent>
+             * </complexType>
+             *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SecondaryStructure { + + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "annotationId", required = true) + protected String annotationId; + @XmlAttribute(name = "gapped") + protected Boolean gapped; + @XmlAttribute(name = "viewerState") + protected String viewerState; + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the annotationId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getAnnotationId() { + return annotationId; + } + + /** + * Sets the value of the annotationId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setAnnotationId(String value) { + this.annotationId = value; + } + + /** + * Gets the value of the gapped property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isGapped() { + return gapped; + } + + /** + * Sets the value of the gapped property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setGapped(Boolean value) { + this.gapped = value; + } + + /** + * Gets the value of the viewerState property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewerState() { + return viewerState; + } + + /** + * Sets the value of the viewerState property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewerState(String value) { + this.viewerState = value; + } + + } + + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence minOccurs="0">
+     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "title", + "newick" + }) + public static class Tree { + + @XmlElement(namespace = "www.jalview.org") + protected String title; + @XmlElement(namespace = "www.jalview.org") + protected String newick; + @XmlAttribute(name = "fontName") + protected String fontName; + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + @XmlAttribute(name = "threshold") + protected Float threshold; + @XmlAttribute(name = "showBootstrap") + protected Boolean showBootstrap; + @XmlAttribute(name = "showDistances") + protected Boolean showDistances; + @XmlAttribute(name = "markUnlinked") + protected Boolean markUnlinked; + @XmlAttribute(name = "fitToWindow") + protected Boolean fitToWindow; + @XmlAttribute(name = "currentTree") + protected Boolean currentTree; + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the newick property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getNewick() { + return newick; + } + + /** + * Sets the value of the newick property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setNewick(String value) { + this.newick = value; + } + + /** + * Gets the value of the fontName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFontName() { + return fontName; + } + + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFontName(String value) { + this.fontName = value; + } + + /** + * Gets the value of the fontSize property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontSize() { + return fontSize; + } + + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontSize(Integer value) { + this.fontSize = value; + } + + /** + * Gets the value of the fontStyle property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontStyle() { + return fontStyle; + } + + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontStyle(Integer value) { + this.fontStyle = value; + } + + /** + * Gets the value of the threshold property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getThreshold() { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setThreshold(Float value) { + this.threshold = value; + } + + /** + * Gets the value of the showBootstrap property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowBootstrap() { + return showBootstrap; + } + + /** + * Sets the value of the showBootstrap property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowBootstrap(Boolean value) { + this.showBootstrap = value; + } + + /** + * Gets the value of the showDistances property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowDistances() { + return showDistances; + } + + /** + * Sets the value of the showDistances property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowDistances(Boolean value) { + this.showDistances = value; + } + + /** + * Gets the value of the markUnlinked property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isMarkUnlinked() { + return markUnlinked; + } + + /** + * Sets the value of the markUnlinked property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setMarkUnlinked(Boolean value) { + this.markUnlinked = value; + } + + /** + * Gets the value of the fitToWindow property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isFitToWindow() { + return fitToWindow; + } + + /** + * Sets the value of the fitToWindow property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setFitToWindow(Boolean value) { + this.fitToWindow = value; + } + + /** + * Gets the value of the currentTree property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isCurrentTree() { + return currentTree; + } + + /** + * Sets the value of the currentTree property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setCurrentTree(Boolean value) { + this.currentTree = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+     *       </sequence>
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "userColourScheme" + }) + public static class UserColours { + + @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true) + protected JalviewUserColours userColourScheme; + @XmlAttribute(name = "id") + protected String id; + + /** + * Gets the value of the userColourScheme property. + * + * @return + * possible object is + * {@link JalviewUserColours } + * + */ + public JalviewUserColours getUserColourScheme() { + return userColourScheme; + } + + /** + * Sets the value of the userColourScheme property. + * + * @param value + * allowed object is + * {@link JalviewUserColours } + * + */ + public void setUserColourScheme(JalviewUserColours value) { + this.userColourScheme = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "annotationColours", + "hiddenColumns", + "calcIdParam" + }) + public static class Viewport { + + @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + @XmlElement(namespace = "www.jalview.org") + protected List hiddenColumns; + @XmlElement(namespace = "www.jalview.org") + protected List calcIdParam; + @XmlAttribute(name = "conservationSelected") + protected Boolean conservationSelected; + @XmlAttribute(name = "pidSelected") + protected Boolean pidSelected; + @XmlAttribute(name = "bgColour") + protected String bgColour; + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "showFullId") + protected Boolean showFullId; + @XmlAttribute(name = "rightAlignIds") + protected Boolean rightAlignIds; + @XmlAttribute(name = "showText") + protected Boolean showText; + @XmlAttribute(name = "showColourText") + protected Boolean showColourText; + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + @XmlAttribute(name = "showBoxes") + protected Boolean showBoxes; + @XmlAttribute(name = "wrapAlignment") + protected Boolean wrapAlignment; + @XmlAttribute(name = "renderGaps") + protected Boolean renderGaps; + @XmlAttribute(name = "showSequenceFeatures") + protected Boolean showSequenceFeatures; + @XmlAttribute(name = "showNPfeatureTooltip") + protected Boolean showNPfeatureTooltip; + @XmlAttribute(name = "showDbRefTooltip") + protected Boolean showDbRefTooltip; + @XmlAttribute(name = "followHighlight") + protected Boolean followHighlight; + @XmlAttribute(name = "followSelection") + protected Boolean followSelection; + @XmlAttribute(name = "showAnnotation") + protected Boolean showAnnotation; + @XmlAttribute(name = "centreColumnLabels") + protected Boolean centreColumnLabels; + @XmlAttribute(name = "showGroupConservation") + protected Boolean showGroupConservation; + @XmlAttribute(name = "showGroupConsensus") + protected Boolean showGroupConsensus; + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; + @XmlAttribute(name = "startRes") + protected Integer startRes; + @XmlAttribute(name = "startSeq") + protected Integer startSeq; + @XmlAttribute(name = "fontName") + protected String fontName; + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + @XmlAttribute(name = "scaleProteinAsCdna") + protected Boolean scaleProteinAsCdna; + @XmlAttribute(name = "viewName") + protected String viewName; + @XmlAttribute(name = "sequenceSetId") + protected String sequenceSetId; + @XmlAttribute(name = "gatheredViews") + protected Boolean gatheredViews; + @XmlAttribute(name = "textCol1") + protected Integer textCol1; + @XmlAttribute(name = "textCol2") + protected Integer textCol2; + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + @XmlAttribute(name = "complementId") + protected String complementId; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the annotationColours property. + * + * @return + * possible object is + * {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() { + return annotationColours; + } + + /** + * Sets the value of the annotationColours property. + * + * @param value + * allowed object is + * {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) { + this.annotationColours = value; + } + + /** + * Gets the value of the hiddenColumns property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the hiddenColumns property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getHiddenColumns().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport.HiddenColumns } + * + * + */ + public List getHiddenColumns() { + if (hiddenColumns == null) { + hiddenColumns = new ArrayList(); + } + return this.hiddenColumns; + } + + /** + * Gets the value of the calcIdParam property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the calcIdParam property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getCalcIdParam().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport.CalcIdParam } + * + * + */ + public List getCalcIdParam() { + if (calcIdParam == null) { + calcIdParam = new ArrayList(); + } + return this.calcIdParam; + } + + /** + * Gets the value of the conservationSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isConservationSelected() { + return conservationSelected; + } + + /** + * Sets the value of the conservationSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setConservationSelected(Boolean value) { + this.conservationSelected = value; + } + + /** + * Gets the value of the pidSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isPidSelected() { + return pidSelected; + } + + /** + * Sets the value of the pidSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setPidSelected(Boolean value) { + this.pidSelected = value; + } + + /** + * Gets the value of the bgColour property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getBgColour() { + return bgColour; + } + + /** + * Sets the value of the bgColour property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setBgColour(String value) { + this.bgColour = value; + } + + /** + * Gets the value of the consThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getConsThreshold() { + return consThreshold; + } + + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setConsThreshold(Integer value) { + this.consThreshold = value; + } + + /** + * Gets the value of the pidThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getPidThreshold() { + return pidThreshold; + } + + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setPidThreshold(Integer value) { + this.pidThreshold = value; + } + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the showFullId property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowFullId() { + return showFullId; + } + + /** + * Sets the value of the showFullId property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowFullId(Boolean value) { + this.showFullId = value; + } + + /** + * Gets the value of the rightAlignIds property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isRightAlignIds() { + return rightAlignIds; + } + + /** + * Sets the value of the rightAlignIds property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setRightAlignIds(Boolean value) { + this.rightAlignIds = value; + } + + /** + * Gets the value of the showText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowText() { + return showText; + } + + /** + * Sets the value of the showText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowText(Boolean value) { + this.showText = value; + } + + /** + * Gets the value of the showColourText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowColourText() { + return showColourText; + } + + /** + * Sets the value of the showColourText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowColourText(Boolean value) { + this.showColourText = value; + } + + /** + * Gets the value of the showUnconserved property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowUnconserved() { + if (showUnconserved == null) { + return false; + } else { + return showUnconserved; + } + } + + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) { + this.showUnconserved = value; + } + + /** + * Gets the value of the showBoxes property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowBoxes() { + return showBoxes; + } + + /** + * Sets the value of the showBoxes property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowBoxes(Boolean value) { + this.showBoxes = value; + } + + /** + * Gets the value of the wrapAlignment property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isWrapAlignment() { + return wrapAlignment; + } + + /** + * Sets the value of the wrapAlignment property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setWrapAlignment(Boolean value) { + this.wrapAlignment = value; + } + + /** + * Gets the value of the renderGaps property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isRenderGaps() { + return renderGaps; + } + + /** + * Sets the value of the renderGaps property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setRenderGaps(Boolean value) { + this.renderGaps = value; + } + + /** + * Gets the value of the showSequenceFeatures property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowSequenceFeatures() { + return showSequenceFeatures; + } + + /** + * Sets the value of the showSequenceFeatures property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowSequenceFeatures(Boolean value) { + this.showSequenceFeatures = value; + } + + /** + * Gets the value of the showNPfeatureTooltip property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowNPfeatureTooltip() { + return showNPfeatureTooltip; + } + + /** + * Sets the value of the showNPfeatureTooltip property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowNPfeatureTooltip(Boolean value) { + this.showNPfeatureTooltip = value; + } + + /** + * Gets the value of the showDbRefTooltip property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowDbRefTooltip() { + return showDbRefTooltip; + } + + /** + * Sets the value of the showDbRefTooltip property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowDbRefTooltip(Boolean value) { + this.showDbRefTooltip = value; + } + + /** + * Gets the value of the followHighlight property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isFollowHighlight() { + if (followHighlight == null) { + return true; + } else { + return followHighlight; + } + } + + /** + * Sets the value of the followHighlight property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setFollowHighlight(Boolean value) { + this.followHighlight = value; + } + + /** + * Gets the value of the followSelection property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isFollowSelection() { + if (followSelection == null) { + return true; + } else { + return followSelection; + } + } + + /** + * Sets the value of the followSelection property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setFollowSelection(Boolean value) { + this.followSelection = value; + } + + /** + * Gets the value of the showAnnotation property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowAnnotation() { + return showAnnotation; + } + + /** + * Sets the value of the showAnnotation property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowAnnotation(Boolean value) { + this.showAnnotation = value; + } + + /** + * Gets the value of the centreColumnLabels property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isCentreColumnLabels() { + if (centreColumnLabels == null) { + return false; + } else { + return centreColumnLabels; + } + } + + /** + * Sets the value of the centreColumnLabels property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setCentreColumnLabels(Boolean value) { + this.centreColumnLabels = value; + } + + /** + * Gets the value of the showGroupConservation property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowGroupConservation() { + if (showGroupConservation == null) { + return false; + } else { + return showGroupConservation; + } + } + + /** + * Sets the value of the showGroupConservation property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowGroupConservation(Boolean value) { + this.showGroupConservation = value; + } + + /** + * Gets the value of the showGroupConsensus property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowGroupConsensus() { + if (showGroupConsensus == null) { + return false; + } else { + return showGroupConsensus; + } + } + + /** + * Sets the value of the showGroupConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowGroupConsensus(Boolean value) { + this.showGroupConsensus = value; + } + + /** + * Gets the value of the showConsensusHistogram property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowConsensusHistogram() { + if (showConsensusHistogram == null) { + return true; + } else { + return showConsensusHistogram; + } + } + + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) { + this.showConsensusHistogram = value; + } + + /** + * Gets the value of the showSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowSequenceLogo() { + if (showSequenceLogo == null) { + return false; + } else { + return showSequenceLogo; + } + } + + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) { + this.showSequenceLogo = value; + } + + /** + * Gets the value of the normaliseSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() { + if (normaliseSequenceLogo == null) { + return false; + } else { + return normaliseSequenceLogo; + } + } + + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) { + this.normaliseSequenceLogo = value; + } + + /** + * Gets the value of the ignoreGapsinConsensus property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() { + if (ignoreGapsinConsensus == null) { + return true; + } else { + return ignoreGapsinConsensus; + } + } + + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) { + this.ignoreGapsinConsensus = value; + } + + /** + * Gets the value of the startRes property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStartRes() { + return startRes; + } + + /** + * Sets the value of the startRes property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStartRes(Integer value) { + this.startRes = value; + } + + /** + * Gets the value of the startSeq property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStartSeq() { + return startSeq; + } + + /** + * Sets the value of the startSeq property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStartSeq(Integer value) { + this.startSeq = value; + } + + /** + * Gets the value of the fontName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFontName() { + return fontName; + } + + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFontName(String value) { + this.fontName = value; + } + + /** + * Gets the value of the fontSize property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontSize() { + return fontSize; + } + + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontSize(Integer value) { + this.fontSize = value; + } + + /** + * Gets the value of the fontStyle property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontStyle() { + return fontStyle; + } + + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontStyle(Integer value) { + this.fontStyle = value; + } + + /** + * Gets the value of the scaleProteinAsCdna property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isScaleProteinAsCdna() { + if (scaleProteinAsCdna == null) { + return true; + } else { + return scaleProteinAsCdna; + } + } + + /** + * Sets the value of the scaleProteinAsCdna property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setScaleProteinAsCdna(Boolean value) { + this.scaleProteinAsCdna = value; + } + + /** + * Gets the value of the viewName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewName() { + return viewName; + } + + /** + * Sets the value of the viewName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewName(String value) { + this.viewName = value; + } + + /** + * Gets the value of the sequenceSetId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSequenceSetId() { + return sequenceSetId; + } + + /** + * Sets the value of the sequenceSetId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSequenceSetId(String value) { + this.sequenceSetId = value; + } + + /** + * Gets the value of the gatheredViews property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isGatheredViews() { + return gatheredViews; + } + + /** + * Sets the value of the gatheredViews property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setGatheredViews(Boolean value) { + this.gatheredViews = value; + } + + /** + * Gets the value of the textCol1 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol1() { + return textCol1; + } + + /** + * Sets the value of the textCol1 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol1(Integer value) { + this.textCol1 = value; + } + + /** + * Gets the value of the textCol2 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol2() { + return textCol2; + } + + /** + * Sets the value of the textCol2 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol2(Integer value) { + this.textCol2 = value; + } + + /** + * Gets the value of the textColThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextColThreshold() { + return textColThreshold; + } + + /** + * Sets the value of the textColThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextColThreshold(Integer value) { + this.textColThreshold = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the complementId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getComplementId() { + return complementId; + } + + /** + * Sets the value of the complementId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setComplementId(String value) { + this.complementId = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+         *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class CalcIdParam + extends WebServiceParameterSet + { + + @XmlAttribute(name = "calcId", required = true) + protected String calcId; + @XmlAttribute(name = "needsUpdate") + protected Boolean needsUpdate; + @XmlAttribute(name = "autoUpdate", required = true) + protected boolean autoUpdate; + + /** + * Gets the value of the calcId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getCalcId() { + return calcId; + } + + /** + * Sets the value of the calcId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setCalcId(String value) { + this.calcId = value; + } + + /** + * Gets the value of the needsUpdate property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isNeedsUpdate() { + if (needsUpdate == null) { + return false; + } else { + return needsUpdate; + } + } + + /** + * Sets the value of the needsUpdate property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setNeedsUpdate(Boolean value) { + this.needsUpdate = value; + } + + /** + * Gets the value of the autoUpdate property. + * + */ + public boolean isAutoUpdate() { + return autoUpdate; + } + + /** + * Sets the value of the autoUpdate property. + * + */ + public void setAutoUpdate(boolean value) { + this.autoUpdate = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class HiddenColumns { + + @XmlAttribute(name = "start") + protected Integer start; + @XmlAttribute(name = "end") + protected Integer end; + + /** + * Gets the value of the start property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStart(Integer value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setEnd(Integer value) { + this.end = value; + } + + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java new file mode 100644 index 0000000..f084bc3 --- /dev/null +++ b/src/jalview/xml/binding/jalview/JalviewModelType.java @@ -0,0 +1,5090 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 01:33:02 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlID; +import javax.xml.bind.annotation.XmlSchemaType; +import javax.xml.bind.annotation.XmlType; +import javax.xml.bind.annotation.XmlValue; +import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; +import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; +import javax.xml.datatype.XMLGregorianCalendar; + + +/** + *

