From e8ca868ba1549b359ab12585147eb4c66cbe2a53 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 25 Jul 2024 14:48:25 +0100 Subject: [PATCH] JAL-4392 JAL-3987 store and restore consensus secondary structure row visualisation and shading settings --- schemas/jalview.xsd | 65 +- src/jalview/project/Jalview2XML.java | 32 +- src/jalview/xml/binding/jalview/AlcodonFrame.java | 516 +- src/jalview/xml/binding/jalview/Annotation.java | 1506 +-- .../binding/jalview/AnnotationColourScheme.java | 464 +- .../xml/binding/jalview/AnnotationElement.java | 355 +- src/jalview/xml/binding/jalview/DoubleMatrix.java | 320 +- src/jalview/xml/binding/jalview/DoubleVector.java | 98 +- src/jalview/xml/binding/jalview/Feature.java | 608 +- .../xml/binding/jalview/FeatureMatcher.java | 258 +- .../xml/binding/jalview/FeatureMatcherSet.java | 294 +- src/jalview/xml/binding/jalview/FilterBy.java | 98 +- src/jalview/xml/binding/jalview/JalviewModel.java |13625 ++++++++++---------- .../xml/binding/jalview/JalviewUserColours.java | 1060 +- src/jalview/xml/binding/jalview/MapListType.java | 545 +- .../xml/binding/jalview/MapOnAMatrixType.java | 262 +- src/jalview/xml/binding/jalview/Mapping.java | 209 +- src/jalview/xml/binding/jalview/MatrixType.java | 600 +- src/jalview/xml/binding/jalview/NoValueColour.java | 98 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 1086 +- src/jalview/xml/binding/jalview/PcaDataType.java | 192 +- src/jalview/xml/binding/jalview/Pdbentry.java | 387 +- src/jalview/xml/binding/jalview/Property.java | 127 +- src/jalview/xml/binding/jalview/Sequence.java | 571 +- src/jalview/xml/binding/jalview/SequenceSet.java | 593 +- src/jalview/xml/binding/jalview/SequenceType.java | 253 +- src/jalview/xml/binding/jalview/ThresholdType.java | 49 +- src/jalview/xml/binding/jalview/VAMSAS.java | 157 +- .../binding/jalview/WebServiceParameterSet.java | 376 +- src/jalview/xml/binding/jalview/package-info.java | 8 +- 30 files changed, 12979 insertions(+), 11833 deletions(-) diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd index c5d35fb..c80eab6 100755 --- a/schemas/jalview.xsd +++ b/schemas/jalview.xsd @@ -360,13 +360,13 @@ + + - - @@ -376,14 +376,7 @@ - - - - + @@ -453,13 +446,11 @@ + - - - - + @@ -483,17 +474,14 @@ + use="optional" default="false"> + whether a new group has conservation displayed by default - - - - + use="optional" default="false" > + whether a new group has consensus displayed by default + + whether a new group has secondary structure consensus displayed by default @@ -729,6 +717,35 @@ --> + + + + base attributes for alignment or group shading + + + + + Conservation shading increment + + + + Percent Identity Threshold + + + Secondary structure consensus shading - since 2.11.4 + + + Secondary structure consensus increment + + + + + + diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index ed57fe7..3af8e76 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -1484,7 +1484,7 @@ public class Jalview2XML List groupSecondaryStructureSources = sg.getSecondaryStructureSources(); if(groupSecondaryStructureSources != null && groupSecondaryStructureSources.size()>0) { - jGroup.setSecondaryStructureSources(groupSecondaryStructureSources); + jGroup.getSecStrProvider().addAll(groupSecondaryStructureSources); } ColourSchemeI colourScheme = sg.getColourScheme(); @@ -1526,10 +1526,10 @@ public class Jalview2XML if(groupColourScheme.isConsensusSecondaryStructureColouring()) { - jGroup.setConsensusSecondaryStructureColouring( + jGroup.setSecstrSelected( groupColourScheme.isConsensusSecondaryStructureColouring()); - jGroup.setConsensusSecondaryStructureThreshold( - groupColourScheme.getConsensusSecondaryStructureThreshold()); + jGroup.setSecstrThreshold(groupColourScheme + .getConsensusSecondaryStructureThreshold()); } } @@ -1654,15 +1654,13 @@ public class Jalview2XML if(vcs.isConsensusSecondaryStructureColouring()) { - view.setConsensusSecondaryStructureThreshold( - vcs.getConsensusSecondaryStructureThreshold()); + view.setSecstrThreshold(vcs.getConsensusSecondaryStructureThreshold()); } } view.setConservationSelected(av.getConservationSelected()); view.setPidSelected(av.getAbovePIDThreshold()); - view.setByConsensusSecondaryStructureSelected( - av.getByConsensusSecondaryStructureSelected()); + view.setSecstrSelected(av.getByConsensusSecondaryStructureSelected()); view.setCharHeight(av.getCharHeight()); view.setCharWidth(av.getCharWidth()); final Font font = av.getFont(); @@ -1691,7 +1689,7 @@ public class Jalview2XML view.setShowSequenceLogo(av.isShowSequenceLogo()); view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo()); view.setShowGroupConsensus(av.isShowGroupConsensus()); - view.setShowGroupSSConsensus(av.isShowGroupSSConsensus()); + view.setShowGroupSecStrConsensus(av.isShowGroupSSConsensus()); view.setShowGroupConservation(av.isShowGroupConservation()); view.setShowNPfeatureTooltip(av.isShowNPFeats()); view.setShowDbRefTooltip(av.isShowDBRefs()); @@ -4271,11 +4269,11 @@ public class Jalview2XML safeInt(jGroup.getStart()), safeInt(jGroup.getEnd())); sg.getGroupColourScheme().setThreshold(pidThreshold, true); sg.getGroupColourScheme().setConsensusSecondaryStructureColouring( - safeBoolean(jGroup.isConsensusSecondaryStructureColouring())); + safeBoolean(jGroup.isSecstrSelected())); sg.getGroupColourScheme() .setConservationInc(safeInt(jGroup.getConsThreshold())); sg.getGroupColourScheme().setConsensusSecondaryStructureThreshold( - safeInt(jGroup.getConsensusSecondaryStructureThreshold())); + safeInt(jGroup.getSecstrThreshold())); sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour()))); @@ -4288,7 +4286,7 @@ public class Jalview2XML sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus()); - sg.setSecondaryStructureSources(jGroup.getSecondaryStructureSources()); + sg.setSecondaryStructureSources(jGroup.getSecStrProvider()); if (jGroup.getConsThreshold() != null && jGroup.getConsThreshold().intValue() != 0) { @@ -5251,9 +5249,9 @@ public class Jalview2XML safeBoolean(view.isConservationSelected())); viewport.setIncrement(safeInt(view.getConsThreshold())); viewport.setByConsensusSecondaryStructureSelected( - safeBoolean(view.isByConsensusSecondaryStructureSelected())); + safeBoolean(view.isSecstrSelected())); viewport.setConsensusSecondaryStructureThreshold( - safeInt(view.getConsensusSecondaryStructureThreshold())); + safeInt(view.getSecstrThreshold())); viewport.setShowJVSuffix(safeBoolean(view.isShowFullId())); viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds())); viewport.setFont( @@ -5353,11 +5351,11 @@ public class Jalview2XML viewport.getResidueShading() .setConservationInc(safeInt(view.getConsThreshold())); } - if (safeBoolean(view.isByConsensusSecondaryStructureSelected()) && cs != null) + if (safeBoolean(view.isSecstrSelected()) && cs != null) { viewport.getResidueShading() .setConsensusSecondaryStructureThreshold( - safeInt(view.getConsensusSecondaryStructureThreshold())); + safeInt(view.getSecstrThreshold())); } af.changeColour(cs); viewport.setColourAppliesToAllGroups(true); @@ -5375,7 +5373,7 @@ public class Jalview2XML viewport.setShowDBRefs(safeBoolean(view.isShowDbRefTooltip())); viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip())); viewport.setShowGroupConsensus(view.isShowGroupConsensus()); - viewport.setShowGroupSSConsensus(view.isShowGroupSSConsensus()); + viewport.setShowGroupSSConsensus(view.isShowGroupSecStrConsensus()); viewport.setShowGroupConservation(view.isShowGroupConservation()); viewport.setShowComplementFeatures(view.isShowComplementFeatures()); viewport.setShowComplementFeaturesOnTop( diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index bb26303..06fab20 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -17,288 +18,329 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for anonymous complex type. + *

Java class for anonymous complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="alcodon" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;attribute name="pos2" - * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; &lt;attribute - * name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt; - * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> + * 
+ * <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" }) +@XmlType(name = "", propOrder = { + "alcodon", + "alcodMap" +}) @XmlRootElement(name = "AlcodonFrame") -public class AlcodonFrame -{ - - protected List alcodon; - - protected List alcodMap; - - /** - * Gets the value of the alcodon property. - * - * <p> 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 - * <CODE>set</CODE> method for the alcodon property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAlcodon().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the alcodMap property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAlcodMap().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt; - * &lt;/sequence&gt; &lt;attribute name="dnasq" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "mapping" }) - public static class AlcodMap - { +public class AlcodonFrame { - @XmlElement(name = "Mapping", required = true) - protected Mapping mapping; - - @XmlAttribute(name = "dnasq", required = true) - protected String dnasq; + protected List alcodon; + protected List alcodMap; /** + * Gets the value of the alcodon property. * - * a Mapping entry and an associated protein sequence + *

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);
+     *
* - * @return possible object is {@link Mapping } * - */ - public Mapping getMapping() - { - return mapping; - } - - /** - * Sets the value of the mapping property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame.Alcodon } + *

* - * @param value - * allowed object is {@link Mapping } * + * @return + * The value of the alcodon property. */ - public void setMapping(Mapping value) - { - this.mapping = value; + public List getAlcodon() { + if (alcodon == null) { + alcodon = new ArrayList(); + } + return this.alcodon; } /** - * Gets the value of the dnasq property. + * Gets the value of the alcodMap property. * - * @return possible object is {@link String } + *

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 } + *

+ * + * + * @return + * The value of the alcodMap property. */ - public String getDnasq() - { - return dnasq; + public List getAlcodMap() { + if (alcodMap == null) { + alcodMap = new ArrayList(); + } + return this.alcodMap; } + /** - * Sets the value of the dnasq property. + *

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>
+     *
* - * @param value - * allowed object is {@link String } * */ - public void setDnasq(String value) - { - this.dnasq = value; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "mapping" + }) + public static class AlcodMap { - } + /** + * a Mapping entry and an associated protein + * sequence + * + */ + @XmlElement(name = "Mapping", required = true) + protected Mapping mapping; + /** + * internal jalview id for the dnasq for this + * mapping. + * + */ + @XmlAttribute(name = "dnasq", required = true) + protected String dnasq; - /** - * - * 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). - * - * - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;attribute name="pos2" - * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;attribute name="pos3" - * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Alcodon - { + /** + * a Mapping entry and an associated protein + * sequence + * + * @return + * possible object is + * {@link Mapping } + * + */ + public Mapping getMapping() { + return mapping; + } - @XmlAttribute(name = "pos1") - protected BigInteger pos1; + /** + * Sets the value of the mapping property. + * + * @param value + * allowed object is + * {@link Mapping } + * + * @see #getMapping() + */ + public void setMapping(Mapping value) { + this.mapping = value; + } - @XmlAttribute(name = "pos2") - protected BigInteger pos2; + /** + * internal jalview id for the dnasq for this + * mapping. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDnasq() { + return dnasq; + } - @XmlAttribute(name = "pos3") - protected BigInteger pos3; + /** + * Sets the value of the dnasq property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getDnasq() + */ + public void setDnasq(String value) { + this.dnasq = value; + } - /** - * 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. + * 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). * - * @return possible object is {@link BigInteger } + *

Java class for anonymous complex type

. * - */ - public BigInteger getPos2() - { - return pos2; - } - - /** - * Sets the value of the pos2 property. - * - * @param value - * allowed object is {@link BigInteger } + *

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

* - */ - public void setPos2(BigInteger value) - { - this.pos2 = value; - } - - /** - * Gets the value of the pos3 property. + * 
+     * <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>
+     *
* - * @return possible object is {@link BigInteger } * */ - public BigInteger getPos3() - { - return pos3; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Alcodon { - /** - * Sets the value of the pos3 property. - * - * @param value - * allowed object is {@link BigInteger } - * - */ - public void setPos3(BigInteger value) - { - this.pos3 = value; - } + @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 index 26e9124..a906543 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -16,794 +17,825 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for anonymous complex type. + *