Java class for JalviewModelType complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="JalviewModelType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ *         <sequence>
+ *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org}pdbentry">
+ *                             <sequence>
+ *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ *                                 <complexType>
+ *                                   <simpleContent>
+ *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </extension>
+ *                                   </simpleContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="secondaryStructure" maxOccurs="unbounded">
+ *                                 <complexType>
+ *                                   <complexContent>
+ *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     </restriction>
+ *                                   </complexContent>
+ *                                 </complexType>
+ *                               </element>
+ *                             </sequence>
+ *                             <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                   </sequence>
+ *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </extension>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ *                   </sequence>
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence minOccurs="0">
+ *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="FeatureSettings" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <sequence>
+ *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ *                             </sequence>
+ *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                   </sequence>
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *         </sequence>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "JalviewModelType", namespace = "www.jalview.org", propOrder = { + "creationDate", + "version", + "vamsasModel", + "jSeq", + "jGroup", + "viewport", + "userColours", + "tree", + "featureSettings" +}) +public class JalviewModelType { + + @XmlElement(required = true) + @XmlSchemaType(name = "dateTime") + protected XMLGregorianCalendar creationDate; + @XmlElement(required = true) + protected String version; + @XmlElement(required = true) + protected VAMSAS vamsasModel; + @XmlElement(name = "JSeq") + protected List jSeq; + @XmlElement(name = "JGroup") + protected List jGroup; + @XmlElement(name = "Viewport") + protected List viewport; + @XmlElement(name = "UserColours") + protected List userColours; + protected List tree; + @XmlElement(name = "FeatureSettings") + protected JalviewModelType.FeatureSettings featureSettings; + + /** + * Gets the value of the creationDate property. + * + * @return + * possible object is + * {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getCreationDate() { + return creationDate; + } + + /** + * Sets the value of the creationDate property. + * + * @param value + * allowed object is + * {@link XMLGregorianCalendar } + * + */ + public void setCreationDate(XMLGregorianCalendar value) { + this.creationDate = value; + } + + /** + * Gets the value of the version property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getVersion() { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setVersion(String value) { + this.version = value; + } + + /** + * Gets the value of the vamsasModel property. + * + * @return + * possible object is + * {@link VAMSAS } + * + */ + public VAMSAS getVamsasModel() { + return vamsasModel; + } + + /** + * Sets the value of the vamsasModel property. + * + * @param value + * allowed object is + * {@link VAMSAS } + * + */ + public void setVamsasModel(VAMSAS value) { + this.vamsasModel = value; + } + + /** + * Gets the value of the jSeq property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the jSeq property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getJSeq().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.JSeq } + * + * + */ + public List getJSeq() { + if (jSeq == null) { + jSeq = new ArrayList(); + } + return this.jSeq; + } + + /** + * Gets the value of the jGroup property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the jGroup property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getJGroup().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.JGroup } + * + * + */ + public List getJGroup() { + if (jGroup == null) { + jGroup = new ArrayList(); + } + return this.jGroup; + } + + /** + * Gets the value of the viewport property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the viewport property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getViewport().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.Viewport } + * + * + */ + public List getViewport() { + if (viewport == null) { + viewport = new ArrayList(); + } + return this.viewport; + } + + /** + * Gets the value of the userColours property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the userColours property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getUserColours().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.UserColours } + * + * + */ + public List getUserColours() { + if (userColours == null) { + userColours = new ArrayList(); + } + return this.userColours; + } + + /** + * Gets the value of the tree property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the tree property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getTree().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.Tree } + * + * + */ + public List getTree() { + if (tree == null) { + tree = new ArrayList(); + } + return this.tree; + } + + /** + * Gets the value of the featureSettings property. + * + * @return + * possible object is + * {@link JalviewModelType.FeatureSettings } + * + */ + public JalviewModelType.FeatureSettings getFeatureSettings() { + return featureSettings; + } + + /** + * Sets the value of the featureSettings property. + * + * @param value + * allowed object is + * {@link JalviewModelType.FeatureSettings } + * + */ + public void setFeatureSettings(JalviewModelType.FeatureSettings value) { + this.featureSettings = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *                 </sequence>
+     *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="group" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "setting", + "group" + }) + public static class FeatureSettings { + + @XmlElement(namespace = "www.jalview.org") + protected List setting; + @XmlElement(namespace = "www.jalview.org") + protected List group; + + /** + * Gets the value of the setting property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the setting property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getSetting().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.FeatureSettings.Setting } + * + * + */ + public List getSetting() { + if (setting == null) { + setting = new ArrayList(); + } + return this.setting; + } + + /** + * Gets the value of the group property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the group property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getGroup().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.FeatureSettings.Group } + * + * + */ + public List getGroup() { + if (group == null) { + group = new ArrayList(); + } + return this.group; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Group { + + @XmlAttribute(name = "name", required = true) + protected String name; + @XmlAttribute(name = "display", required = true) + protected boolean display; + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) { + this.display = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+         *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+         *       </sequence>
+         *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+         *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "attributeName", + "matcherSet" + }) + public static class Setting { + + @XmlElement(namespace = "www.jalview.org") + protected List attributeName; + @XmlElement(namespace = "www.jalview.org") + protected FeatureMatcherSet matcherSet; + @XmlAttribute(name = "type", required = true) + protected String type; + @XmlAttribute(name = "colour", required = true) + protected int colour; + @XmlAttribute(name = "display", required = true) + protected boolean display; + @XmlAttribute(name = "order") + protected Float order; + @XmlAttribute(name = "mincolour") + protected Integer mincolour; + @XmlAttribute(name = "noValueColour") + protected NoValueColour noValueColour; + @XmlAttribute(name = "threshold") + protected Float threshold; + @XmlAttribute(name = "threshstate") + protected Integer threshstate; + @XmlAttribute(name = "max") + protected Float max; + @XmlAttribute(name = "min") + protected Float min; + @XmlAttribute(name = "colourByLabel") + protected Boolean colourByLabel; + @XmlAttribute(name = "autoScale") + protected Boolean autoScale; + + /** + * Gets the value of the attributeName property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the attributeName property. + * + *

+ * For example, to add a new item, do as follows: + * 

+             *    getAttributeName().add(newItem);
+             *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getAttributeName() { + if (attributeName == null) { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * Gets the value of the matcherSet property. + * + * @return + * possible object is + * {@link FeatureMatcherSet } + * + */ + public FeatureMatcherSet getMatcherSet() { + return matcherSet; + } + + /** + * Sets the value of the matcherSet property. + * + * @param value + * allowed object is + * {@link FeatureMatcherSet } + * + */ + public void setMatcherSet(FeatureMatcherSet value) { + this.matcherSet = value; + } + + /** + * Gets the value of the type property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getType() { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setType(String value) { + this.type = value; + } + + /** + * Gets the value of the colour property. + * + */ + public int getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + */ + public void setColour(int value) { + this.colour = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) { + this.display = value; + } + + /** + * Gets the value of the order property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getOrder() { + return order; + } + + /** + * Sets the value of the order property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setOrder(Float value) { + this.order = value; + } + + /** + * Gets the value of the mincolour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getMincolour() { + return mincolour; + } + + /** + * Sets the value of the mincolour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setMincolour(Integer value) { + this.mincolour = value; + } + + /** + * Gets the value of the noValueColour property. + * + * @return + * possible object is + * {@link NoValueColour } + * + */ + public NoValueColour getNoValueColour() { + if (noValueColour == null) { + return NoValueColour.MIN; + } else { + return noValueColour; + } + } + + /** + * Sets the value of the noValueColour property. + * + * @param value + * allowed object is + * {@link NoValueColour } + * + */ + public void setNoValueColour(NoValueColour value) { + this.noValueColour = value; + } + + /** + * Gets the value of the threshold property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getThreshold() { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setThreshold(Float value) { + this.threshold = value; + } + + /** + * Gets the value of the threshstate property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getThreshstate() { + return threshstate; + } + + /** + * Sets the value of the threshstate property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setThreshstate(Integer value) { + this.threshstate = value; + } + + /** + * Gets the value of the max property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getMax() { + return max; + } + + /** + * Sets the value of the max property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setMax(Float value) { + this.max = value; + } + + /** + * Gets the value of the min property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getMin() { + return min; + } + + /** + * Sets the value of the min property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setMin(Float value) { + this.min = value; + } + + /** + * Gets the value of the colourByLabel property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isColourByLabel() { + return colourByLabel; + } + + /** + * Sets the value of the colourByLabel property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourByLabel(Boolean value) { + this.colourByLabel = value; + } + + /** + * Gets the value of the autoScale property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isAutoScale() { + return autoScale; + } + + /** + * Sets the value of the autoScale property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setAutoScale(Boolean value) { + this.autoScale = value; + } + + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "seq", + "annotationColours" + }) + public static class JGroup { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List seq; + @XmlElement(namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + @XmlAttribute(name = "start") + protected Integer start; + @XmlAttribute(name = "end") + protected Integer end; + @XmlAttribute(name = "name") + protected String name; + @XmlAttribute(name = "colour") + protected String colour; + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + @XmlAttribute(name = "outlineColour") + protected Integer outlineColour; + @XmlAttribute(name = "displayBoxes") + protected Boolean displayBoxes; + @XmlAttribute(name = "displayText") + protected Boolean displayText; + @XmlAttribute(name = "colourText") + protected Boolean colourText; + @XmlAttribute(name = "textCol1") + protected Integer textCol1; + @XmlAttribute(name = "textCol2") + protected Integer textCol2; + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + @XmlAttribute(name = "id") + protected String id; + + /** + * Gets the value of the seq property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the seq property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getSeq().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getSeq() { + if (seq == null) { + seq = new ArrayList(); + } + return this.seq; + } + + /** + * Gets the value of the annotationColours property. + * + * @return + * possible object is + * {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() { + return annotationColours; + } + + /** + * Sets the value of the annotationColours property. + * + * @param value + * allowed object is + * {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) { + this.annotationColours = value; + } + + /** + * Gets the value of the start property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStart(Integer value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setEnd(Integer value) { + this.end = value; + } + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the colour property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setColour(String value) { + this.colour = value; + } + + /** + * Gets the value of the consThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getConsThreshold() { + return consThreshold; + } + + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setConsThreshold(Integer value) { + this.consThreshold = value; + } + + /** + * Gets the value of the pidThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getPidThreshold() { + return pidThreshold; + } + + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setPidThreshold(Integer value) { + this.pidThreshold = value; + } + + /** + * Gets the value of the outlineColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getOutlineColour() { + return outlineColour; + } + + /** + * Sets the value of the outlineColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setOutlineColour(Integer value) { + this.outlineColour = value; + } + + /** + * Gets the value of the displayBoxes property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isDisplayBoxes() { + return displayBoxes; + } + + /** + * Sets the value of the displayBoxes property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setDisplayBoxes(Boolean value) { + this.displayBoxes = value; + } + + /** + * Gets the value of the displayText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isDisplayText() { + return displayText; + } + + /** + * Sets the value of the displayText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setDisplayText(Boolean value) { + this.displayText = value; + } + + /** + * Gets the value of the colourText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isColourText() { + return colourText; + } + + /** + * Sets the value of the colourText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourText(Boolean value) { + this.colourText = value; + } + + /** + * Gets the value of the textCol1 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol1() { + return textCol1; + } + + /** + * Sets the value of the textCol1 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol1(Integer value) { + this.textCol1 = value; + } + + /** + * Gets the value of the textCol2 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol2() { + return textCol2; + } + + /** + * Sets the value of the textCol2 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol2(Integer value) { + this.textCol2 = value; + } + + /** + * Gets the value of the textColThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextColThreshold() { + return textColThreshold; + } + + /** + * Sets the value of the textColThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextColThreshold(Integer value) { + this.textColThreshold = value; + } + + /** + * Gets the value of the showUnconserved property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowUnconserved() { + return showUnconserved; + } + + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) { + this.showUnconserved = value; + } + + /** + * Gets the value of the ignoreGapsinConsensus property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() { + if (ignoreGapsinConsensus == null) { + return true; + } else { + return ignoreGapsinConsensus; + } + } + + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) { + this.ignoreGapsinConsensus = value; + } + + /** + * Gets the value of the showConsensusHistogram property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowConsensusHistogram() { + if (showConsensusHistogram == null) { + return true; + } else { + return showConsensusHistogram; + } + } + + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) { + this.showConsensusHistogram = value; + } + + /** + * Gets the value of the showSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowSequenceLogo() { + if (showSequenceLogo == null) { + return false; + } else { + return showSequenceLogo; + } + } + + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) { + this.showSequenceLogo = value; + } + + /** + * Gets the value of the normaliseSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() { + if (normaliseSequenceLogo == null) { + return false; + } else { + return normaliseSequenceLogo; + } + } + + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) { + this.normaliseSequenceLogo = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org}pdbentry">
+     *                 <sequence>
+     *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *                     <complexType>
+     *                       <simpleContent>
+     *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *                           <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </extension>
+     *                       </simpleContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="secondaryStructure" maxOccurs="unbounded">
+     *                     <complexType>
+     *                       <complexContent>
+     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </restriction>
+     *                       </complexContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "features", + "pdbids", + "hiddenSequences", + "rnaViewer" + }) + public static class JSeq { + + @XmlElement(namespace = "www.jalview.org") + protected List features; + @XmlElement(namespace = "www.jalview.org") + protected List pdbids; + @XmlElement(namespace = "www.jalview.org", type = Integer.class) + protected List hiddenSequences; + @XmlElement(namespace = "www.jalview.org") + protected List rnaViewer; + @XmlAttribute(name = "colour") + protected Integer colour; + @XmlAttribute(name = "start", required = true) + protected int start; + @XmlAttribute(name = "end", required = true) + protected int end; + @XmlAttribute(name = "id", required = true) + protected String id; + @XmlAttribute(name = "hidden") + protected Boolean hidden; + @XmlAttribute(name = "viewreference") + protected Boolean viewreference; + + /** + * Gets the value of the features property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the features property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getFeatures().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Feature } + * + * + */ + public List getFeatures() { + if (features == null) { + features = new ArrayList(); + } + return this.features; + } + + /** + * Gets the value of the pdbids property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the pdbids property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getPdbids().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.JSeq.Pdbids } + * + * + */ + public List getPdbids() { + if (pdbids == null) { + pdbids = new ArrayList(); + } + return this.pdbids; + } + + /** + * Gets the value of the hiddenSequences property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the hiddenSequences property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getHiddenSequences().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Integer } + * + * + */ + public List getHiddenSequences() { + if (hiddenSequences == null) { + hiddenSequences = new ArrayList(); + } + return this.hiddenSequences; + } + + /** + * Gets the value of the rnaViewer property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the rnaViewer property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getRnaViewer().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.JSeq.RnaViewer } + * + * + */ + public List getRnaViewer() { + if (rnaViewer == null) { + rnaViewer = new ArrayList(); + } + return this.rnaViewer; + } + + /** + * Gets the value of the colour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getColour() { + return colour; + } + + /** + * Sets the value of the colour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setColour(Integer value) { + this.colour = value; + } + + /** + * Gets the value of the start property. + * + */ + public int getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + */ + public void setStart(int value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + */ + public int getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + */ + public void setEnd(int value) { + this.end = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the hidden property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isHidden() { + return hidden; + } + + /** + * Sets the value of the hidden property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setHidden(Boolean value) { + this.hidden = value; + } + + /** + * Gets the value of the viewreference property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isViewreference() { + return viewreference; + } + + /** + * Sets the value of the viewreference property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setViewreference(Boolean value) { + this.viewreference = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org}pdbentry">
+         *       <sequence>
+         *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+         *           <complexType>
+         *             <simpleContent>
+         *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
+         *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+         *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </extension>
+         *             </simpleContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "structureState" + }) + public static class Pdbids + extends Pdbentry + { + + @XmlElement(namespace = "www.jalview.org") + protected List structureState; + + /** + * Gets the value of the structureState property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the structureState property. + * + *