Java class for anonymous complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" - * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="label" - * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element - * name="description" type="{http://www.w3.org/2001/XMLSchema}string" - * minOccurs="0"/&gt; &lt;element name="thresholdLine" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" - * /&gt; &lt;attribute name="colour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="contactmatrix" - * type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType" - * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="property" - * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute - * name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="graphType" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="groupRef" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="graphGroup" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="scoreOnly" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="score" - * type="{http://www.w3.org/2001/XMLSchema}double" /&gt; &lt;attribute - * name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="centreColLabels" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="showAllColLabels" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="false" /&gt; &lt;attribute name="belowAlignment" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="calcId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
+ *       </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", - "contactmatrix", "property" }) +@XmlType(name = "", propOrder = { + "annotationElement", + "label", + "description", + "thresholdLine", + "contactmatrix", + "property" +}) @XmlRootElement(name = "Annotation") -public class Annotation -{ +public class Annotation { - protected List annotationElement; + protected List annotationElement; + @XmlElement(required = true) + protected String label; + protected String description; + protected Annotation.ThresholdLine thresholdLine; + protected List contactmatrix; + 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; + /** + * height in pixels for the graph if this is a + * graph-type annotation. + * + */ + @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; + /** + * is an autocalculated annotation row + * + */ + @XmlAttribute(name = "autoCalculated") + protected Boolean autoCalculated; + /** + * is to be shown below the alignment - introduced + * in Jalview 2.8 for visualizing T-COFFEE alignment scores + * + */ + @XmlAttribute(name = "belowAlignment") + protected Boolean belowAlignment; + /** + * Optional string identifier used to group sets of + * annotation produced by a particular calculation. Values are opaque + * strings but have semantic meaning to Jalview's renderer, data + * importer and calculation system. + * + */ + @XmlAttribute(name = "calcId") + protected String calcId; - @XmlElement(required = true) - protected String label; + /** + * 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 } + *

+ * + * + * @return + * The value of the annotationElement property. + */ + public List getAnnotationElement() { + if (annotationElement == null) { + annotationElement = new ArrayList(); + } + return this.annotationElement; + } - protected String description; + /** + * Gets the value of the label property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getLabel() { + return label; + } - protected Annotation.ThresholdLine thresholdLine; - - protected List contactmatrix; - - 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. - * - * <p> 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 - * <CODE>set</CODE> method for the annotationElement property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAnnotationElement().add(newItem); </pre> - * - * - * <p> 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 contactmatrix property. - * - * <p> 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 - * <CODE>set</CODE> method for the contactmatrix property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getContactmatrix().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link MapOnAMatrixType } - * - * - */ - public List getContactmatrix() - { - if (contactmatrix == null) - { - contactmatrix = new ArrayList(); - } - return this.contactmatrix; - } - - /** - * Gets the value of the property property. - * - * <p> 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 - * <CODE>set</CODE> method for the property property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getProperty().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="value" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class ThresholdLine - { - - @XmlAttribute(name = "label") - protected String label; + /** + * Sets the value of the label property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setLabel(String value) { + this.label = value; + } - @XmlAttribute(name = "value") - protected Float value; + /** + * Gets the value of the description property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDescription() { + return description; + } - @XmlAttribute(name = "colour") - protected Integer colour; + /** + * 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 label property. + * Gets the value of the thresholdLine property. * - * @return possible object is {@link String } + * @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 String getLabel() - { - return label; + public void setThresholdLine(Annotation.ThresholdLine value) { + this.thresholdLine = value; } /** - * Sets the value of the label property. + * Gets the value of the contactmatrix 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 contactmatrix property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link MapOnAMatrixType } + *

+ * + * + * @return + * The value of the contactmatrix property. + */ + public List getContactmatrix() { + if (contactmatrix == null) { + contactmatrix = new ArrayList(); + } + return this.contactmatrix; + } + + /** + * 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 Property } + *

+ * + * + * @return + * The value of the property 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 String } + * 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 void setLabel(String value) - { - this.label = value; + public Integer getGraphGroup() { + return graphGroup; } /** - * Gets the value of the value property. + * Sets the value of the graphGroup property. * - * @return possible object is {@link Float } + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGraphGroup(Integer value) { + this.graphGroup = value; + } + + /** + * height in pixels for the graph if this is a + * graph-type annotation. * + * @return + * possible object is + * {@link Integer } + * */ - public Float getValue() - { - return value; + public Integer getGraphHeight() { + return graphHeight; } /** - * Sets the value of the value property. + * Sets the value of the graphHeight property. * * @param value - * allowed object is {@link Float } + * allowed object is + * {@link Integer } + * + * @see #getGraphHeight() + */ + public void setGraphHeight(Integer value) { + this.graphHeight = value; + } + + /** + * Gets the value of the id property. * + * @return + * possible object is + * {@link String } + * */ - public void setValue(Float value) - { - this.value = value; + public String getId() { + return id; } /** - * Gets the value of the colour property. + * Sets the value of the id property. * - * @return possible object is {@link Integer } + * @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 Integer getColour() - { - return colour; + public boolean isScoreOnly() { + if (scoreOnly == null) { + return false; + } else { + return scoreOnly; + } } /** - * Sets the value of the colour property. + * Sets the value of the scoreOnly property. * * @param value - * allowed object is {@link Integer } + * 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 void setColour(Integer value) - { - this.colour = value; + 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; + } + + /** + * is an autocalculated annotation row + * + * @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 } + * + * @see #isAutoCalculated() + */ + public void setAutoCalculated(Boolean value) { + this.autoCalculated = value; + } + + /** + * is to be shown below the alignment - introduced + * in Jalview 2.8 for visualizing T-COFFEE alignment scores + * + * @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 } + * + * @see #isBelowAlignment() + */ + public void setBelowAlignment(Boolean value) { + this.belowAlignment = value; + } + + /** + * Optional string identifier used to group sets of + * annotation produced by a particular calculation. Values are opaque + * strings but have semantic meaning to Jalview's renderer, data + * importer and calculation system. + * + * @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 } + * + * @see #getCalcId() + */ + 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="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 index 427c84d..de46d74 100644 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -12,243 +13,242 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for AnnotationColourScheme complex type. + *

Java class for AnnotationColourScheme complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="AnnotationColourScheme"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="annotation" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="maxColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="threshold" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="predefinedColours" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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; - } +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 index cd0dce9..d074219 100644 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -13,186 +14,190 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for anonymous complex type. + *

Java class for anonymous complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="displayCharacter" - * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; - * &lt;element name="description" - * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; - * &lt;element name="secondaryStructure" minOccurs="0"&gt; - * &lt;simpleType&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;length - * value="1"/&gt; &lt;/restriction&gt; &lt;/simpleType&gt; - * &lt;/element&gt; &lt;element name="value" - * type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="position" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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" }) +@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; - } +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/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index b46439a..aad7c25 100644 --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -15,167 +16,174 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for DoubleMatrix complex type. + *

Java class for DoubleMatrix complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="DoubleMatrix"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="row" - * type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="D" - * type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt; &lt;element - * name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="rows" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <complexType name="DoubleMatrix">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ *         <element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       <attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType( - name = "DoubleMatrix", - namespace = "www.jalview.org", - propOrder = - { "row", "d", "e" }) -public class DoubleMatrix -{ - - protected List row; - - @XmlElement(name = "D") - protected DoubleVector d; - - @XmlElement(name = "E") - protected DoubleVector e; - - @XmlAttribute(name = "rows") - protected Integer rows; - - @XmlAttribute(name = "columns") - protected Integer columns; - - /** - * Gets the value of the row property. - * - * <p> 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 - * <CODE>set</CODE> method for the row property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getRow().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link DoubleVector } - * - * - */ - public List getRow() - { - if (row == null) - { - row = new ArrayList(); +@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = { + "row", + "d", + "e" +}) +public class DoubleMatrix { + + protected List row; + @XmlElement(name = "D") + protected DoubleVector d; + @XmlElement(name = "E") + protected DoubleVector e; + @XmlAttribute(name = "rows") + protected Integer rows; + @XmlAttribute(name = "columns") + protected Integer columns; + + /** + * Gets the value of the row 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 row property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link DoubleVector } + *

+ * + * + * @return + * The value of the row property. + */ + public List getRow() { + if (row == null) { + row = new ArrayList(); + } + return this.row; + } + + /** + * Gets the value of the d property. + * + * @return + * possible object is + * {@link DoubleVector } + * + */ + public DoubleVector getD() { + return d; + } + + /** + * Sets the value of the d property. + * + * @param value + * allowed object is + * {@link DoubleVector } + * + */ + public void setD(DoubleVector value) { + this.d = value; + } + + /** + * Gets the value of the e property. + * + * @return + * possible object is + * {@link DoubleVector } + * + */ + public DoubleVector getE() { + return e; + } + + /** + * Sets the value of the e property. + * + * @param value + * allowed object is + * {@link DoubleVector } + * + */ + public void setE(DoubleVector value) { + this.e = value; + } + + /** + * Gets the value of the rows property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getRows() { + return rows; + } + + /** + * Sets the value of the rows property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setRows(Integer value) { + this.rows = value; + } + + /** + * Gets the value of the columns property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getColumns() { + return columns; + } + + /** + * Sets the value of the columns property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setColumns(Integer value) { + this.columns = value; } - return this.row; - } - - /** - * Gets the value of the d property. - * - * @return possible object is {@link DoubleVector } - * - */ - public DoubleVector getD() - { - return d; - } - - /** - * Sets the value of the d property. - * - * @param value - * allowed object is {@link DoubleVector } - * - */ - public void setD(DoubleVector value) - { - this.d = value; - } - - /** - * Gets the value of the e property. - * - * @return possible object is {@link DoubleVector } - * - */ - public DoubleVector getE() - { - return e; - } - - /** - * Sets the value of the e property. - * - * @param value - * allowed object is {@link DoubleVector } - * - */ - public void setE(DoubleVector value) - { - this.e = value; - } - - /** - * Gets the value of the rows property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getRows() - { - return rows; - } - - /** - * Sets the value of the rows property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setRows(Integer value) - { - this.rows = value; - } - - /** - * Gets the value of the columns property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getColumns() - { - return columns; - } - - /** - * Sets the value of the columns property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setColumns(Integer value) - { - this.columns = value; - } } diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index ad1b19c..f1ba7ee 100644 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -14,58 +15,65 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for DoubleVector complex type. + *

Java class for DoubleVector complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="DoubleVector"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="v" - * type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> + * 
+ * <complexType name="DoubleVector">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType( - name = "DoubleVector", - namespace = "www.jalview.org", - propOrder = - { "v" }) -public class DoubleVector -{ +@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = { + "v" +}) +public class DoubleVector { - @XmlElement(type = Double.class) - protected List v; + @XmlElement(type = Double.class) + protected List v; - /** - * Gets the value of the v property. - * - * <p> 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 - * <CODE>set</CODE> method for the v property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getV().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link Double } - * - * - */ - public List getV() - { - if (v == null) - { - v = new ArrayList(); + /** + * Gets the value of the v 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 v property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link Double } + *

+ * + * + * @return + * The value of the v property. + */ + public List getV() { + if (v == null) { + v = new ArrayList(); + } + return this.v; } - return this.v; - } } diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index a8f2006..17b5c9f 100644 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -14,350 +15,357 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for feature complex type. + *

Java class for feature complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="feature"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="otherData" - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="key2" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attribute name="begin" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="type" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="status" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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. - * - * <p> 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 - * <CODE>set</CODE> method for the otherData property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getOtherData().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link Feature.OtherData } - * - * - */ - public List getOtherData() - { - if (otherData == null) - { - otherData = new ArrayList(); +@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 } + *

+ * + * + * @return + * The value of the otherData property. + */ + public List getOtherData() { + if (otherData == null) { + otherData = new ArrayList(); + } + return this.otherData; } - 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="key2" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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. + * Gets the value of the begin property. * - * @return possible object is {@link String } + */ + public int getBegin() { + return begin; + } + + /** + * Sets the value of the begin property. * */ - public String getKey() - { - return key; + public void setBegin(int value) { + this.begin = value; } /** - * Sets the value of the key property. + * Gets the value of the end property. * - * @param value - * allowed object is {@link String } + */ + 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 void setKey(String value) - { - this.key = value; + public String getType() { + return type; } /** - * Gets the value of the key2 property. + * Sets the value of the type property. * - * @return possible object is {@link String } + * @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 getKey2() - { - return key2; + public String getDescription() { + return description; } /** - * Sets the value of the key2 property. + * Sets the value of the description property. * * @param value - * allowed object is {@link String } + * 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 void setKey2(String value) - { - this.key2 = value; + public String getStatus() { + return status; } /** - * Gets the value of the value property. + * Sets the value of the status property. * - * @return possible object is {@link String } + * @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 getValue() - { - return value; + public String getFeatureGroup() { + return featureGroup; } /** - * Sets the value of the value property. + * Sets the value of the featureGroup property. * * @param value - * allowed object is {@link String } + * 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 void setValue(String value) - { - this.value = value; + 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; + /** + * key2 may be used for a sub-attribute of 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; + } + + /** + * key2 may be used for a sub-attribute of key + * + * @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 } + * + * @see #getKey2() + */ + 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 index d9ff117..5c1cdeb 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -15,141 +16,154 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for FeatureMatcher complex type. + *