+ * For example, to add a new item, do as follows: + * 

+             *    getStructureState().add(newItem);
+             *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.JSeq.Pdbids.StructureState } + * + * + */ + public List getStructureState() { + if (structureState == null) { + structureState = new ArrayList(); + } + return this.structureState; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+             * <complexType>
+             *   <simpleContent>
+             *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+             *       <attGroup ref="{www.jalview.org}swingwindow"/>
+             *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+             *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </extension>
+             *   </simpleContent>
+             * </complexType>
+             *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "value" + }) + public static class StructureState { + + @XmlValue + protected String value; + @XmlAttribute(name = "visible") + protected Boolean visible; + @XmlAttribute(name = "viewId") + protected String viewId; + @XmlAttribute(name = "alignwithAlignPanel") + protected Boolean alignwithAlignPanel; + @XmlAttribute(name = "colourwithAlignPanel") + protected Boolean colourwithAlignPanel; + @XmlAttribute(name = "colourByJmol") + protected Boolean colourByJmol; + @XmlAttribute(name = "type") + protected String type; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + /** + * Gets the value of the visible property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isVisible() { + return visible; + } + + /** + * Sets the value of the visible property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setVisible(Boolean value) { + this.visible = value; + } + + /** + * Gets the value of the viewId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewId() { + return viewId; + } + + /** + * Sets the value of the viewId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewId(String value) { + this.viewId = value; + } + + /** + * Gets the value of the alignwithAlignPanel property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isAlignwithAlignPanel() { + if (alignwithAlignPanel == null) { + return true; + } else { + return alignwithAlignPanel; + } + } + + /** + * Sets the value of the alignwithAlignPanel property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setAlignwithAlignPanel(Boolean value) { + this.alignwithAlignPanel = value; + } + + /** + * Gets the value of the colourwithAlignPanel property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isColourwithAlignPanel() { + if (colourwithAlignPanel == null) { + return false; + } else { + return colourwithAlignPanel; + } + } + + /** + * Sets the value of the colourwithAlignPanel property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourwithAlignPanel(Boolean value) { + this.colourwithAlignPanel = value; + } + + /** + * Gets the value of the colourByJmol property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isColourByJmol() { + if (colourByJmol == null) { + return true; + } else { + return colourByJmol; + } + } + + /** + * Sets the value of the colourByJmol property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourByJmol(Boolean value) { + this.colourByJmol = value; + } + + /** + * Gets the value of the type property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getType() { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setType(String value) { + this.type = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="secondaryStructure" maxOccurs="unbounded">
+         *           <complexType>
+         *             <complexContent>
+         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </restriction>
+         *             </complexContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "secondaryStructure" + }) + public static class RnaViewer { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List secondaryStructure; + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "viewId") + protected String viewId; + @XmlAttribute(name = "dividerLocation") + protected Integer dividerLocation; + @XmlAttribute(name = "selectedRna") + protected Integer selectedRna; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the secondaryStructure property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the secondaryStructure property. + * + *