Java class for FeatureMatcher complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="FeatureMatcher"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="attributeName" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" - * minOccurs="0"/&gt; &lt;element name="condition" - * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element - * name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; - * &lt;/sequence&gt; &lt;attribute name="by" - * type="{www.jalview.org/colours}FilterBy" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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; +@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = { + "attributeName", + "condition", + "value" +}) +public class FeatureMatcher { - @XmlElement(namespace = "", required = true) - protected String condition; + /** + * name of feature attribute to filter on, or attribute and sub-attribute + * + */ + @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; - @XmlElement(namespace = "", required = true) - protected String value; - - @XmlAttribute(name = "by") - protected FilterBy by; - - /** - * Gets the value of the attributeName property. - * - * <p> 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 - * <CODE>set</CODE> method for the attributeName property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAttributeName().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getAttributeName() - { - if (attributeName == null) - { - attributeName = new ArrayList(); + /** + * name of feature attribute to filter on, or attribute and sub-attribute + * + * 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 } + *

+ * + * + * @return + * The value of the attributeName property. + */ + public List getAttributeName() { + if (attributeName == null) { + attributeName = new ArrayList(); + } + return this.attributeName; } - return this.attributeName; - } - /** - * Gets the value of the condition property. - * - * @return possible object is {@link String } - * - */ - public String getCondition() - { - return condition; - } + /** + * 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; - } + /** + * 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; - } + /** + * 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; - } + /** + * 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; - } + /** + * 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; - } + /** + * 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 index cf81588..22f938d 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -15,167 +16,184 @@ 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 * - * <p>Java class for FeatureMatcherSet complex type. + *

Java class for FeatureMatcherSet complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="FeatureMatcherSet"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;choice&gt; &lt;element name="matchCondition" - * type="{www.jalview.org/colours}FeatureMatcher"/&gt; &lt;element - * name="compoundMatcher"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="matcherSet" - * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" - * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute name="and" - * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;/choice&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="matcherSet" - * type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" - * minOccurs="2"/&gt; &lt;/sequence&gt; &lt;attribute - * name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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; +@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 matcherSet property. - * - * <p> 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 - * <CODE>set</CODE> method for the matcherSet property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getMatcherSet().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link FeatureMatcherSet } + * 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 List getMatcherSet() - { - if (matcherSet == null) - { - matcherSet = new ArrayList(); - } - return this.matcherSet; + public void setMatchCondition(FeatureMatcher value) { + this.matchCondition = value; } /** - * Gets the value of the and property. + * Gets the value of the compoundMatcher property. * + * @return + * possible object is + * {@link FeatureMatcherSet.CompoundMatcher } + * */ - public boolean isAnd() - { - return and; + public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() { + return compoundMatcher; } /** - * Sets the value of the and property. + * Sets the value of the compoundMatcher property. * + * @param value + * allowed object is + * {@link FeatureMatcherSet.CompoundMatcher } + * */ - public void setAnd(boolean value) - { - this.and = value; + 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; + /** + * If true, matchers are AND-ed, if false they are OR-ed + * + */ + @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 } + *

+ * + * + * @return + * The value of the matcherSet property. + */ + public List getMatcherSet() { + if (matcherSet == null) { + matcherSet = new ArrayList(); + } + return this.matcherSet; + } + + /** + * If true, matchers are AND-ed, if false they are OR-ed + * + */ + 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 index cfb0293..fa80470 100644 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@ -1,60 +1,78 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 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; + /** - * <p>Java class for FilterBy. + * Filter may apply to label, score or some feature attribute + * + *

Java class for FilterBy

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. <pre> &lt;simpleType - * name="FilterBy"&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration - * value="byLabel"/&gt; &lt;enumeration value="byScore"/&gt; - * &lt;enumeration value="byAttribute"/&gt; &lt;/restriction&gt; - * &lt;/simpleType&gt; </pre> + *

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; - } +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; + } + + /** + * Gets the value associated to the enum constant. + * + * @return + * The value linked to the enum. + */ + public String value() { + return value; + } + + /** + * Gets the enum associated to the value passed as parameter. + * + * @param v + * The value to get the enum from. + * @return + * The enum which corresponds to the value, if it exists. + * @throws IllegalArgumentException + * If no value matches in the enum declaration. + */ + public static FilterBy fromValue(String v) { + for (FilterBy c: FilterBy.values()) { + if (c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); } - throw new IllegalArgumentException(v); - } } diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index dda2352..0300df2 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -21,7047 +22,7707 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; import javax.xml.datatype.XMLGregorianCalendar; + /** - * <p>Java class for JalviewModel complex type. + *

Java class for JalviewModel complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="JalviewModel"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="creationDate" - * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; &lt;element - * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; - * &lt;element name="vamsasModel" - * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt; - * &lt;sequence&gt; &lt;element name="JSeq" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="features" - * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt; - * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension - * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt; - * &lt;element name="structureState" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;simpleContent&gt; &lt;extension - * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; - * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; - * &lt;attribute name="visible" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="alignwithAlignPanel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="colourwithAlignPanel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="colourByJmol" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/extension&gt; &lt;/simpleContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;/extension&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;element name="hiddenSequences" - * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="rnaViewer" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="secondaryStructure" - * maxOccurs="unbounded"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="annotationId" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewerState" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="dividerLocation" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attribute name="colour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="end" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="hidden" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="seq" - * type="{http://www.w3.org/2001/XMLSchema}string" - * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours" - * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="start" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="colour" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="pidThreshold" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="displayBoxes" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="colourText" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="textCol2" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="showUnconserved" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="true" /&gt; &lt;attribute name="showConsensusHistogram" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="showSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="normaliseSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="AnnotationColours" - * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt; - * &lt;element name="hiddenColumns" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension - * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt; - * &lt;attribute name="calcId" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="false" /&gt; &lt;attribute name="autoUpdate" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/extension&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="overview" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute - * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="residueColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="hiddenColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute - * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="pidSelected" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="consThreshold" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="title" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="rightAlignIds" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="showColourText" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="false" /&gt; &lt;attribute name="showBoxes" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="renderGaps" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="showNPfeatureTooltip" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="followHighlight" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="followSelection" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="showAnnotation" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="false" /&gt; &lt;attribute name="showGroupConservation" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showGroupConsensus" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showConsensusHistogram" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="showSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="normaliseSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="ignoreGapsinConsensus" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="startRes" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="charWidth" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="fontName" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="fontStyle" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="idWidthManuallyAdjusted" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="true" /&gt; &lt;attribute name="viewName" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="gatheredViews" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="textCol2" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="id" - * type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; &lt;attribute - * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="showComplementFeatures" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showComplementFeaturesOnTop" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="UserColourScheme" - * type="{www.jalview.org/colours}JalviewUserColours"/&gt; - * &lt;/sequence&gt; &lt;attribute name="id" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="tree" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence minOccurs="0"&gt; &lt;element name="title" - * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element - * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; - * &lt;/sequence&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="fontName" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="fontStyle" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="showBootstrap" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="markUnlinked" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="currentTree" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="false" /&gt; &lt;attribute name="columnReference" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; - * &lt;attribute name="linkToAllViews" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="sequencePoint" - * maxOccurs="unbounded"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;attribute name="sequenceRef" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;element name="seqPointMin"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attGroup ref="{www.jalview.org}position"/&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="seqPointMax"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;element name="pcaData" - * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt; - * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt; - * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; - * &lt;attribute name="title" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="xDim" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="bgColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="showLabels" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="FeatureSettings" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="setting" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="attributeName" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" - * minOccurs="0"/&gt; &lt;element name="matcherSet" - * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="type" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="display" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute - * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="mincolour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="noValueColour" type="{www.jalview.org/colours}NoValueColour" - * default="Min" /&gt; &lt;attribute name="threshold" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" - * /&gt; &lt;attribute name="min" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="autoScale" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="group" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attribute name="name" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="display" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;/sequence&gt; &lt;/sequence&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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"/>
+ *                     <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}conservationShading"/>
+ *                   <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="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="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>
+ *                     <element name="overview" minOccurs="0">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attGroup ref="{www.jalview.org}conservationShading"/>
+ *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <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="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="charHeight" 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="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <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" />
+ *                   <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 </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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 </restriction>
+ *               </complexContent>
+ *             </complexType>
+ *           </element>
+ *           <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
+ *             <complexType>
+ *               <complexContent>
+ *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   <sequence>
+ *                     <element name="sequencePoint" maxOccurs="unbounded">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                             <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="axis" maxOccurs="3" minOccurs="3">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="seqPointMin">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="seqPointMax">
+ *                       <complexType>
+ *                         <complexContent>
+ *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             <attGroup ref="{www.jalview.org}position"/>
+ *                           </restriction>
+ *                         </complexContent>
+ *                       </complexType>
+ *                     </element>
+ *                     <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ *                   </sequence>
+ *                   <attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 </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", "pcaViewer", "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 = "PcaViewer") - protected List pcaViewer; - - @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. - * - * <p> 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 - * <CODE>set</CODE> method for the jSeq property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getJSeq().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the jGroup property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getJGroup().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the viewport property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getViewport().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the userColours property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getUserColours().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the tree property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getTree().add(newItem); </pre> - * - * - * <p> 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 pcaViewer property. - * - * <p> 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 - * <CODE>set</CODE> method for the pcaViewer property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getPcaViewer().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link JalviewModel.PcaViewer } - * - * - */ - public List getPcaViewer() - { - if (pcaViewer == null) - { - pcaViewer = new ArrayList(); - } - return this.pcaViewer; - } - - /** - * 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="setting" - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="attributeName" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" - * minOccurs="0"/&gt; &lt;element name="matcherSet" - * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="type" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="display" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="order" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="noValueColour" - * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt; - * &lt;attribute name="threshold" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" - * /&gt; &lt;attribute name="min" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="autoScale" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="group" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="display" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> - * - * - */ - @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. - * - * <p> 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 - * <CODE>set</CODE> method for the setting property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getSetting().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the group property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getGroup().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attribute name="name" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="display" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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; - } - - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="attributeName" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" - * minOccurs="0"/&gt; &lt;element name="matcherSet" - * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="type" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="colour" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="display" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="order" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="mincolour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="noValueColour" type="{www.jalview.org/colours}NoValueColour" - * default="Min" /&gt; &lt;attribute name="threshold" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="threshstate" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="min" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="colourByLabel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="autoScale" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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. - * - * <p> 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 - * <CODE>set</CODE> method for the attributeName property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAttributeName().add(newItem); </pre> - * - * - * <p> 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; - } - - } - - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="seq" - * type="{http://www.w3.org/2001/XMLSchema}string" - * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours" - * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="start" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="name" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="consThreshold" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="outlineColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="displayText" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="colourText" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="textCol1" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="textColThreshold" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="ignoreGapsinConsensus" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="showConsensusHistogram" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="showSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="normaliseSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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 = "consensusSecondaryStructureThreshold") - protected Integer consensusSecondaryStructureThreshold; - - @XmlAttribute(name = "consensusSecondaryStructureColouring") - private boolean consensusSecondaryStructureColouring; - - @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; - - @XmlAttribute(name = "secondaryStructureSources") - protected List secondaryStructureSources; - - - /** - * Gets the value of the seq property. - * - * <p> 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 - * <CODE>set</CODE> method for the seq property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getSeq().add(newItem); </pre> - * - * - * <p> 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. +@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = { + "creationDate", + "version", + "vamsasModel", + "jSeq", + "jGroup", + "viewport", + "userColours", + "tree", + "pcaViewer", + "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 = "PcaViewer") + protected List pcaViewer; + @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 AnnotationColourScheme } - * + * allowed object is + * {@link XMLGregorianCalendar } + * */ - public void setAnnotationColours(AnnotationColourScheme value) - { - this.annotationColours = value; + public void setCreationDate(XMLGregorianCalendar value) { + this.creationDate = value; } /** - * Gets the value of the start property. - * - * @return possible object is {@link Integer } + * Gets the value of the version property. * + * @return + * possible object is + * {@link String } + * */ - public Integer getStart() - { - return start; + public String getVersion() { + return version; } /** - * Sets the value of the start property. + * Sets the value of the version property. * * @param value - * allowed object is {@link Integer } - * + * allowed object is + * {@link String } + * */ - public void setStart(Integer value) - { - this.start = value; + public void setVersion(String value) { + this.version = value; } /** - * Gets the value of the end property. - * - * @return possible object is {@link Integer } + * Gets the value of the vamsasModel property. * + * @return + * possible object is + * {@link VAMSAS } + * */ - public Integer getEnd() - { - return end; + public VAMSAS getVamsasModel() { + return vamsasModel; } /** - * Sets the value of the end property. + * Sets the value of the vamsasModel property. * * @param value - * allowed object is {@link Integer } - * + * allowed object is + * {@link VAMSAS } + * */ - public void setEnd(Integer value) - { - this.end = value; + public void setVamsasModel(VAMSAS value) { + this.vamsasModel = value; } /** - * Gets the value of the name property. + * Gets the value of the jSeq property. * - * @return possible object is {@link String } + *

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.

* - */ - public String getName() - { - return name; - } - - /** - * Sets the value of the name property. + *

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

+ * 
+     * getJSeq().add(newItem);
+     *
* - * @param value - * allowed object is {@link String } * - */ - public void setName(String value) - { - this.name = value; - } - - /** - * Gets the value of the colour property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq } + *

* - * @return possible object is {@link String } * + * @return + * The value of the jSeq property. */ - public String getColour() - { - return colour; + public List getJSeq() { + if (jSeq == null) { + jSeq = new ArrayList(); + } + return this.jSeq; } /** - * Sets the value of the colour property. + * Gets the value of the jGroup property. * - * @param value - * allowed object is {@link String } + *

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.

* - */ - public void setColour(String value) - { - this.colour = value; - } - - /** - * Gets the value of the consThreshold property. + *

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

+ * 
+     * getJGroup().add(newItem);
+     *
* - * @return possible object is {@link Integer } * - */ - public Integer getConsThreshold() - { - return consThreshold; - } - - /** - * Sets the value of the consThreshold property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JGroup } + *

* - * @param value - * allowed object is {@link Integer } * + * @return + * The value of the jGroup property. */ - public void setConsThreshold(Integer value) - { - this.consThreshold = value; + public List getJGroup() { + if (jGroup == null) { + jGroup = new ArrayList(); + } + return this.jGroup; } /** - * Gets the value of the pidThreshold property. + * Gets the value of the viewport property. * - * @return possible object is {@link Integer } + *

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.

* - */ - public Integer getPidThreshold() - { - return pidThreshold; - } - - /** - * Sets the value of the pidThreshold property. + *

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

+ * 
+     * getViewport().add(newItem);
+     *
* - * @param value - * allowed object is {@link Integer } * - */ - public void setPidThreshold(Integer value) - { - this.pidThreshold = value; - } - - /** - * Gets the value of the consensusSecondaryStructureThreshold property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport } + *

* - * @return possible object is {@link Integer } * + * @return + * The value of the viewport property. */ - public Integer getConsensusSecondaryStructureThreshold() - { - return consensusSecondaryStructureThreshold; + public List getViewport() { + if (viewport == null) { + viewport = new ArrayList(); + } + return this.viewport; } /** - * Sets the value of the consensusSecondaryStructureThreshold property. + * Gets the value of the userColours property. * - * @param value - * allowed object is {@link Integer } + *

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.

* - */ - public void setConsensusSecondaryStructureThreshold(Integer value) - { - this.consensusSecondaryStructureThreshold = value; - } - - /** - * Sets the value of the consensusSecondaryStructureColouring property. + *

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

+ * 
+     * getUserColours().add(newItem);
+     *
* - * @param value - * allowed object is {@link boolean } * - */ - public void setConsensusSecondaryStructureColouring(boolean value) - { - this.consensusSecondaryStructureColouring = value; - } - - - /** - * Sets the value of the consensusSecondaryStructureColouring property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.UserColours } + *

* - * @param value - * allowed object is {@link boolean } * + * @return + * The value of the userColours property. */ - public boolean isConsensusSecondaryStructureColouring() - { - return consensusSecondaryStructureColouring; + public List getUserColours() { + if (userColours == null) { + userColours = new ArrayList(); + } + return this.userColours; } /** - * Gets the value of the outlineColour property. + * Gets the value of the tree property. * - * @return possible object is {@link Integer } + *

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.

* - */ - public Integer getOutlineColour() - { - return outlineColour; - } - - /** - * Sets the value of the outlineColour property. + *

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

+ * 
+     * getTree().add(newItem);
+     *
* - * @param value - * allowed object is {@link Integer } * - */ - public void setOutlineColour(Integer value) - { - this.outlineColour = value; - } - - /** - * Gets the value of the displayBoxes property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Tree } + *

* - * @return possible object is {@link Boolean } * + * @return + * The value of the tree property. */ - public Boolean isDisplayBoxes() - { - return displayBoxes; + public List getTree() { + if (tree == null) { + tree = new ArrayList(); + } + return this.tree; } /** - * Sets the value of the displayBoxes property. + * Gets the value of the pcaViewer property. * - * @param value - * allowed object is {@link Boolean } + *

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 pcaViewer property.

* - */ - public void setDisplayBoxes(Boolean value) - { - this.displayBoxes = value; - } - - /** - * Gets the value of the displayText property. + *

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

+ * 
+     * getPcaViewer().add(newItem);
+     *
* - * @return possible object is {@link Boolean } * - */ - public Boolean isDisplayText() - { - return displayText; - } - - /** - * Sets the value of the displayText property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.PcaViewer } + *

* - * @param value - * allowed object is {@link Boolean } * + * @return + * The value of the pcaViewer property. */ - public void setDisplayText(Boolean value) - { - this.displayText = value; + public List getPcaViewer() { + if (pcaViewer == null) { + pcaViewer = new ArrayList(); + } + return this.pcaViewer; } /** - * Gets the value of the colourText property. - * - * @return possible object is {@link Boolean } + * Gets the value of the featureSettings property. * + * @return + * possible object is + * {@link JalviewModel.FeatureSettings } + * */ - public Boolean isColourText() - { - return colourText; + public JalviewModel.FeatureSettings getFeatureSettings() { + return featureSettings; } /** - * Sets the value of the colourText property. + * Sets the value of the featureSettings 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. + * 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>
+     *
* - * @param value - * allowed object is {@link Integer } * */ - public void setTextCol1(Integer value) - { - this.textCol1 = value; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "setting", + "group" + }) + public static class FeatureSettings { - /** - * Gets the value of the textCol2 property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getTextCol2() - { - return textCol2; - } + @XmlElement(namespace = "www.jalview.org") + protected List setting; + @XmlElement(namespace = "www.jalview.org") + protected List group; - /** - * 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 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 } + *

+ * + * + * @return + * The value of the setting property. + */ + public List getSetting() { + if (setting == null) { + setting = new ArrayList(); + } + return this.setting; + } - /** - * Gets the value of the textColThreshold property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getTextColThreshold() - { - return textColThreshold; - } + /** + * 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 } + *

+ * + * + * @return + * The value of the group property. + */ + public List getGroup() { + if (group == null) { + group = new ArrayList(); + } + return this.group; + } - /** - * 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; - } + /** + *

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; + } - /** - * 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; - } + /** + *

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 { + + /** + * name of feature attribute to colour by, or attribute and sub-attribute + * + */ + @XmlElement(namespace = "www.jalview.org") + protected List attributeName; + /** + * optional filter(s) applied to the feature type + * + */ + @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; + /** + * Optional minimum colour + * for graduated + * feature + * colour + * + */ + @XmlAttribute(name = "mincolour") + protected Integer mincolour; + @XmlAttribute(name = "noValueColour") + protected NoValueColour noValueColour; + /** + * threshold value for + * graduated feature colour + * + */ + @XmlAttribute(name = "threshold") + protected Float threshold; + /** + * threshold type for + * graduated feature colour + * + */ + @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; + + /** + * name of feature attribute to colour by, or attribute and sub-attribute + * + * 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 } + *

+ * + * + * @return + * The value of the attributeName property. + */ + public List getAttributeName() { + if (attributeName == null) { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * optional filter(s) applied to the feature type + * + * @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 } + * + * @see #getMatcherSet() + */ + 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; + } + + /** + * Optional minimum colour + * for graduated + * feature + * colour + * + * @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 } + * + * @see #getMincolour() + */ + 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; + } + + /** + * threshold value for + * graduated feature colour + * + * @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 } + * + * @see #getThreshold() + */ + public void setThreshold(Float value) { + this.threshold = value; + } + + /** + * threshold type for + * graduated feature colour + * + * @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 } + * + * @see #getThreshstate() + */ + 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; + } - /** - * 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. + *

Java class for anonymous complex type

. * - * @param value - * allowed object is {@link Boolean } + *

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

* - */ - 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; - } - - - public List getSecondaryStructureSources() - { - return secondaryStructureSources; - } - - public void setSecondaryStructureSources( - List secondaryStructureSources) - { - this.secondaryStructureSources = secondaryStructureSources; - } - - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="features" - * type="{www.jalview.org}feature" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="pdbids" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;extension - * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt; - * &lt;element name="structureState" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;simpleContent&gt; &lt;extension - * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; - * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; - * &lt;attribute name="visible" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="true" /&gt; &lt;attribute name="colourwithAlignPanel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="colourByJmol" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="type" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/extension&gt; &lt;/simpleContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;/extension&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;element name="hiddenSequences" - * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="rnaViewer" - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="secondaryStructure" - * maxOccurs="unbounded"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="annotationId" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewerState" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="dividerLocation" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attribute name="colour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="end" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="hidden" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewreference" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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. - * - * <p> 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 - * <CODE>set</CODE> method for the features property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getFeatures().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the pdbids property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getPdbids().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the hiddenSequences property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getHiddenSequences().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the rnaViewer property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getRnaViewer().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;extension base="{www.jalview.org}pdbentry"&gt; - * &lt;sequence&gt; &lt;element name="structureState" - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;simpleContent&gt; &lt;extension - * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; - * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; - * &lt;attribute name="visible" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="alignwithAlignPanel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="colourwithAlignPanel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" - * /&gt; &lt;attribute name="colourByJmol" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="type" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/extension&gt; &lt;/simpleContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;/extension&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> + * 
+     * <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"/>
+     *         <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}conservationShading"/>
+     *       <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="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="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </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. - * - * <p> 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 - * <CODE>set</CODE> method for the structureState property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getStructureState().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;simpleContent&gt; - * &lt;extension - * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; - * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; - * &lt;attribute name="visible" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="alignwithAlignPanel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" - * /&gt; &lt;attribute name="colourwithAlignPanel" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" - * /&gt; &lt;attribute name="colourByJmol" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" - * /&gt; &lt;attribute name="type" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/extension&gt; &lt;/simpleContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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; - + @XmlType(name = "", propOrder = { + "seq", + "annotationColours", + "secStrProvider" + }) + public static class JGroup { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List seq; + @XmlElement(namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org") + protected List secStrProvider; + @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 = "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; /** - * Gets the value of the value property. + * Optional sequence group ID (only + * needs to be + * unique for this + * alignment) * - * @return possible object is {@link String } + */ + @XmlAttribute(name = "id") + protected String id; + @XmlAttribute(name = "conservationSelected") + protected Boolean conservationSelected; + /** + * Conservation shading increment * */ - public String getValue() - { - return value; - } - + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + @XmlAttribute(name = "pidSelected") + protected Boolean pidSelected; /** - * Sets the value of the value property. + * Percent Identity Threshold * - * @param value - * allowed object is {@link String } + */ + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + /** + * Secondary structure consensus shading - since 2.11.4 * */ - public void setValue(String value) - { - this.value = value; - } + @XmlAttribute(name = "secstrSelected") + protected Boolean secstrSelected; + /** + * Secondary structure consensus increment + * + */ + @XmlAttribute(name = "secstrThreshold") + protected Integer secstrThreshold; + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; /** - * Gets the value of the visible property. + * 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);
+         *
+ * * - * @return possible object is {@link Boolean } + *

+ * Objects of the following type(s) are allowed in the list + * {@link String } + *