+ * For example, to add a new item, do as follows: + * 

+             *    getSecondaryStructure().add(newItem);
+             *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure } + * + * + */ + public List getSecondaryStructure() { + if (secondaryStructure == null) { + secondaryStructure = new ArrayList(); + } + return this.secondaryStructure; + } + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the viewId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewId() { + return viewId; + } + + /** + * Sets the value of the viewId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewId(String value) { + this.viewId = value; + } + + /** + * Gets the value of the dividerLocation property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getDividerLocation() { + return dividerLocation; + } + + /** + * Sets the value of the dividerLocation property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setDividerLocation(Integer value) { + this.dividerLocation = value; + } + + /** + * Gets the value of the selectedRna property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getSelectedRna() { + return selectedRna; + } + + /** + * Sets the value of the selectedRna property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setSelectedRna(Integer value) { + this.selectedRna = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+             * <complexType>
+             *   <complexContent>
+             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </restriction>
+             *   </complexContent>
+             * </complexType>
+             *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SecondaryStructure { + + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "annotationId", required = true) + protected String annotationId; + @XmlAttribute(name = "gapped") + protected Boolean gapped; + @XmlAttribute(name = "viewerState") + protected String viewerState; + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the annotationId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getAnnotationId() { + return annotationId; + } + + /** + * Sets the value of the annotationId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setAnnotationId(String value) { + this.annotationId = value; + } + + /** + * Gets the value of the gapped property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isGapped() { + return gapped; + } + + /** + * Sets the value of the gapped property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setGapped(Boolean value) { + this.gapped = value; + } + + /** + * Gets the value of the viewerState property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewerState() { + return viewerState; + } + + /** + * Sets the value of the viewerState property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewerState(String value) { + this.viewerState = value; + } + + } + + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence minOccurs="0">
+     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "title", + "newick" + }) + public static class Tree { + + @XmlElement(namespace = "www.jalview.org") + protected String title; + @XmlElement(namespace = "www.jalview.org") + protected String newick; + @XmlAttribute(name = "fontName") + protected String fontName; + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + @XmlAttribute(name = "threshold") + protected Float threshold; + @XmlAttribute(name = "showBootstrap") + protected Boolean showBootstrap; + @XmlAttribute(name = "showDistances") + protected Boolean showDistances; + @XmlAttribute(name = "markUnlinked") + protected Boolean markUnlinked; + @XmlAttribute(name = "fitToWindow") + protected Boolean fitToWindow; + @XmlAttribute(name = "currentTree") + protected Boolean currentTree; + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the newick property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getNewick() { + return newick; + } + + /** + * Sets the value of the newick property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setNewick(String value) { + this.newick = value; + } + + /** + * Gets the value of the fontName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFontName() { + return fontName; + } + + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFontName(String value) { + this.fontName = value; + } + + /** + * Gets the value of the fontSize property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontSize() { + return fontSize; + } + + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontSize(Integer value) { + this.fontSize = value; + } + + /** + * Gets the value of the fontStyle property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontStyle() { + return fontStyle; + } + + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontStyle(Integer value) { + this.fontStyle = value; + } + + /** + * Gets the value of the threshold property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getThreshold() { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setThreshold(Float value) { + this.threshold = value; + } + + /** + * Gets the value of the showBootstrap property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowBootstrap() { + return showBootstrap; + } + + /** + * Sets the value of the showBootstrap property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowBootstrap(Boolean value) { + this.showBootstrap = value; + } + + /** + * Gets the value of the showDistances property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowDistances() { + return showDistances; + } + + /** + * Sets the value of the showDistances property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowDistances(Boolean value) { + this.showDistances = value; + } + + /** + * Gets the value of the markUnlinked property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isMarkUnlinked() { + return markUnlinked; + } + + /** + * Sets the value of the markUnlinked property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setMarkUnlinked(Boolean value) { + this.markUnlinked = value; + } + + /** + * Gets the value of the fitToWindow property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isFitToWindow() { + return fitToWindow; + } + + /** + * Sets the value of the fitToWindow property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setFitToWindow(Boolean value) { + this.fitToWindow = value; + } + + /** + * Gets the value of the currentTree property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isCurrentTree() { + return currentTree; + } + + /** + * Sets the value of the currentTree property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setCurrentTree(Boolean value) { + this.currentTree = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+     *       </sequence>
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "userColourScheme" + }) + public static class UserColours { + + @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true) + protected JalviewUserColours userColourScheme; + @XmlAttribute(name = "id") + protected String id; + + /** + * Gets the value of the userColourScheme property. + * + * @return + * possible object is + * {@link JalviewUserColours } + * + */ + public JalviewUserColours getUserColourScheme() { + return userColourScheme; + } + + /** + * Sets the value of the userColourScheme property. + * + * @param value + * allowed object is + * {@link JalviewUserColours } + * + */ + public void setUserColourScheme(JalviewUserColours value) { + this.userColourScheme = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "annotationColours", + "hiddenColumns", + "calcIdParam" + }) + public static class Viewport { + + @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + @XmlElement(namespace = "www.jalview.org") + protected List hiddenColumns; + @XmlElement(namespace = "www.jalview.org") + protected List calcIdParam; + @XmlAttribute(name = "conservationSelected") + protected Boolean conservationSelected; + @XmlAttribute(name = "pidSelected") + protected Boolean pidSelected; + @XmlAttribute(name = "bgColour") + protected String bgColour; + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "showFullId") + protected Boolean showFullId; + @XmlAttribute(name = "rightAlignIds") + protected Boolean rightAlignIds; + @XmlAttribute(name = "showText") + protected Boolean showText; + @XmlAttribute(name = "showColourText") + protected Boolean showColourText; + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + @XmlAttribute(name = "showBoxes") + protected Boolean showBoxes; + @XmlAttribute(name = "wrapAlignment") + protected Boolean wrapAlignment; + @XmlAttribute(name = "renderGaps") + protected Boolean renderGaps; + @XmlAttribute(name = "showSequenceFeatures") + protected Boolean showSequenceFeatures; + @XmlAttribute(name = "showNPfeatureTooltip") + protected Boolean showNPfeatureTooltip; + @XmlAttribute(name = "showDbRefTooltip") + protected Boolean showDbRefTooltip; + @XmlAttribute(name = "followHighlight") + protected Boolean followHighlight; + @XmlAttribute(name = "followSelection") + protected Boolean followSelection; + @XmlAttribute(name = "showAnnotation") + protected Boolean showAnnotation; + @XmlAttribute(name = "centreColumnLabels") + protected Boolean centreColumnLabels; + @XmlAttribute(name = "showGroupConservation") + protected Boolean showGroupConservation; + @XmlAttribute(name = "showGroupConsensus") + protected Boolean showGroupConsensus; + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; + @XmlAttribute(name = "startRes") + protected Integer startRes; + @XmlAttribute(name = "startSeq") + protected Integer startSeq; + @XmlAttribute(name = "fontName") + protected String fontName; + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + @XmlAttribute(name = "scaleProteinAsCdna") + protected Boolean scaleProteinAsCdna; + @XmlAttribute(name = "viewName") + protected String viewName; + @XmlAttribute(name = "sequenceSetId") + protected String sequenceSetId; + @XmlAttribute(name = "gatheredViews") + protected Boolean gatheredViews; + @XmlAttribute(name = "textCol1") + protected Integer textCol1; + @XmlAttribute(name = "textCol2") + protected Integer textCol2; + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + @XmlAttribute(name = "complementId") + protected String complementId; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the annotationColours property. + * + * @return + * possible object is + * {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() { + return annotationColours; + } + + /** + * Sets the value of the annotationColours property. + * + * @param value + * allowed object is + * {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) { + this.annotationColours = value; + } + + /** + * Gets the value of the hiddenColumns property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the hiddenColumns property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getHiddenColumns().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.Viewport.HiddenColumns } + * + * + */ + public List getHiddenColumns() { + if (hiddenColumns == null) { + hiddenColumns = new ArrayList(); + } + return this.hiddenColumns; + } + + /** + * Gets the value of the calcIdParam property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the calcIdParam property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getCalcIdParam().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModelType.Viewport.CalcIdParam } + * + * + */ + public List getCalcIdParam() { + if (calcIdParam == null) { + calcIdParam = new ArrayList(); + } + return this.calcIdParam; + } + + /** + * Gets the value of the conservationSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isConservationSelected() { + return conservationSelected; + } + + /** + * Sets the value of the conservationSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setConservationSelected(Boolean value) { + this.conservationSelected = value; + } + + /** + * Gets the value of the pidSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isPidSelected() { + return pidSelected; + } + + /** + * Sets the value of the pidSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setPidSelected(Boolean value) { + this.pidSelected = value; + } + + /** + * Gets the value of the bgColour property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getBgColour() { + return bgColour; + } + + /** + * Sets the value of the bgColour property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setBgColour(String value) { + this.bgColour = value; + } + + /** + * Gets the value of the consThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getConsThreshold() { + return consThreshold; + } + + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setConsThreshold(Integer value) { + this.consThreshold = value; + } + + /** + * Gets the value of the pidThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getPidThreshold() { + return pidThreshold; + } + + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setPidThreshold(Integer value) { + this.pidThreshold = value; + } + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the showFullId property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowFullId() { + return showFullId; + } + + /** + * Sets the value of the showFullId property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowFullId(Boolean value) { + this.showFullId = value; + } + + /** + * Gets the value of the rightAlignIds property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isRightAlignIds() { + return rightAlignIds; + } + + /** + * Sets the value of the rightAlignIds property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setRightAlignIds(Boolean value) { + this.rightAlignIds = value; + } + + /** + * Gets the value of the showText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowText() { + return showText; + } + + /** + * Sets the value of the showText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowText(Boolean value) { + this.showText = value; + } + + /** + * Gets the value of the showColourText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowColourText() { + return showColourText; + } + + /** + * Sets the value of the showColourText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowColourText(Boolean value) { + this.showColourText = value; + } + + /** + * Gets the value of the showUnconserved property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowUnconserved() { + if (showUnconserved == null) { + return false; + } else { + return showUnconserved; + } + } + + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) { + this.showUnconserved = value; + } + + /** + * Gets the value of the showBoxes property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowBoxes() { + return showBoxes; + } + + /** + * Sets the value of the showBoxes property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowBoxes(Boolean value) { + this.showBoxes = value; + } + + /** + * Gets the value of the wrapAlignment property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isWrapAlignment() { + return wrapAlignment; + } + + /** + * Sets the value of the wrapAlignment property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setWrapAlignment(Boolean value) { + this.wrapAlignment = value; + } + + /** + * Gets the value of the renderGaps property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isRenderGaps() { + return renderGaps; + } + + /** + * Sets the value of the renderGaps property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setRenderGaps(Boolean value) { + this.renderGaps = value; + } + + /** + * Gets the value of the showSequenceFeatures property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowSequenceFeatures() { + return showSequenceFeatures; + } + + /** + * Sets the value of the showSequenceFeatures property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowSequenceFeatures(Boolean value) { + this.showSequenceFeatures = value; + } + + /** + * Gets the value of the showNPfeatureTooltip property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowNPfeatureTooltip() { + return showNPfeatureTooltip; + } + + /** + * Sets the value of the showNPfeatureTooltip property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowNPfeatureTooltip(Boolean value) { + this.showNPfeatureTooltip = value; + } + + /** + * Gets the value of the showDbRefTooltip property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowDbRefTooltip() { + return showDbRefTooltip; + } + + /** + * Sets the value of the showDbRefTooltip property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowDbRefTooltip(Boolean value) { + this.showDbRefTooltip = value; + } + + /** + * Gets the value of the followHighlight property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isFollowHighlight() { + if (followHighlight == null) { + return true; + } else { + return followHighlight; + } + } + + /** + * Sets the value of the followHighlight property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setFollowHighlight(Boolean value) { + this.followHighlight = value; + } + + /** + * Gets the value of the followSelection property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isFollowSelection() { + if (followSelection == null) { + return true; + } else { + return followSelection; + } + } + + /** + * Sets the value of the followSelection property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setFollowSelection(Boolean value) { + this.followSelection = value; + } + + /** + * Gets the value of the showAnnotation property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowAnnotation() { + return showAnnotation; + } + + /** + * Sets the value of the showAnnotation property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowAnnotation(Boolean value) { + this.showAnnotation = value; + } + + /** + * Gets the value of the centreColumnLabels property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isCentreColumnLabels() { + if (centreColumnLabels == null) { + return false; + } else { + return centreColumnLabels; + } + } + + /** + * Sets the value of the centreColumnLabels property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setCentreColumnLabels(Boolean value) { + this.centreColumnLabels = value; + } + + /** + * Gets the value of the showGroupConservation property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowGroupConservation() { + if (showGroupConservation == null) { + return false; + } else { + return showGroupConservation; + } + } + + /** + * Sets the value of the showGroupConservation property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowGroupConservation(Boolean value) { + this.showGroupConservation = value; + } + + /** + * Gets the value of the showGroupConsensus property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowGroupConsensus() { + if (showGroupConsensus == null) { + return false; + } else { + return showGroupConsensus; + } + } + + /** + * Sets the value of the showGroupConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowGroupConsensus(Boolean value) { + this.showGroupConsensus = value; + } + + /** + * Gets the value of the showConsensusHistogram property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowConsensusHistogram() { + if (showConsensusHistogram == null) { + return true; + } else { + return showConsensusHistogram; + } + } + + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) { + this.showConsensusHistogram = value; + } + + /** + * Gets the value of the showSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowSequenceLogo() { + if (showSequenceLogo == null) { + return false; + } else { + return showSequenceLogo; + } + } + + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) { + this.showSequenceLogo = value; + } + + /** + * Gets the value of the normaliseSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() { + if (normaliseSequenceLogo == null) { + return false; + } else { + return normaliseSequenceLogo; + } + } + + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) { + this.normaliseSequenceLogo = value; + } + + /** + * Gets the value of the ignoreGapsinConsensus property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() { + if (ignoreGapsinConsensus == null) { + return true; + } else { + return ignoreGapsinConsensus; + } + } + + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) { + this.ignoreGapsinConsensus = value; + } + + /** + * Gets the value of the startRes property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStartRes() { + return startRes; + } + + /** + * Sets the value of the startRes property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStartRes(Integer value) { + this.startRes = value; + } + + /** + * Gets the value of the startSeq property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStartSeq() { + return startSeq; + } + + /** + * Sets the value of the startSeq property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStartSeq(Integer value) { + this.startSeq = value; + } + + /** + * Gets the value of the fontName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFontName() { + return fontName; + } + + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFontName(String value) { + this.fontName = value; + } + + /** + * Gets the value of the fontSize property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontSize() { + return fontSize; + } + + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontSize(Integer value) { + this.fontSize = value; + } + + /** + * Gets the value of the fontStyle property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontStyle() { + return fontStyle; + } + + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontStyle(Integer value) { + this.fontStyle = value; + } + + /** + * Gets the value of the scaleProteinAsCdna property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isScaleProteinAsCdna() { + if (scaleProteinAsCdna == null) { + return true; + } else { + return scaleProteinAsCdna; + } + } + + /** + * Sets the value of the scaleProteinAsCdna property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setScaleProteinAsCdna(Boolean value) { + this.scaleProteinAsCdna = value; + } + + /** + * Gets the value of the viewName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewName() { + return viewName; + } + + /** + * Sets the value of the viewName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setViewName(String value) { + this.viewName = value; + } + + /** + * Gets the value of the sequenceSetId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSequenceSetId() { + return sequenceSetId; + } + + /** + * Sets the value of the sequenceSetId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSequenceSetId(String value) { + this.sequenceSetId = value; + } + + /** + * Gets the value of the gatheredViews property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isGatheredViews() { + return gatheredViews; + } + + /** + * Sets the value of the gatheredViews property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setGatheredViews(Boolean value) { + this.gatheredViews = value; + } + + /** + * Gets the value of the textCol1 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol1() { + return textCol1; + } + + /** + * Sets the value of the textCol1 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol1(Integer value) { + this.textCol1 = value; + } + + /** + * Gets the value of the textCol2 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol2() { + return textCol2; + } + + /** + * Sets the value of the textCol2 property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextCol2(Integer value) { + this.textCol2 = value; + } + + /** + * Gets the value of the textColThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextColThreshold() { + return textColThreshold; + } + + /** + * Sets the value of the textColThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setTextColThreshold(Integer value) { + this.textColThreshold = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the complementId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getComplementId() { + return complementId; + } + + /** + * Sets the value of the complementId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setComplementId(String value) { + this.complementId = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+         *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class CalcIdParam + extends WebServiceParameterSet + { + + @XmlAttribute(name = "calcId", required = true) + protected String calcId; + @XmlAttribute(name = "needsUpdate") + protected Boolean needsUpdate; + @XmlAttribute(name = "autoUpdate", required = true) + protected boolean autoUpdate; + + /** + * Gets the value of the calcId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getCalcId() { + return calcId; + } + + /** + * Sets the value of the calcId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setCalcId(String value) { + this.calcId = value; + } + + /** + * Gets the value of the needsUpdate property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isNeedsUpdate() { + if (needsUpdate == null) { + return false; + } else { + return needsUpdate; + } + } + + /** + * Sets the value of the needsUpdate property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setNeedsUpdate(Boolean value) { + this.needsUpdate = value; + } + + /** + * Gets the value of the autoUpdate property. + * + */ + public boolean isAutoUpdate() { + return autoUpdate; + } + + /** + * Sets the value of the autoUpdate property. + * + */ + public void setAutoUpdate(boolean value) { + this.autoUpdate = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class HiddenColumns { + + @XmlAttribute(name = "start") + protected Integer start; + @XmlAttribute(name = "end") + protected Integer end; + + /** + * Gets the value of the start property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStart(Integer value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setEnd(Integer value) { + this.end = value; + } + + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java new file mode 100644 index 0000000..b6f6b83 --- /dev/null +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@ -0,0 +1,612 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for JalviewUserColours complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="JalviewUserColours">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="colour" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                 </sequence>
+ *                 <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                 <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="filter" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ *                 </sequence>
+ *                 <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = { + "version", + "colour", + "filter" +}) +public class JalviewUserColours { + + @XmlElement(name = "Version", namespace = "") + protected String version; + @XmlElement(namespace = "") + protected List colour; + @XmlElement(namespace = "") + protected List filter; + @XmlAttribute(name = "schemeName") + protected String schemeName; + + /** + * Gets the value of the version property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getVersion() { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setVersion(String value) { + this.version = value; + } + + /** + * Gets the value of the colour property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the colour property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getColour().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewUserColours.Colour } + * + * + */ + public List getColour() { + if (colour == null) { + colour = new ArrayList(); + } + return this.colour; + } + + /** + * Gets the value of the filter property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the filter property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getFilter().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewUserColours.Filter } + * + * + */ + public List getFilter() { + if (filter == null) { + filter = new ArrayList(); + } + return this.filter; + } + + /** + * Gets the value of the schemeName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSchemeName() { + return schemeName; + } + + /** + * Sets the value of the schemeName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSchemeName(String value) { + this.schemeName = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "attributeName" + }) + public static class Colour { + + @XmlElement(namespace = "") + protected List attributeName; + @XmlAttribute(name = "Name") + protected String name; + @XmlAttribute(name = "RGB", required = true) + protected String rgb; + @XmlAttribute(name = "minRGB") + protected String minRGB; + @XmlAttribute(name = "noValueColour") + protected NoValueColour noValueColour; + @XmlAttribute(name = "threshType") + protected ThresholdType threshType; + @XmlAttribute(name = "threshold") + protected Float threshold; + @XmlAttribute(name = "max") + protected Float max; + @XmlAttribute(name = "min") + protected Float min; + @XmlAttribute(name = "colourByLabel") + protected Boolean colourByLabel; + @XmlAttribute(name = "autoScale") + protected Boolean autoScale; + + /** + * Gets the value of the attributeName property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the attributeName property. + * + *