* + * + * @return + * The value of the seq property. */ - public Boolean isVisible() - { - return visible; + public List getSeq() { + if (seq == null) { + seq = new ArrayList(); + } + return this.seq; } /** - * Sets the value of the visible property. - * - * @param value - * allowed object is {@link Boolean } + * Gets the value of the annotationColours property. * + * @return + * possible object is + * {@link AnnotationColourScheme } + * */ - public void setVisible(Boolean value) - { - this.visible = value; + public AnnotationColourScheme getAnnotationColours() { + return annotationColours; } /** - * Gets the value of the viewId property. - * - * @return possible object is {@link String } + * Sets the value of the annotationColours property. * + * @param value + * allowed object is + * {@link AnnotationColourScheme } + * */ - public String getViewId() - { - return viewId; + public void setAnnotationColours(AnnotationColourScheme value) { + this.annotationColours = value; } /** - * Sets the value of the viewId property. + * Gets the value of the secStrProvider property. * - * @param value - * allowed object is {@link String } + *

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 secStrProvider property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link String } + *

* + * + * @return + * The value of the secStrProvider property. */ - public void setViewId(String value) - { - this.viewId = value; + public List getSecStrProvider() { + if (secStrProvider == null) { + secStrProvider = new ArrayList(); + } + return this.secStrProvider; } /** - * Gets the value of the alignwithAlignPanel property. - * - * @return possible object is {@link Boolean } + * Gets the value of the start property. * + * @return + * possible object is + * {@link Integer } + * */ - public boolean isAlignwithAlignPanel() - { - if (alignwithAlignPanel == null) - { - return true; - } - else - { - return alignwithAlignPanel; - } + public Integer getStart() { + return start; } /** - * Sets the value of the alignwithAlignPanel property. + * Sets the value of the start property. * * @param value - * allowed object is {@link Boolean } - * + * allowed object is + * {@link Integer } + * */ - public void setAlignwithAlignPanel(Boolean value) - { - this.alignwithAlignPanel = value; + public void setStart(Integer value) { + this.start = value; } /** - * Gets the value of the colourwithAlignPanel property. - * - * @return possible object is {@link Boolean } + * Gets the value of the end property. * + * @return + * possible object is + * {@link Integer } + * */ - public boolean isColourwithAlignPanel() - { - if (colourwithAlignPanel == null) - { - return false; - } - else - { - return colourwithAlignPanel; - } + public Integer getEnd() { + return end; } /** - * Sets the value of the colourwithAlignPanel property. + * Sets the value of the end property. * * @param value - * allowed object is {@link Boolean } - * + * allowed object is + * {@link Integer } + * */ - public void setColourwithAlignPanel(Boolean value) - { - this.colourwithAlignPanel = value; + public void setEnd(Integer value) { + this.end = value; } /** - * Gets the value of the colourByJmol property. - * - * @return possible object is {@link Boolean } + * Gets the value of the name property. * + * @return + * possible object is + * {@link String } + * */ - public boolean isColourByJmol() - { - if (colourByJmol == null) - { - return true; - } - else - { - return colourByJmol; - } + public String getName() { + return name; } /** - * Sets the value of the colourByJmol property. + * Sets the value of the name property. * * @param value - * allowed object is {@link Boolean } - * + * allowed object is + * {@link String } + * */ - public void setColourByJmol(Boolean value) - { - this.colourByJmol = value; + public void setName(String value) { + this.name = value; } /** - * Gets the value of the type property. - * - * @return possible object is {@link String } + * Gets the value of the colour property. * + * @return + * possible object is + * {@link String } + * */ - public String getType() - { - return type; + public String getColour() { + return colour; } /** - * Sets the value of the type property. + * Sets the value of the colour property. * * @param value - * allowed object is {@link String } - * + * allowed object is + * {@link String } + * */ - public void setType(String value) - { - this.type = value; + public void setColour(String value) { + this.colour = value; } /** - * Gets the value of the width property. - * - * @return possible object is {@link Integer } + * Gets the value of the outlineColour property. * + * @return + * possible object is + * {@link Integer } + * */ - public Integer getWidth() - { - return width; + public Integer getOutlineColour() { + return outlineColour; } /** - * Sets the value of the width property. + * Sets the value of the outlineColour property. * * @param value - * allowed object is {@link Integer } - * + * allowed object is + * {@link Integer } + * */ - public void setWidth(Integer value) - { - this.width = value; + public void setOutlineColour(Integer value) { + this.outlineColour = value; } /** - * Gets the value of the height property. - * - * @return possible object is {@link Integer } + * Gets the value of the displayBoxes property. * + * @return + * possible object is + * {@link Boolean } + * */ - public Integer getHeight() - { - return height; + public Boolean isDisplayBoxes() { + return displayBoxes; } /** - * Sets the value of the height property. + * Sets the value of the displayBoxes property. * * @param value - * allowed object is {@link Integer } - * + * allowed object is + * {@link Boolean } + * */ - public void setHeight(Integer value) - { - this.height = value; + public void setDisplayBoxes(Boolean value) { + this.displayBoxes = value; } /** - * Gets the value of the xpos property. - * - * @return possible object is {@link Integer } + * Gets the value of the displayText property. * + * @return + * possible object is + * {@link Boolean } + * */ - public Integer getXpos() - { - return xpos; + public Boolean isDisplayText() { + return displayText; } /** - * Sets the value of the xpos property. + * Sets the value of the displayText property. * * @param value - * allowed object is {@link Integer } - * + * allowed object is + * {@link Boolean } + * */ - public void setXpos(Integer value) - { - this.xpos = value; + public void setDisplayText(Boolean value) { + this.displayText = value; } /** - * Gets the value of the ypos property. - * - * @return possible object is {@link Integer } + * Gets the value of the colourText property. * + * @return + * possible object is + * {@link Boolean } + * */ - public Integer getYpos() - { - return ypos; + public Boolean isColourText() { + return colourText; } /** - * Sets the value of the ypos property. + * Sets the value of the colourText property. * * @param value - * allowed object is {@link Integer } - * + * allowed object is + * {@link Boolean } + * */ - public void setYpos(Integer value) - { - this.ypos = value; + public void setColourText(Boolean value) { + this.colourText = value; } - } - - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="secondaryStructure" - * maxOccurs="unbounded"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attribute name="title" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="annotationId" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="gapped" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewerState" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute - * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="viewId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="dividerLocation" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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. - * - * <p> 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 - * <CODE>set</CODE> method for the secondaryStructure - * property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getSecondaryStructure().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attribute name="title" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="annotationId" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="gapped" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="viewerState" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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 } + * Gets the value of the textCol1 property. * + * @return + * possible object is + * {@link Integer } + * */ - public String getTitle() - { - return title; + public Integer getTextCol1() { + return textCol1; } /** - * Sets the value of the title property. + * Sets the value of the textCol1 property. * * @param value - * allowed object is {@link String } - * + * allowed object is + * {@link Integer } + * */ - public void setTitle(String value) - { - this.title = value; + public void setTextCol1(Integer value) { + this.textCol1 = value; } /** - * Gets the value of the annotationId property. - * - * @return possible object is {@link String } + * Gets the value of the textCol2 property. * + * @return + * possible object is + * {@link Integer } + * */ - public String getAnnotationId() - { - return annotationId; + public Integer getTextCol2() { + return textCol2; } /** - * Sets the value of the annotationId property. + * Sets the value of the textCol2 property. * * @param value - * allowed object is {@link String } - * + * allowed object is + * {@link Integer } + * */ - public void setAnnotationId(String value) - { - this.annotationId = value; + public void setTextCol2(Integer value) { + this.textCol2 = value; } /** - * Gets the value of the gapped property. - * - * @return possible object is {@link Boolean } + * Gets the value of the textColThreshold property. * + * @return + * possible object is + * {@link Integer } + * */ - public Boolean isGapped() - { - return gapped; + public Integer getTextColThreshold() { + return textColThreshold; } /** - * Sets the value of the gapped property. + * Sets the value of the textColThreshold property. * * @param value - * allowed object is {@link Boolean } - * + * allowed object is + * {@link Integer } + * */ - public void setGapped(Boolean value) - { - this.gapped = value; + public void setTextColThreshold(Integer value) { + this.textColThreshold = value; } /** - * Gets the value of the viewerState property. - * - * @return possible object is {@link String } + * Gets the value of the showUnconserved property. * + * @return + * possible object is + * {@link Boolean } + * */ - public String getViewerState() - { - return viewerState; + public Boolean isShowUnconserved() { + return showUnconserved; } /** - * Sets the value of the viewerState property. + * Sets the value of the showUnconserved property. * * @param value - * allowed object is {@link String } + * allowed object is + * {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) { + this.showUnconserved = value; + } + + /** + * Optional sequence group ID (only + * needs to be + * unique for this + * alignment) * + * @return + * possible object is + * {@link String } + * */ - public void setViewerState(String value) - { - this.viewerState = value; + public String getId() { + return id; } - } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getId() + */ + public void setId(String value) { + this.id = value; + } - } + /** + * Gets the value of the conservationSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isConservationSelected() { + return conservationSelected; + } - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="sequencePoint" - * maxOccurs="unbounded"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;attribute - * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;element name="seqPointMin"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;element name="seqPointMax"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; - * &lt;/element&gt; &lt;element name="pcaData" - * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt; - * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt; - * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; - * &lt;attribute name="title" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="xDim" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="bgColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="showLabels" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="linkToAllViews" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType( - name = "", - propOrder = - { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" }) - public static class PcaViewer - { - - @XmlElement(namespace = "www.jalview.org", required = true) - protected List sequencePoint; - - @XmlElement(namespace = "www.jalview.org", required = true) - protected List axis; - - @XmlElement(namespace = "www.jalview.org", required = true) - protected JalviewModel.PcaViewer.SeqPointMin seqPointMin; - - @XmlElement(namespace = "www.jalview.org", required = true) - protected JalviewModel.PcaViewer.SeqPointMax seqPointMax; - - @XmlElement(namespace = "www.jalview.org", required = true) - protected PcaDataType pcaData; - - @XmlAttribute(name = "title") - protected String title; - - @XmlAttribute(name = "scoreModelName") - protected String scoreModelName; - - @XmlAttribute(name = "xDim") - protected Integer xDim; - - @XmlAttribute(name = "yDim") - protected Integer yDim; - - @XmlAttribute(name = "zDim") - protected Integer zDim; - - @XmlAttribute(name = "bgColour") - protected Integer bgColour; - - @XmlAttribute(name = "scaleFactor") - protected Float scaleFactor; - - @XmlAttribute(name = "showLabels") - protected Boolean showLabels; - - @XmlAttribute(name = "linkToAllViews") - protected Boolean linkToAllViews; - - @XmlAttribute(name = "includeGaps") - protected Boolean includeGaps; - - @XmlAttribute(name = "matchGaps") - protected Boolean matchGaps; - - @XmlAttribute(name = "includeGappedColumns") - protected Boolean includeGappedColumns; - - @XmlAttribute(name = "denominateByShortestLength") - protected Boolean denominateByShortestLength; - - @XmlAttribute(name = "width") - protected Integer width; - - @XmlAttribute(name = "height") - protected Integer height; - - @XmlAttribute(name = "xpos") - protected Integer xpos; - - @XmlAttribute(name = "ypos") - protected Integer ypos; + /** + * 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 sequencePoint property. - * - * <p> 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 - * <CODE>set</CODE> method for the sequencePoint property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getSequencePoint().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link JalviewModel.PcaViewer.SequencePoint } - * - * - */ - public List getSequencePoint() - { - if (sequencePoint == null) - { - sequencePoint = new ArrayList(); - } - return this.sequencePoint; - } + /** + * Conservation shading increment + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getConsThreshold() { + return consThreshold; + } - /** - * Gets the value of the axis property. - * - * <p> 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 - * <CODE>set</CODE> method for the axis property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAxis().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link JalviewModel.PcaViewer.Axis } - * - * - */ - public List getAxis() - { - if (axis == null) - { - axis = new ArrayList(); - } - return this.axis; - } + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + * @see #getConsThreshold() + */ + public void setConsThreshold(Integer value) { + this.consThreshold = value; + } - /** - * Gets the value of the seqPointMin property. - * - * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin } - * - */ - public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() - { - return seqPointMin; - } + /** + * Gets the value of the pidSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isPidSelected() { + return pidSelected; + } - /** - * Sets the value of the seqPointMin property. - * - * @param value - * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin } - * - */ - public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) - { - this.seqPointMin = value; - } + /** + * 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 seqPointMax property. - * - * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax } - * - */ - public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() - { - return seqPointMax; - } + /** + * Percent Identity Threshold + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getPidThreshold() { + return pidThreshold; + } - /** - * Sets the value of the seqPointMax property. - * - * @param value - * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax } - * - */ - public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) - { - this.seqPointMax = value; - } + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + * @see #getPidThreshold() + */ + public void setPidThreshold(Integer value) { + this.pidThreshold = value; + } - /** - * Gets the value of the pcaData property. - * - * @return possible object is {@link PcaDataType } - * - */ - public PcaDataType getPcaData() - { - return pcaData; - } + /** + * Secondary structure consensus shading - since 2.11.4 + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isSecstrSelected() { + if (secstrSelected == null) { + return false; + } else { + return secstrSelected; + } + } - /** - * Sets the value of the pcaData property. - * - * @param value - * allowed object is {@link PcaDataType } - * - */ - public void setPcaData(PcaDataType value) - { - this.pcaData = value; - } + /** + * Sets the value of the secstrSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + * @see #isSecstrSelected() + */ + public void setSecstrSelected(Boolean value) { + this.secstrSelected = value; + } - /** - * Gets the value of the title property. - * - * @return possible object is {@link String } - * - */ - public String getTitle() - { - return title; - } + /** + * Secondary structure consensus increment + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getSecstrThreshold() { + return secstrThreshold; + } - /** - * Sets the value of the title property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setTitle(String value) - { - this.title = value; - } + /** + * Sets the value of the secstrThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + * @see #getSecstrThreshold() + */ + public void setSecstrThreshold(Integer value) { + this.secstrThreshold = value; + } - /** - * Gets the value of the scoreModelName property. - * - * @return possible object is {@link String } - * - */ - public String getScoreModelName() - { - return scoreModelName; - } + /** + * 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 scoreModelName property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setScoreModelName(String value) - { - this.scoreModelName = value; - } + /** + * 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 xDim property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getXDim() - { - return xDim; - } + /** + * 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 xDim property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setXDim(Integer value) - { - this.xDim = value; - } + /** + * 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 yDim property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getYDim() - { - return yDim; - } + /** + * 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 yDim property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setYDim(Integer value) - { - this.yDim = value; - } + /** + * 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 zDim property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getZDim() - { - return zDim; - } + /** + * 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 zDim property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setZDim(Integer value) - { - this.zDim = value; - } + /** + * 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 bgColour property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getBgColour() - { - return bgColour; } - /** - * Sets the value of the bgColour property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setBgColour(Integer value) - { - this.bgColour = value; - } /** - * Gets the value of the scaleFactor property. + *