+ * For example, to add a new item, do as follows: + * 

+         *    getAttributeName().add(newItem);
+         *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getAttributeName() { + if (attributeName == null) { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the rgb property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getRGB() { + return rgb; + } + + /** + * Sets the value of the rgb property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setRGB(String value) { + this.rgb = value; + } + + /** + * Gets the value of the minRGB property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getMinRGB() { + return minRGB; + } + + /** + * Sets the value of the minRGB property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setMinRGB(String value) { + this.minRGB = value; + } + + /** + * Gets the value of the noValueColour property. + * + * @return + * possible object is + * {@link NoValueColour } + * + */ + public NoValueColour getNoValueColour() { + if (noValueColour == null) { + return NoValueColour.MIN; + } else { + return noValueColour; + } + } + + /** + * Sets the value of the noValueColour property. + * + * @param value + * allowed object is + * {@link NoValueColour } + * + */ + public void setNoValueColour(NoValueColour value) { + this.noValueColour = value; + } + + /** + * Gets the value of the threshType property. + * + * @return + * possible object is + * {@link ThresholdType } + * + */ + public ThresholdType getThreshType() { + return threshType; + } + + /** + * Sets the value of the threshType property. + * + * @param value + * allowed object is + * {@link ThresholdType } + * + */ + public void setThreshType(ThresholdType value) { + this.threshType = value; + } + + /** + * Gets the value of the threshold property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getThreshold() { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setThreshold(Float value) { + this.threshold = value; + } + + /** + * Gets the value of the max property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getMax() { + return max; + } + + /** + * Sets the value of the max property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setMax(Float value) { + this.max = value; + } + + /** + * Gets the value of the min property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getMin() { + return min; + } + + /** + * Sets the value of the min property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setMin(Float value) { + this.min = value; + } + + /** + * Gets the value of the colourByLabel property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isColourByLabel() { + return colourByLabel; + } + + /** + * Sets the value of the colourByLabel property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setColourByLabel(Boolean value) { + this.colourByLabel = value; + } + + /** + * Gets the value of the autoScale property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isAutoScale() { + return autoScale; + } + + /** + * Sets the value of the autoScale property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setAutoScale(Boolean value) { + this.autoScale = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+     *       </sequence>
+     *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "matcherSet" + }) + public static class Filter { + + @XmlElement(namespace = "", required = true) + protected FeatureMatcherSet matcherSet; + @XmlAttribute(name = "featureType", required = true) + protected String featureType; + + /** + * Gets the value of the matcherSet property. + * + * @return + * possible object is + * {@link FeatureMatcherSet } + * + */ + public FeatureMatcherSet getMatcherSet() { + return matcherSet; + } + + /** + * Sets the value of the matcherSet property. + * + * @param value + * allowed object is + * {@link FeatureMatcherSet } + * + */ + public void setMatcherSet(FeatureMatcherSet value) { + this.matcherSet = value; + } + + /** + * Gets the value of the featureType property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFeatureType() { + return featureType; + } + + /** + * Sets the value of the featureType property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFeatureType(String value) { + this.featureType = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java new file mode 100644 index 0000000..8e5f553 --- /dev/null +++ b/src/jalview/xml/binding/jalview/MapListType.java @@ -0,0 +1,315 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.math.BigInteger; +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlSchemaType; +import javax.xml.bind.annotation.XmlSeeAlso; +import javax.xml.bind.annotation.XmlType; + + +/** + * + * This effectively represents a java.util.MapList object + * + * + *

Java class for mapListType complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="mapListType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *       <attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "mapListType", propOrder = { + "mapListFrom", + "mapListTo" +}) +@XmlSeeAlso({ + Mapping.class +}) +public class MapListType { + + protected List mapListFrom; + protected List mapListTo; + @XmlAttribute(name = "mapFromUnit", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger mapFromUnit; + @XmlAttribute(name = "mapToUnit", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger mapToUnit; + + /** + * Gets the value of the mapListFrom property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the mapListFrom property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getMapListFrom().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link MapListType.MapListFrom } + * + * + */ + public List getMapListFrom() { + if (mapListFrom == null) { + mapListFrom = new ArrayList(); + } + return this.mapListFrom; + } + + /** + * Gets the value of the mapListTo property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the mapListTo property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getMapListTo().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link MapListType.MapListTo } + * + * + */ + public List getMapListTo() { + if (mapListTo == null) { + mapListTo = new ArrayList(); + } + return this.mapListTo; + } + + /** + * Gets the value of the mapFromUnit property. + * + * @return + * possible object is + * {@link BigInteger } + * + */ + public BigInteger getMapFromUnit() { + return mapFromUnit; + } + + /** + * Sets the value of the mapFromUnit property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setMapFromUnit(BigInteger value) { + this.mapFromUnit = value; + } + + /** + * Gets the value of the mapToUnit property. + * + * @return + * possible object is + * {@link BigInteger } + * + */ + public BigInteger getMapToUnit() { + return mapToUnit; + } + + /** + * Sets the value of the mapToUnit property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setMapToUnit(BigInteger value) { + this.mapToUnit = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class MapListFrom { + + @XmlAttribute(name = "start", required = true) + protected int start; + @XmlAttribute(name = "end", required = true) + protected int end; + + /** + * Gets the value of the start property. + * + */ + public int getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + */ + public void setStart(int value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + */ + public int getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + */ + public void setEnd(int value) { + this.end = value; + } + + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class MapListTo { + + @XmlAttribute(name = "start", required = true) + protected int start; + @XmlAttribute(name = "end", required = true) + protected int end; + + /** + * Gets the value of the start property. + * + */ + public int getStart() { + return start; + } + + /** + * Sets the value of the start property. + * + */ + public void setStart(int value) { + this.start = value; + } + + /** + * Gets the value of the end property. + * + */ + public int getEnd() { + return end; + } + + /** + * Sets the value of the end property. + * + */ + public void setEnd(int value) { + this.end = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java new file mode 100644 index 0000000..da64ed2 --- /dev/null +++ b/src/jalview/xml/binding/jalview/Mapping.java @@ -0,0 +1,113 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + + +/** + * + * Represent the jalview.datamodel.Mapping object - it also provides + * a way of storing sequences that are mapped 'to' without adding them + * to the sequence set (which will mean they are then added to the alignment too). + * + * + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType>
+ *   <complexContent>
+ *     <extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
+ *       <sequence>
+ *         <choice minOccurs="0">
+ *           <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
+ *           <element name="dseqFor">
+ *             <simpleType>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               </restriction>
+ *             </simpleType>
+ *           </element>
+ *         </choice>
+ *       </sequence>
+ *     </extension>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = { + "sequence", + "dseqFor" +}) +@XmlRootElement(name = "Mapping") +public class Mapping + extends MapListType +{ + + @XmlElement(name = "Sequence") + protected Sequence sequence; + protected String dseqFor; + + /** + * Gets the value of the sequence property. + * + * @return + * possible object is + * {@link Sequence } + * + */ + public Sequence getSequence() { + return sequence; + } + + /** + * Sets the value of the sequence property. + * + * @param value + * allowed object is + * {@link Sequence } + * + */ + public void setSequence(Sequence value) { + this.sequence = value; + } + + /** + * Gets the value of the dseqFor property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDseqFor() { + return dseqFor; + } + + /** + * Sets the value of the dseqFor property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDseqFor(String value) { + this.dseqFor = value; + } + +} diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java new file mode 100644 index 0000000..9bce64b --- /dev/null +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@ -0,0 +1,61 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.annotation.XmlEnum; +import javax.xml.bind.annotation.XmlEnumValue; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for NoValueColour. + * + *

The following schema fragment specifies the expected content contained within this class. + *

+ * 

+ * <simpleType name="NoValueColour">
+ *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     <enumeration value="None"/>
+ *     <enumeration value="Min"/>
+ *     <enumeration value="Max"/>
+ *   </restriction>
+ * </simpleType>
+ *
+ * + */ +@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours") +@XmlEnum +public enum NoValueColour { + + @XmlEnumValue("None") + NONE("None"), + @XmlEnumValue("Min") + MIN("Min"), + @XmlEnumValue("Max") + MAX("Max"); + private final String value; + + NoValueColour(String v) { + value = v; + } + + public String value() { + return value; + } + + public static NoValueColour fromValue(String v) { + for (NoValueColour c: NoValueColour.values()) { + if (c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); + } + +} diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java new file mode 100644 index 0000000..3b9cae3 --- /dev/null +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@ -0,0 +1,404 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.JAXBElement; +import javax.xml.bind.annotation.XmlElementDecl; +import javax.xml.bind.annotation.XmlRegistry; +import javax.xml.namespace.QName; + + +/** + * This object contains factory methods for each + * Java content interface and Java element interface + * generated in the jalview.xml.binding.jalview package. + *

An ObjectFactory allows you to programatically + * construct new instances of the Java representation + * for XML content. The Java representation of XML + * content can consist of schema derived interfaces + * and classes representing the binding of schema + * type definitions, element declarations and model + * groups. Factory methods for each of these are + * provided in this class. + * + */ +@XmlRegistry +public class ObjectFactory { + + private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel"); + + /** + * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview + * + */ + public ObjectFactory() { + } + + /** + * Create an instance of {@link AlcodonFrame } + * + */ + public AlcodonFrame createAlcodonFrame() { + return new AlcodonFrame(); + } + + /** + * Create an instance of {@link MapListType } + * + */ + public MapListType createMapListType() { + return new MapListType(); + } + + /** + * Create an instance of {@link Sequence } + * + */ + public Sequence createSequence() { + return new Sequence(); + } + + /** + * Create an instance of {@link Annotation } + * + */ + public Annotation createAnnotation() { + return new Annotation(); + } + + /** + * Create an instance of {@link SequenceSet } + * + */ + public SequenceSet createSequenceSet() { + return new SequenceSet(); + } + + /** + * Create an instance of {@link FeatureMatcherSet } + * + */ + public FeatureMatcherSet createFeatureMatcherSet() { + return new FeatureMatcherSet(); + } + + /** + * Create an instance of {@link JalviewUserColours } + * + */ + public JalviewUserColours createJalviewUserColours() { + return new JalviewUserColours(); + } + + /** + * Create an instance of {@link Pdbentry } + * + */ + public Pdbentry createPdbentry() { + return new Pdbentry(); + } + + /** + * Create an instance of {@link Feature } + * + */ + public Feature createFeature() { + return new Feature(); + } + + /** + * Create an instance of {@link JalviewModel } + * + */ + public JalviewModel createJalviewModel() { + return new JalviewModel(); + } + + /** + * Create an instance of {@link JalviewModel.FeatureSettings } + * + */ + public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() { + return new JalviewModel.FeatureSettings(); + } + + /** + * Create an instance of {@link JalviewModel.Viewport } + * + */ + public JalviewModel.Viewport createJalviewModelViewport() { + return new JalviewModel.Viewport(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq } + * + */ + public JalviewModel.JSeq createJalviewModelJSeq() { + return new JalviewModel.JSeq(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq.RnaViewer } + * + */ + public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() { + return new JalviewModel.JSeq.RnaViewer(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq.Pdbids } + * + */ + public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() { + return new JalviewModel.JSeq.Pdbids(); + } + + /** + * Create an instance of {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme createAnnotationColourScheme() { + return new AnnotationColourScheme(); + } + + /** + * Create an instance of {@link AlcodonFrame.Alcodon } + * + */ + public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() { + return new AlcodonFrame.Alcodon(); + } + + /** + * Create an instance of {@link AlcodonFrame.AlcodMap } + * + */ + public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() { + return new AlcodonFrame.AlcodMap(); + } + + /** + * Create an instance of {@link AnnotationElement } + * + */ + public AnnotationElement createAnnotationElement() { + return new AnnotationElement(); + } + + /** + * Create an instance of {@link Mapping } + * + */ + public Mapping createMapping() { + return new Mapping(); + } + + /** + * Create an instance of {@link MapListType.MapListFrom } + * + */ + public MapListType.MapListFrom createMapListTypeMapListFrom() { + return new MapListType.MapListFrom(); + } + + /** + * Create an instance of {@link MapListType.MapListTo } + * + */ + public MapListType.MapListTo createMapListTypeMapListTo() { + return new MapListType.MapListTo(); + } + + /** + * Create an instance of {@link SequenceType } + * + */ + public SequenceType createSequenceType() { + return new SequenceType(); + } + + /** + * Create an instance of {@link Sequence.DBRef } + * + */ + public Sequence.DBRef createSequenceDBRef() { + return new Sequence.DBRef(); + } + + /** + * Create an instance of {@link Annotation.ThresholdLine } + * + */ + public Annotation.ThresholdLine createAnnotationThresholdLine() { + return new Annotation.ThresholdLine(); + } + + /** + * Create an instance of {@link Annotation.Property } + * + */ + public Annotation.Property createAnnotationProperty() { + return new Annotation.Property(); + } + + /** + * Create an instance of {@link SequenceSet.SequenceSetProperties } + * + */ + public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() { + return new SequenceSet.SequenceSetProperties(); + } + + /** + * Create an instance of {@link VAMSAS } + * + */ + public VAMSAS createVAMSAS() { + return new VAMSAS(); + } + + /** + * Create an instance of {@link FeatureMatcher } + * + */ + public FeatureMatcher createFeatureMatcher() { + return new FeatureMatcher(); + } + + /** + * Create an instance of {@link WebServiceParameterSet } + * + */ + public WebServiceParameterSet createWebServiceParameterSet() { + return new WebServiceParameterSet(); + } + + /** + * Create an instance of {@link FeatureMatcherSet.CompoundMatcher } + * + */ + public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() { + return new FeatureMatcherSet.CompoundMatcher(); + } + + /** + * Create an instance of {@link JalviewUserColours.Colour } + * + */ + public JalviewUserColours.Colour createJalviewUserColoursColour() { + return new JalviewUserColours.Colour(); + } + + /** + * Create an instance of {@link JalviewUserColours.Filter } + * + */ + public JalviewUserColours.Filter createJalviewUserColoursFilter() { + return new JalviewUserColours.Filter(); + } + + /** + * Create an instance of {@link Pdbentry.Property } + * + */ + public Pdbentry.Property createPdbentryProperty() { + return new Pdbentry.Property(); + } + + /** + * Create an instance of {@link Feature.OtherData } + * + */ + public Feature.OtherData createFeatureOtherData() { + return new Feature.OtherData(); + } + + /** + * Create an instance of {@link JalviewModel.JGroup } + * + */ + public JalviewModel.JGroup createJalviewModelJGroup() { + return new JalviewModel.JGroup(); + } + + /** + * Create an instance of {@link JalviewModel.UserColours } + * + */ + public JalviewModel.UserColours createJalviewModelUserColours() { + return new JalviewModel.UserColours(); + } + + /** + * Create an instance of {@link JalviewModel.Tree } + * + */ + public JalviewModel.Tree createJalviewModelTree() { + return new JalviewModel.Tree(); + } + + /** + * Create an instance of {@link JalviewModel.FeatureSettings.Setting } + * + */ + public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() { + return new JalviewModel.FeatureSettings.Setting(); + } + + /** + * Create an instance of {@link JalviewModel.FeatureSettings.Group } + * + */ + public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() { + return new JalviewModel.FeatureSettings.Group(); + } + + /** + * Create an instance of {@link JalviewModel.Viewport.HiddenColumns } + * + */ + public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() { + return new JalviewModel.Viewport.HiddenColumns(); + } + + /** + * Create an instance of {@link JalviewModel.Viewport.CalcIdParam } + * + */ + public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() { + return new JalviewModel.Viewport.CalcIdParam(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } + * + */ + public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() { + return new JalviewModel.JSeq.RnaViewer.SecondaryStructure(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState } + * + */ + public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() { + return new JalviewModel.JSeq.Pdbids.StructureState(); + } + + /** + * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}} + * + */ + @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel") + public JAXBElement createJalviewModel(JalviewModel value) { + return new JAXBElement(_JalviewModel_QNAME, JalviewModel.class, null, value); + } + +} diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java new file mode 100644 index 0000000..acb0f78 --- /dev/null +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@ -0,0 +1,247 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlSeeAlso; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for pdbentry complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="pdbentry">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence maxOccurs="unbounded" minOccurs="0">
+ *         <element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = { + "property" +}) +@XmlSeeAlso({ + jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class +}) +public class Pdbentry { + + protected List property; + @XmlAttribute(name = "id", required = true) + protected String id; + @XmlAttribute(name = "type") + protected String type; + @XmlAttribute(name = "file") + protected String file; + + /** + * Gets the value of the property property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the property property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getProperty().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Pdbentry.Property } + * + * + */ + public List getProperty() { + if (property == null) { + property = new ArrayList(); + } + return this.property; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the type property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getType() { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setType(String value) { + this.type = value; + } + + /** + * Gets the value of the file property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFile() { + return file; + } + + /** + * Sets the value of the file property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFile(String value) { + this.file = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Property { + + @XmlAttribute(name = "name", required = true) + protected String name; + @XmlAttribute(name = "value", required = true) + protected String value; + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java new file mode 100644 index 0000000..d5e1d33 --- /dev/null +++ b/src/jalview/xml/binding/jalview/Sequence.java @@ -0,0 +1,257 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType>
+ *   <complexContent>
+ *     <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
+ *       <sequence>
+ *         <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ *                 </sequence>
+ *                 <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </extension>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = { + "dbRef" +}) +@XmlRootElement(name = "Sequence") +public class Sequence + extends SequenceType +{ + + @XmlElement(name = "DBRef") + protected List dbRef; + @XmlAttribute(name = "dsseqid") + protected String dsseqid; + + /** + * Gets the value of the dbRef property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the dbRef property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getDBRef().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Sequence.DBRef } + * + * + */ + public List getDBRef() { + if (dbRef == null) { + dbRef = new ArrayList(); + } + return this.dbRef; + } + + /** + * Gets the value of the dsseqid property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDsseqid() { + return dsseqid; + } + + /** + * Sets the value of the dsseqid property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDsseqid(String value) { + this.dsseqid = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "mapping" + }) + public static class DBRef { + + @XmlElement(name = "Mapping") + protected Mapping mapping; + @XmlAttribute(name = "source") + protected String source; + @XmlAttribute(name = "version") + protected String version; + @XmlAttribute(name = "accessionId") + protected String accessionId; + + /** + * Gets the value of the mapping property. + * + * @return + * possible object is + * {@link Mapping } + * + */ + public Mapping getMapping() { + return mapping; + } + + /** + * Sets the value of the mapping property. + * + * @param value + * allowed object is + * {@link Mapping } + * + */ + public void setMapping(Mapping value) { + this.mapping = value; + } + + /** + * Gets the value of the source property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSource() { + return source; + } + + /** + * Sets the value of the source property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSource(String value) { + this.source = value; + } + + /** + * Gets the value of the version property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getVersion() { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setVersion(String value) { + this.version = value; + } + + /** + * Gets the value of the accessionId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getAccessionId() { + return accessionId; + } + + /** + * Sets the value of the accessionId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setAccessionId(String value) { + this.accessionId = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java new file mode 100644 index 0000000..1ac96eb --- /dev/null +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -0,0 +1,318 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlRootElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "", propOrder = { + "sequence", + "annotation", + "sequenceSetProperties", + "alcodonFrame" +}) +@XmlRootElement(name = "SequenceSet") +public class SequenceSet { + + @XmlElement(name = "Sequence") + protected List sequence; + @XmlElement(name = "Annotation") + protected List annotation; + protected List sequenceSetProperties; + @XmlElement(name = "AlcodonFrame") + protected List alcodonFrame; + @XmlAttribute(name = "gapChar", required = true) + protected String gapChar; + @XmlAttribute(name = "datasetId") + protected String datasetId; + + /** + * Gets the value of the sequence property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the sequence property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getSequence().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Sequence } + * + * + */ + public List getSequence() { + if (sequence == null) { + sequence = new ArrayList(); + } + return this.sequence; + } + + /** + * Gets the value of the annotation property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the annotation property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAnnotation().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link Annotation } + * + * + */ + public List getAnnotation() { + if (annotation == null) { + annotation = new ArrayList(); + } + return this.annotation; + } + + /** + * Gets the value of the sequenceSetProperties property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the sequenceSetProperties property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getSequenceSetProperties().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link SequenceSet.SequenceSetProperties } + * + * + */ + public List getSequenceSetProperties() { + if (sequenceSetProperties == null) { + sequenceSetProperties = new ArrayList(); + } + return this.sequenceSetProperties; + } + + /** + * Gets the value of the alcodonFrame property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the alcodonFrame property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getAlcodonFrame().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame } + * + * + */ + public List getAlcodonFrame() { + if (alcodonFrame == null) { + alcodonFrame = new ArrayList(); + } + return this.alcodonFrame; + } + + /** + * Gets the value of the gapChar property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getGapChar() { + return gapChar; + } + + /** + * Sets the value of the gapChar property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setGapChar(String value) { + this.gapChar = value; + } + + /** + * Gets the value of the datasetId property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDatasetId() { + return datasetId; + } + + /** + * Sets the value of the datasetId property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDatasetId(String value) { + this.datasetId = value; + } + + + /** + *