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>
+     *
* - * @return possible object is {@link Float } * */ - public Float getScaleFactor() - { - return scaleFactor; - } + @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; + /** + * Reference to a viewer showing + * RNA structure for this sequence. + * Schema supports one viewer + * showing multiple annotations for + * multiple sequences, though + * currently only one annotation + * for one sequence (gapped or + * trimmed) is used + * + */ + @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; - /** - * Sets the value of the scaleFactor property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setScaleFactor(Float value) - { - this.scaleFactor = value; - } + /** + * 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 } + *

+ * + * + * @return + * The value of the features property. + */ + public List getFeatures() { + if (features == null) { + features = new ArrayList(); + } + return this.features; + } - /** - * Gets the value of the showLabels property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowLabels() - { - return showLabels; - } + /** + * 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 } + *

+ * + * + * @return + * The value of the pdbids property. + */ + public List getPdbids() { + if (pdbids == null) { + pdbids = new ArrayList(); + } + return this.pdbids; + } - /** - * Sets the value of the showLabels property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowLabels(Boolean value) - { - this.showLabels = value; - } - - /** - * Gets the value of the linkToAllViews property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isLinkToAllViews() - { - return linkToAllViews; - } + /** + * 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 } + *

+ * + * + * @return + * The value of the hiddenSequences property. + */ + public List getHiddenSequences() { + if (hiddenSequences == null) { + hiddenSequences = new ArrayList(); + } + return this.hiddenSequences; + } - /** - * Sets the value of the linkToAllViews property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setLinkToAllViews(Boolean value) - { - this.linkToAllViews = value; - } + /** + * Reference to a viewer showing + * RNA structure for this sequence. + * Schema supports one viewer + * showing multiple annotations for + * multiple sequences, though + * currently only one annotation + * for one sequence (gapped or + * trimmed) is used + * + * 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 } + *

+ * + * + * @return + * The value of the rnaViewer property. + */ + public List getRnaViewer() { + if (rnaViewer == null) { + rnaViewer = new ArrayList(); + } + return this.rnaViewer; + } - /** - * Gets the value of the includeGaps property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isIncludeGaps() - { - return includeGaps; - } + /** + * Gets the value of the colour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getColour() { + return colour; + } - /** - * Sets the value of the includeGaps property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setIncludeGaps(Boolean value) - { - this.includeGaps = value; - } + /** + * 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 matchGaps property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isMatchGaps() - { - return matchGaps; - } + /** + * Gets the value of the start property. + * + */ + public int getStart() { + return start; + } - /** - * Sets the value of the matchGaps property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setMatchGaps(Boolean value) - { - this.matchGaps = value; - } + /** + * Sets the value of the start property. + * + */ + public void setStart(int value) { + this.start = value; + } - /** - * Gets the value of the includeGappedColumns property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isIncludeGappedColumns() - { - return includeGappedColumns; - } + /** + * Gets the value of the end property. + * + */ + public int getEnd() { + return end; + } - /** - * Sets the value of the includeGappedColumns property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setIncludeGappedColumns(Boolean value) - { - this.includeGappedColumns = value; - } + /** + * Sets the value of the end property. + * + */ + public void setEnd(int value) { + this.end = value; + } - /** - * Gets the value of the denominateByShortestLength property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isDenominateByShortestLength() - { - return denominateByShortestLength; - } + /** + * Gets the value of the id property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } - /** - * Sets the value of the denominateByShortestLength property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setDenominateByShortestLength(Boolean value) - { - this.denominateByShortestLength = value; - } + /** + * 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; - } + /** + * Gets the value of the hidden property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isHidden() { + return hidden; + } - /** - * Sets the value of the width property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setWidth(Integer value) - { - this.width = value; - } + /** + * 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 height property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getHeight() - { - return height; - } + /** + * Gets the value of the viewreference property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isViewreference() { + return viewreference; + } - /** - * Sets the value of the height property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setHeight(Integer value) - { - this.height = value; - } + /** + * Sets the value of the viewreference property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setViewreference(Boolean value) { + this.viewreference = 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; - } + /** + *

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 + { - /** - * Gets the value of the ypos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getYpos() - { - return ypos; - } + @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 } + *

+ * + * + * @return + * The value of the structureState property. + */ + 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; + /** + * additional + * identifier + * which + * properly + * disambiguates + * the + * structure + * view + * from + * any + * other + * view + * with + * the + * same + * attributes. + * This + * is + * not + * an + * ID, + * because + * it + * is + * possible + * to + * have + * many + * references + * to + * the + * same + * physical + * structure + * view + * from + * different + * sequences + * in + * an + * alignment. + * A + * structureState + * element + * citing + * the + * same + * viewId + * will + * appear + * for + * each + * instance. + * + */ + @XmlAttribute(name = "viewId") + protected String viewId; + /** + * Flag + * set + * if + * the + * alignment + * panel + * containing + * this + * JSeq + * should + * be + * included + * in + * those + * used + * to + * perform + * a + * structure + * superposition + * (since + * Jalview + * 2.7). + * + */ + @XmlAttribute(name = "alignwithAlignPanel") + protected Boolean alignwithAlignPanel; + /** + * Flag + * set + * if + * the + * alignment + * panel + * containing + * this + * JSeq + * should + * be + * included + * in + * those + * used + * to + * colour + * its + * associated + * sequences + * in + * this + * structureState(since + * Jalview + * 2.7). + * + */ + @XmlAttribute(name = "colourwithAlignPanel") + protected Boolean colourwithAlignPanel; + /** + * Flag + * set + * if + * the + * structure + * display + * is + * coloured + * by + * the + * Jmol + * state, + * rather + * than + * by + * one + * or + * more + * linked + * alignment + * views. + * + */ + @XmlAttribute(name = "colourByJmol") + protected Boolean colourByJmol; + /** + * An + * identifier + * for + * the + * viewer + * type, + * currently + * either + * JMOL + * or + * CHIMERA + * + */ + @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; + } + + /** + * additional + * identifier + * which + * properly + * disambiguates + * the + * structure + * view + * from + * any + * other + * view + * with + * the + * same + * attributes. + * This + * is + * not + * an + * ID, + * because + * it + * is + * possible + * to + * have + * many + * references + * to + * the + * same + * physical + * structure + * view + * from + * different + * sequences + * in + * an + * alignment. + * A + * structureState + * element + * citing + * the + * same + * viewId + * will + * appear + * for + * each + * instance. + * + * @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 } + * + * @see #getViewId() + */ + public void setViewId(String value) { + this.viewId = value; + } + + /** + * Flag + * set + * if + * the + * alignment + * panel + * containing + * this + * JSeq + * should + * be + * included + * in + * those + * used + * to + * perform + * a + * structure + * superposition + * (since + * Jalview + * 2.7). + * + * @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 } + * + * @see #isAlignwithAlignPanel() + */ + public void setAlignwithAlignPanel(Boolean value) { + this.alignwithAlignPanel = value; + } + + /** + * Flag + * set + * if + * the + * alignment + * panel + * containing + * this + * JSeq + * should + * be + * included + * in + * those + * used + * to + * colour + * its + * associated + * sequences + * in + * this + * structureState(since + * Jalview + * 2.7). + * + * @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 } + * + * @see #isColourwithAlignPanel() + */ + public void setColourwithAlignPanel(Boolean value) { + this.colourwithAlignPanel = value; + } + + /** + * Flag + * set + * if + * the + * structure + * display + * is + * coloured + * by + * the + * Jmol + * state, + * rather + * than + * by + * one + * or + * more + * linked + * alignment + * views. + * + * @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 } + * + * @see #isColourByJmol() + */ + public void setColourByJmol(Boolean value) { + this.colourByJmol = value; + } + + /** + * An + * identifier + * for + * the + * viewer + * type, + * currently + * either + * JMOL + * or + * CHIMERA + * + * @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 } + * + * @see #getType() + */ + 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; + } + + } - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setYpos(Integer value) - { - this.ypos = value; - } + } - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Axis - { - - @XmlAttribute(name = "xPos") - protected Float xPos; - - @XmlAttribute(name = "yPos") - protected Float yPos; - - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * Gets the value of the xPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getXPos() - { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setXPos(Float value) - { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getYPos() - { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setYPos(Float value) - { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getZPos() - { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setZPos(Float value) - { - this.zPos = 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; + /** + * An id unique to the RNA + * viewer panel + * + */ + @XmlAttribute(name = "viewId") + protected String viewId; + /** + * horizontal position of + * split pane divider + * + */ + @XmlAttribute(name = "dividerLocation") + protected Integer dividerLocation; + /** + * Index of the selected + * structure in the viewer + * panel + * + */ + @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 } + *

+ * + * + * @return + * The value of the secondaryStructure property. + */ + 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; + } + + /** + * An id unique to the RNA + * viewer panel + * + * @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 } + * + * @see #getViewId() + */ + public void setViewId(String value) { + this.viewId = value; + } + + /** + * horizontal position of + * split pane divider + * + * @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 } + * + * @see #getDividerLocation() + */ + public void setDividerLocation(Integer value) { + this.dividerLocation = value; + } + + /** + * Index of the selected + * structure in the viewer + * panel + * + * @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 } + * + * @see #getSelectedRna() + */ + 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; + /** + * id attribute + * of + * Annotation + * in + * vamsasModel + * for the + * secondary + * structure + * annotation + * shown in the + * viewer + * + */ + @XmlAttribute(name = "annotationId", required = true) + protected String annotationId; + /** + * if true the + * RNA + * structure is + * shown with + * gaps, if + * false + * without + * + */ + @XmlAttribute(name = "gapped") + protected Boolean gapped; + /** + * name of the + * project jar + * entry that + * holds the + * VARNA viewer + * state for + * the + * structure + * + */ + @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; + } + + /** + * id attribute + * of + * Annotation + * in + * vamsasModel + * for the + * secondary + * structure + * annotation + * shown in the + * viewer + * + * @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 } + * + * @see #getAnnotationId() + */ + public void setAnnotationId(String value) { + this.annotationId = value; + } + + /** + * if true the + * RNA + * structure is + * shown with + * gaps, if + * false + * without + * + * @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 } + * + * @see #isGapped() + */ + public void setGapped(Boolean value) { + this.gapped = value; + } + + /** + * name of the + * project jar + * entry that + * holds the + * VARNA viewer + * state for + * the + * structure + * + * @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 } + * + * @see #getViewerState() + */ + public void setViewerState(String value) { + this.viewerState = value; + } + + } - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SeqPointMax - { - - @XmlAttribute(name = "xPos") - protected Float xPos; - - @XmlAttribute(name = "yPos") - protected Float yPos; - - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * Gets the value of the xPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getXPos() - { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setXPos(Float value) - { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getYPos() - { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setYPos(Float value) - { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getZPos() - { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setZPos(Float value) - { - this.zPos = value; - } + } } - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SeqPointMin - { - - @XmlAttribute(name = "xPos") - protected Float xPos; - - @XmlAttribute(name = "yPos") - protected Float yPos; - - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * Gets the value of the xPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getXPos() - { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setXPos(Float value) - { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getYPos() - { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setYPos(Float value) - { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getZPos() - { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setZPos(Float value) - { - this.zPos = value; - } - - } /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}position"/&gt; &lt;attribute - * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + *

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="sequencePoint" maxOccurs="unbounded">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="axis" maxOccurs="3" minOccurs="3">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="seqPointMin">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="seqPointMax">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
* * */ @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SequencePoint - { - - @XmlAttribute(name = "sequenceRef") - protected String sequenceRef; - - @XmlAttribute(name = "xPos") - protected Float xPos; - - @XmlAttribute(name = "yPos") - protected Float yPos; - - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * 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 xPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getXPos() - { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setXPos(Float value) - { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getYPos() - { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setYPos(Float value) - { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return possible object is {@link Float } - * - */ - public Float getZPos() - { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setZPos(Float value) - { - this.zPos = value; - } + @XmlType(name = "", propOrder = { + "sequencePoint", + "axis", + "seqPointMin", + "seqPointMax", + "pcaData" + }) + public static class PcaViewer { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List sequencePoint; + /** + * endpoints of X, Y and Z axes in that order + * + */ + @XmlElement(namespace = "www.jalview.org", required = true) + protected List axis; + @XmlElement(namespace = "www.jalview.org", required = true) + protected JalviewModel.PcaViewer.SeqPointMin seqPointMin; + @XmlElement(namespace = "www.jalview.org", required = true) + protected JalviewModel.PcaViewer.SeqPointMax seqPointMax; + @XmlElement(namespace = "www.jalview.org", required = true) + protected PcaDataType pcaData; + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "scoreModelName") + protected String scoreModelName; + @XmlAttribute(name = "xDim") + protected Integer xDim; + @XmlAttribute(name = "yDim") + protected Integer yDim; + @XmlAttribute(name = "zDim") + protected Integer zDim; + @XmlAttribute(name = "bgColour") + protected Integer bgColour; + @XmlAttribute(name = "scaleFactor") + protected Float scaleFactor; + @XmlAttribute(name = "showLabels") + protected Boolean showLabels; + @XmlAttribute(name = "linkToAllViews") + protected Boolean linkToAllViews; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + @XmlAttribute(name = "includeGaps") + protected Boolean includeGaps; + @XmlAttribute(name = "matchGaps") + protected Boolean matchGaps; + @XmlAttribute(name = "includeGappedColumns") + protected Boolean includeGappedColumns; + @XmlAttribute(name = "denominateByShortestLength") + protected Boolean denominateByShortestLength; - } + /** + * Gets the value of the sequencePoint 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 sequencePoint property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.PcaViewer.SequencePoint } + *

+ * + * + * @return + * The value of the sequencePoint property. + */ + public List getSequencePoint() { + if (sequencePoint == null) { + sequencePoint = new ArrayList(); + } + return this.sequencePoint; + } - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence - * minOccurs="0"&gt; &lt;element name="title" - * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element - * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; - * &lt;/sequence&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute - * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="fontSize" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="threshold" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="showDistances" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="markUnlinked" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="fitToWindow" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="currentTree" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="columnWise" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="columnReference" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; - * &lt;attribute name="linkToAllViews" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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 = "columnWise") - protected Boolean columnWise; - - @XmlAttribute(name = "columnReference") - protected String columnReference; - - @XmlAttribute(name = "id") - @XmlJavaTypeAdapter(CollapsedStringAdapter.class) - @XmlID - @XmlSchemaType(name = "ID") - protected String id; - - @XmlAttribute(name = "linkToAllViews") - protected Boolean linkToAllViews; - - @XmlAttribute(name = "width") - protected Integer width; - - @XmlAttribute(name = "height") - protected Integer height; - - @XmlAttribute(name = "xpos") - protected Integer xpos; - - @XmlAttribute(name = "ypos") - protected Integer ypos; + /** + * endpoints of X, Y and Z axes in that order + * + * Gets the value of the axis 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 axis property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.PcaViewer.Axis } + *

+ * + * + * @return + * The value of the axis property. + */ + public List getAxis() { + if (axis == null) { + axis = new ArrayList(); + } + return this.axis; + } - /** - * Gets the value of the title property. - * - * @return possible object is {@link String } - * - */ - public String getTitle() - { - return title; - } + /** + * Gets the value of the seqPointMin property. + * + * @return + * possible object is + * {@link JalviewModel.PcaViewer.SeqPointMin } + * + */ + public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() { + return seqPointMin; + } - /** - * Sets the value of the title property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setTitle(String value) - { - this.title = value; - } + /** + * Sets the value of the seqPointMin property. + * + * @param value + * allowed object is + * {@link JalviewModel.PcaViewer.SeqPointMin } + * + */ + public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) { + this.seqPointMin = value; + } - /** - * Gets the value of the newick property. - * - * @return possible object is {@link String } - * - */ - public String getNewick() - { - return newick; - } + /** + * Gets the value of the seqPointMax property. + * + * @return + * possible object is + * {@link JalviewModel.PcaViewer.SeqPointMax } + * + */ + public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() { + return seqPointMax; + } - /** - * Sets the value of the newick property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setNewick(String value) - { - this.newick = value; - } + /** + * Sets the value of the seqPointMax property. + * + * @param value + * allowed object is + * {@link JalviewModel.PcaViewer.SeqPointMax } + * + */ + public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) { + this.seqPointMax = value; + } - /** - * Gets the value of the fontName property. - * - * @return possible object is {@link String } - * - */ - public String getFontName() - { - return fontName; - } + /** + * Gets the value of the pcaData property. + * + * @return + * possible object is + * {@link PcaDataType } + * + */ + public PcaDataType getPcaData() { + return pcaData; + } - /** - * Sets the value of the fontName property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setFontName(String value) - { - this.fontName = value; - } + /** + * Sets the value of the pcaData property. + * + * @param value + * allowed object is + * {@link PcaDataType } + * + */ + public void setPcaData(PcaDataType value) { + this.pcaData = value; + } - /** - * Gets the value of the fontSize property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getFontSize() - { - return fontSize; - } + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } - /** - * Sets the value of the fontSize property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setFontSize(Integer value) - { - this.fontSize = value; - } + /** + * 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 fontStyle property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getFontStyle() - { - return fontStyle; - } + /** + * Gets the value of the scoreModelName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getScoreModelName() { + return scoreModelName; + } - /** - * Sets the value of the fontStyle property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setFontStyle(Integer value) - { - this.fontStyle = value; - } + /** + * Sets the value of the scoreModelName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setScoreModelName(String value) { + this.scoreModelName = value; + } - /** - * Gets the value of the threshold property. - * - * @return possible object is {@link Float } - * - */ - public Float getThreshold() - { - return threshold; - } + /** + * Gets the value of the xDim property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXDim() { + return xDim; + } - /** - * Sets the value of the threshold property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setThreshold(Float value) - { - this.threshold = value; - } + /** + * Sets the value of the xDim property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXDim(Integer value) { + this.xDim = value; + } - /** - * Gets the value of the showBootstrap property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowBootstrap() - { - return showBootstrap; - } + /** + * Gets the value of the yDim property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYDim() { + return yDim; + } - /** - * Sets the value of the showBootstrap property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowBootstrap(Boolean value) - { - this.showBootstrap = value; - } + /** + * Sets the value of the yDim property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYDim(Integer value) { + this.yDim = value; + } - /** - * Gets the value of the showDistances property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowDistances() - { - return showDistances; - } + /** + * Gets the value of the zDim property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getZDim() { + return zDim; + } - /** - * Sets the value of the showDistances property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowDistances(Boolean value) - { - this.showDistances = value; - } + /** + * Sets the value of the zDim property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setZDim(Integer value) { + this.zDim = value; + } - /** - * Gets the value of the markUnlinked property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isMarkUnlinked() - { - return markUnlinked; - } + /** + * Gets the value of the bgColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getBgColour() { + return bgColour; + } - /** - * Sets the value of the markUnlinked property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setMarkUnlinked(Boolean value) - { - this.markUnlinked = value; - } + /** + * Sets the value of the bgColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setBgColour(Integer value) { + this.bgColour = value; + } - /** - * Gets the value of the fitToWindow property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isFitToWindow() - { - return fitToWindow; - } + /** + * Gets the value of the scaleFactor property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getScaleFactor() { + return scaleFactor; + } - /** - * Sets the value of the fitToWindow property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setFitToWindow(Boolean value) - { - this.fitToWindow = value; - } + /** + * Sets the value of the scaleFactor property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setScaleFactor(Float value) { + this.scaleFactor = value; + } - /** - * Gets the value of the currentTree property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isCurrentTree() - { - return currentTree; - } + /** + * Gets the value of the showLabels property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowLabels() { + return showLabels; + } - /** - * Sets the value of the currentTree property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setCurrentTree(Boolean value) - { - this.currentTree = value; - } + /** + * Sets the value of the showLabels property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowLabels(Boolean value) { + this.showLabels = value; + } - /** - * Gets the value of the columnWise property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isColumnWise() - { - if (columnWise == null) - { - return false; - } - else - { - return columnWise; - } - } + /** + * Gets the value of the linkToAllViews property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isLinkToAllViews() { + return linkToAllViews; + } - /** - * Sets the value of the columnWise property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setColumnWise(Boolean value) - { - this.columnWise = value; - } + /** + * Sets the value of the linkToAllViews property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setLinkToAllViews(Boolean value) { + this.linkToAllViews = value; + } - /** - * Gets the value of the columnReference property. - * - * @return possible object is {@link String } - * - */ - public String getColumnReference() - { - return columnReference; - } + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } - /** - * Sets the value of the columnReference property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setColumnReference(String value) - { - this.columnReference = value; - } + /** + * 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 id property. - * - * @return possible object is {@link String } - * - */ - public String getId() - { - return id; - } + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setId(String value) - { - this.id = value; - } + /** + * 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 linkToAllViews property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isLinkToAllViews() - { - if (linkToAllViews == null) - { - return false; - } - else - { - return linkToAllViews; - } - } + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } - /** - * Sets the value of the linkToAllViews property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setLinkToAllViews(Boolean value) - { - this.linkToAllViews = value; - } + /** + * 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 width property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getWidth() - { - return width; - } + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } - /** - * Sets the value of the width property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setWidth(Integer value) - { - this.width = value; - } + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } - /** - * Gets the value of the height property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getHeight() - { - return height; - } + /** + * Gets the value of the includeGaps property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isIncludeGaps() { + return includeGaps; + } - /** - * Sets the value of the height property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setHeight(Integer value) - { - this.height = value; - } + /** + * Sets the value of the includeGaps property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIncludeGaps(Boolean value) { + this.includeGaps = value; + } - /** - * Gets the value of the xpos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getXpos() - { - return xpos; - } + /** + * Gets the value of the matchGaps property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isMatchGaps() { + return matchGaps; + } - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setXpos(Integer value) - { - this.xpos = value; - } + /** + * Sets the value of the matchGaps property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setMatchGaps(Boolean value) { + this.matchGaps = value; + } - /** - * Gets the value of the ypos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getYpos() - { - return ypos; - } + /** + * Gets the value of the includeGappedColumns property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isIncludeGappedColumns() { + return includeGappedColumns; + } - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setYpos(Integer value) - { - this.ypos = value; - } + /** + * Sets the value of the includeGappedColumns property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIncludeGappedColumns(Boolean value) { + this.includeGappedColumns = value; + } - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="UserColourScheme" - * type="{www.jalview.org/colours}JalviewUserColours"/&gt; - * &lt;/sequence&gt; &lt;attribute name="id" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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 denominateByShortestLength property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isDenominateByShortestLength() { + return denominateByShortestLength; + } - /** - * Gets the value of the userColourScheme property. - * - * @return possible object is {@link JalviewUserColours } - * - */ - public JalviewUserColours getUserColourScheme() - { - return userColourScheme; - } + /** + * Sets the value of the denominateByShortestLength property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setDenominateByShortestLength(Boolean value) { + this.denominateByShortestLength = value; + } - /** - * 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; - } + /** + *