Java class for anonymous complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SequenceSetProperties { + + @XmlAttribute(name = "key") + protected String key; + @XmlAttribute(name = "value") + protected String value; + + /** + * Gets the value of the key property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getKey() { + return key; + } + + /** + * Sets the value of the key property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setKey(String value) { + this.key = value; + } + + /** + * Gets the value of the value property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getValue() { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setValue(String value) { + this.value = value; + } + + } + +} diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java new file mode 100644 index 0000000..d59b714 --- /dev/null +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@ -0,0 +1,153 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlSeeAlso; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for SequenceType complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="SequenceType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "SequenceType", propOrder = { + "sequence", + "name" +}) +@XmlSeeAlso({ + Sequence.class +}) +public class SequenceType { + + protected String sequence; + protected String name; + @XmlAttribute(name = "id") + protected String id; + @XmlAttribute(name = "description") + protected String description; + + /** + * Gets the value of the sequence property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getSequence() { + return sequence; + } + + /** + * Sets the value of the sequence property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setSequence(String value) { + this.sequence = value; + } + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } + + /** + * Gets the value of the description property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDescription() { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDescription(String value) { + this.description = value; + } + +} diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java new file mode 100644 index 0000000..a987524 --- /dev/null +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@ -0,0 +1,47 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import javax.xml.bind.annotation.XmlEnum; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for ThresholdType. + * + *

The following schema fragment specifies the expected content contained within this class. + *

+ * 

+ * <simpleType name="ThresholdType">
+ *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     <enumeration value="NONE"/>
+ *     <enumeration value="ABOVE"/>
+ *     <enumeration value="BELOW"/>
+ *   </restriction>
+ * </simpleType>
+ *
+ * + */ +@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours") +@XmlEnum +public enum ThresholdType { + + NONE, + ABOVE, + BELOW; + + public String value() { + return name(); + } + + public static ThresholdType fromValue(String v) { + return valueOf(v); + } + +} diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java new file mode 100644 index 0000000..bcefa96 --- /dev/null +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@ -0,0 +1,109 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for VAMSAS complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="VAMSAS">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "VAMSAS", propOrder = { + "tree", + "sequenceSet" +}) +public class VAMSAS { + + @XmlElement(name = "Tree") + protected List tree; + @XmlElement(name = "SequenceSet") + protected List sequenceSet; + + /** + * Gets the value of the tree property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the tree property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getTree().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getTree() { + if (tree == null) { + tree = new ArrayList(); + } + return this.tree; + } + + /** + * Gets the value of the sequenceSet property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the sequenceSet property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getSequenceSet().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link SequenceSet } + * + * + */ + public List getSequenceSet() { + if (sequenceSet == null) { + sequenceSet = new ArrayList(); + } + return this.sequenceSet; + } + +} diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java new file mode 100644 index 0000000..8bd69a1 --- /dev/null +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@ -0,0 +1,194 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + + +package jalview.xml.binding.jalview; + +import java.util.ArrayList; +import java.util.List; +import javax.xml.bind.annotation.XmlAccessType; +import javax.xml.bind.annotation.XmlAccessorType; +import javax.xml.bind.annotation.XmlAttribute; +import javax.xml.bind.annotation.XmlElement; +import javax.xml.bind.annotation.XmlSchemaType; +import javax.xml.bind.annotation.XmlSeeAlso; +import javax.xml.bind.annotation.XmlType; + + +/** + *

Java class for WebServiceParameterSet complex type. + * + *

The following schema fragment specifies the expected content contained within this class. + * + * 

+ * <complexType name="WebServiceParameterSet">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         <element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
+ *         <element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       </sequence>
+ *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
+ * + * + */ +@XmlAccessorType(XmlAccessType.FIELD) +@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = { + "version", + "description", + "serviceURL", + "parameters" +}) +@XmlSeeAlso({ + jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class +}) +public class WebServiceParameterSet { + + @XmlElement(name = "Version", namespace = "") + protected String version; + @XmlElement(namespace = "") + protected String description; + @XmlElement(namespace = "", required = true) + @XmlSchemaType(name = "anyURI") + protected List serviceURL; + @XmlElement(namespace = "", required = true) + protected String parameters; + @XmlAttribute(name = "name", required = true) + protected String name; + + /** + * Gets the value of the version property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getVersion() { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setVersion(String value) { + this.version = value; + } + + /** + * Gets the value of the description property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDescription() { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDescription(String value) { + this.description = value; + } + + /** + * Gets the value of the serviceURL property. + * + *

+ * This accessor method returns a reference to the live list, + * not a snapshot. Therefore any modification you make to the + * returned list will be present inside the JAXB object. + * This is why there is not a set method for the serviceURL property. + * + *

+ * For example, to add a new item, do as follows: + * 

+     *    getServiceURL().add(newItem);
+     *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + * + * + */ + public List getServiceURL() { + if (serviceURL == null) { + serviceURL = new ArrayList(); + } + return this.serviceURL; + } + + /** + * Gets the value of the parameters property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getParameters() { + return parameters; + } + + /** + * Sets the value of the parameters property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setParameters(String value) { + this.parameters = value; + } + + /** + * Gets the value of the name property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getName() { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setName(String value) { + this.name = value; + } + +} diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java new file mode 100644 index 0000000..de1dd05 --- /dev/null +++ b/src/jalview/xml/binding/jalview/package-info.java @@ -0,0 +1,9 @@ +// +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb +// Any modifications to this file will be lost upon recompilation of the source schema. +// Generated on: 2018.09.18 at 02:23:07 PM BST +// + +@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) +package jalview.xml.binding.jalview; -- 1.7.10.2