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">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Axis { + + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setId(String value) - { - this.id = value; - } + } - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="AnnotationColours" - * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt; - * &lt;element name="hiddenColumns" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;extension - * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt; - * &lt;attribute name="calcId" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="false" /&gt; &lt;attribute name="autoUpdate" - * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/extension&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="overview" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute - * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="residueColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="hiddenColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute - * name="conservationSelected" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="pidSelected" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="bgColour" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="pidThreshold" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="showFullId" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="rightAlignIds" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="showText" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="showColourText" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="showUnconserved" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showBoxes" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="wrapAlignment" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="renderGaps" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="showSequenceFeatures" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="showNPfeatureTooltip" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="showDbRefTooltip" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="followHighlight" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="followSelection" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="showAnnotation" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="centreColumnLabels" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showGroupConservation" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showGroupConsensus" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showConsensusHistogram" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="showSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="normaliseSequenceLogo" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="ignoreGapsinConsensus" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="startRes" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="charWidth" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="fontName" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="fontStyle" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="idWidthManuallyAdjusted" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="scaleProteinAsCdna" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; - * &lt;attribute name="viewName" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="gatheredViews" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;attribute name="textCol1" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="textColThreshold" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; - * &lt;attribute name="complementId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="showComplementFeatures" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;attribute name="showComplementFeaturesOnTop" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType( - name = "", - propOrder = - { "annotationColours", "hiddenColumns", "calcIdParam", "overview" }) - 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; - - @XmlElement(namespace = "www.jalview.org") - protected JalviewModel.Viewport.Overview overview; - - @XmlAttribute(name = "conservationSelected") - protected Boolean conservationSelected; - - @XmlAttribute(name = "pidSelected") - protected Boolean pidSelected; - - @XmlAttribute(name = "byConsensusSecondaryStructureSelected") - protected Boolean byConsensusSecondaryStructureSelected; - - @XmlAttribute(name = "bgColour") - protected String bgColour; - - @XmlAttribute(name = "consThreshold") - protected Integer consThreshold; - - @XmlAttribute(name = "pidThreshold") - protected Integer pidThreshold; - - @XmlAttribute(name = "consensusSecondaryStructureThreshold") - protected Integer consensusSecondaryStructureThreshold; - - @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; + /** + *

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">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SeqPointMax { + + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } - @XmlAttribute(name = "showSequenceFeatures") - protected Boolean showSequenceFeatures; + } - @XmlAttribute(name = "showNPfeatureTooltip") - protected Boolean showNPfeatureTooltip; - @XmlAttribute(name = "showDbRefTooltip") - protected Boolean showDbRefTooltip; + /** + *

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">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SeqPointMin { + + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } - @XmlAttribute(name = "followHighlight") - protected Boolean followHighlight; + } - @XmlAttribute(name = "followSelection") - protected Boolean followSelection; - @XmlAttribute(name = "showAnnotation") - protected Boolean showAnnotation; + /** + *

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">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SequencePoint { + + @XmlAttribute(name = "sequenceRef") + protected String sequenceRef; + @XmlAttribute(name = "xPos") + protected Float xPos; + @XmlAttribute(name = "yPos") + protected Float yPos; + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * 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 xPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getXPos() { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setXPos(Float value) { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getYPos() { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setYPos(Float value) { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getZPos() { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setZPos(Float value) { + this.zPos = value; + } - @XmlAttribute(name = "centreColumnLabels") - protected Boolean centreColumnLabels; + } - @XmlAttribute(name = "showGroupConservation") - protected Boolean showGroupConservation; + } - @XmlAttribute(name = "showGroupConsensus") - protected Boolean showGroupConsensus; - - @XmlAttribute(name = "showGroupSSConsensus") - protected Boolean showGroupSSConsensus; - @XmlAttribute(name = "showConsensusHistogram") - protected Boolean showConsensusHistogram; + /** + *

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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "title", + "newick" + }) + public static class Tree { - @XmlAttribute(name = "showSequenceLogo") - protected Boolean showSequenceLogo; + @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; + /** + * Set for trees associated with columns of an alignment, sequence or annotation row + * + */ + @XmlAttribute(name = "columnWise") + protected Boolean columnWise; + /** + * Refers to annotation row the tree is provided by + * + */ + @XmlAttribute(name = "columnReference") + protected String columnReference; + /** + * Tree ID added for binding tree + * visualization + * settings to vamsas + * document trees in jalview 2.4.1 + * + */ + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + @XmlAttribute(name = "linkToAllViews") + protected Boolean linkToAllViews; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; - @XmlAttribute(name = "normaliseSequenceLogo") - protected Boolean normaliseSequenceLogo; + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } - @XmlAttribute(name = "ignoreGapsinConsensus") - protected Boolean ignoreGapsinConsensus; + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } - @XmlAttribute(name = "startRes") - protected Integer startRes; + /** + * Gets the value of the newick property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getNewick() { + return newick; + } - @XmlAttribute(name = "startSeq") - protected Integer startSeq; + /** + * Sets the value of the newick property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setNewick(String value) { + this.newick = value; + } - @XmlAttribute(name = "charWidth") - protected Integer charWidth; + /** + * Gets the value of the fontName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFontName() { + return fontName; + } - @XmlAttribute(name = "charHeight") - protected Integer charHeight; + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFontName(String value) { + this.fontName = value; + } - @XmlAttribute(name = "fontName") - protected String fontName; + /** + * Gets the value of the fontSize property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontSize() { + return fontSize; + } - @XmlAttribute(name = "fontSize") - protected Integer fontSize; + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontSize(Integer value) { + this.fontSize = value; + } - @XmlAttribute(name = "fontStyle") - protected Integer fontStyle; + /** + * Gets the value of the fontStyle property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontStyle() { + return fontStyle; + } - @XmlAttribute(name = "idWidth") - protected Integer idWidth; + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontStyle(Integer value) { + this.fontStyle = value; + } - @XmlAttribute(name = "idWidthManuallyAdjusted") - protected Boolean idWidthManuallyAdjusted; + /** + * Gets the value of the threshold property. + * + * @return + * possible object is + * {@link Float } + * + */ + public Float getThreshold() { + return threshold; + } - @XmlAttribute(name = "scaleProteinAsCdna") - protected Boolean scaleProteinAsCdna; + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is + * {@link Float } + * + */ + public void setThreshold(Float value) { + this.threshold = value; + } - @XmlAttribute(name = "viewName") - protected String viewName; + /** + * Gets the value of the showBootstrap property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowBootstrap() { + return showBootstrap; + } - @XmlAttribute(name = "sequenceSetId") - protected String sequenceSetId; + /** + * Sets the value of the showBootstrap property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowBootstrap(Boolean value) { + this.showBootstrap = value; + } - @XmlAttribute(name = "gatheredViews") - protected Boolean gatheredViews; + /** + * Gets the value of the showDistances property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowDistances() { + return showDistances; + } - @XmlAttribute(name = "textCol1") - protected Integer textCol1; + /** + * Sets the value of the showDistances property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowDistances(Boolean value) { + this.showDistances = value; + } - @XmlAttribute(name = "textCol2") - protected Integer textCol2; + /** + * Gets the value of the markUnlinked property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isMarkUnlinked() { + return markUnlinked; + } - @XmlAttribute(name = "textColThreshold") - protected Integer textColThreshold; + /** + * Sets the value of the markUnlinked property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setMarkUnlinked(Boolean value) { + this.markUnlinked = value; + } - @XmlAttribute(name = "id") - @XmlJavaTypeAdapter(CollapsedStringAdapter.class) - @XmlID - @XmlSchemaType(name = "ID") - protected String id; + /** + * Gets the value of the fitToWindow property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isFitToWindow() { + return fitToWindow; + } - @XmlAttribute(name = "complementId") - protected String complementId; + /** + * Sets the value of the fitToWindow property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setFitToWindow(Boolean value) { + this.fitToWindow = value; + } - @XmlAttribute(name = "showComplementFeatures") - protected Boolean showComplementFeatures; + /** + * Gets the value of the currentTree property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isCurrentTree() { + return currentTree; + } - @XmlAttribute(name = "showComplementFeaturesOnTop") - protected Boolean showComplementFeaturesOnTop; + /** + * Sets the value of the currentTree property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setCurrentTree(Boolean value) { + this.currentTree = value; + } - @XmlAttribute(name = "width") - protected Integer width; + /** + * Set for trees associated with columns of an alignment, sequence or annotation row + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isColumnWise() { + if (columnWise == null) { + return false; + } else { + return columnWise; + } + } - @XmlAttribute(name = "height") - protected Integer height; + /** + * Sets the value of the columnWise property. + * + * @param value + * allowed object is + * {@link Boolean } + * + * @see #isColumnWise() + */ + public void setColumnWise(Boolean value) { + this.columnWise = value; + } - @XmlAttribute(name = "xpos") - protected Integer xpos; + /** + * Refers to annotation row the tree is provided by + * + * @return + * possible object is + * {@link String } + * + */ + public String getColumnReference() { + return columnReference; + } - @XmlAttribute(name = "ypos") - protected Integer ypos; + /** + * Sets the value of the columnReference property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getColumnReference() + */ + public void setColumnReference(String value) { + this.columnReference = value; + } - /** - * Gets the value of the annotationColours property. - * - * @return possible object is {@link AnnotationColourScheme } - * - */ - public AnnotationColourScheme getAnnotationColours() - { - return annotationColours; - } + /** + * Tree ID added for binding tree + * visualization + * settings to vamsas + * document trees in jalview 2.4.1 + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } - /** - * Sets the value of the annotationColours property. - * - * @param value - * allowed object is {@link AnnotationColourScheme } - * - */ - public void setAnnotationColours(AnnotationColourScheme value) - { - this.annotationColours = value; - } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getId() + */ + public void setId(String value) { + this.id = value; + } - /** - * Gets the value of the hiddenColumns property. - * - * <p> 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 - * <CODE>set</CODE> method for the hiddenColumns property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getHiddenColumns().add(newItem); </pre> - * - * - * <p> 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 linkToAllViews property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isLinkToAllViews() { + if (linkToAllViews == null) { + return false; + } else { + return linkToAllViews; + } + } - /** - * Gets the value of the calcIdParam property. - * - * <p> 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 - * <CODE>set</CODE> method for the calcIdParam property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getCalcIdParam().add(newItem); </pre> - * - * - * <p> 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; - } + /** + * Sets the value of the linkToAllViews property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setLinkToAllViews(Boolean value) { + this.linkToAllViews = value; + } - /** - * Gets the value of the overview property. - * - * @return possible object is {@link JalviewModel.Viewport.Overview } - * - */ - public JalviewModel.Viewport.Overview getOverview() - { - return overview; - } + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } - /** - * Sets the value of the overview property. - * - * @param value - * allowed object is {@link JalviewModel.Viewport.Overview } - * - */ - public void setOverview(JalviewModel.Viewport.Overview value) - { - this.overview = value; - } + /** + * 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 conservationSelected property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isConservationSelected() - { - return conservationSelected; - } + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } - /** - * Sets the value of the conservationSelected property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setConservationSelected(Boolean value) - { - this.conservationSelected = value; - } + /** + * 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 pidSelected property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isPidSelected() - { - return pidSelected; - } + /** + * 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; + } - /** - * 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 byConsensusSecondaryStructureSelected property. + *

Java class for anonymous complex type

. * - * @return possible object is {@link Boolean } + *

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

* - */ - public Boolean isByConsensusSecondaryStructureSelected() - { - return byConsensusSecondaryStructureSelected; - } - - /** - * Sets the value of the byConsensusSecondaryStructureSelected property. + * 
+     * <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>
+     *
* - * @param value - * allowed object is {@link Boolean } * */ - public void setByConsensusSecondaryStructureSelected(Boolean value) - { - this.byConsensusSecondaryStructureSelected = value; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "userColourScheme" + }) + public static class UserColours { - /** - * Gets the value of the bgColour property. - * - * @return possible object is {@link String } - * - */ - public String getBgColour() - { - return bgColour; - } + @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true) + protected JalviewUserColours userColourScheme; + @XmlAttribute(name = "id") + protected String id; - /** - * 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 userColourScheme property. + * + * @return + * possible object is + * {@link JalviewUserColours } + * + */ + public JalviewUserColours getUserColourScheme() { + return userColourScheme; + } - /** - * Gets the value of the consThreshold property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getConsThreshold() - { - return consThreshold; - } + /** + * Sets the value of the userColourScheme property. + * + * @param value + * allowed object is + * {@link JalviewUserColours } + * + */ + public void setUserColourScheme(JalviewUserColours value) { + this.userColourScheme = value; + } - /** - * 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 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 pidThreshold property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getPidThreshold() - { - return pidThreshold; } + /** - * Sets the value of the pidThreshold property. + *

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>
+     *         <element name="overview" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attGroup ref="{www.jalview.org}conservationShading"/>
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <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="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="charHeight" 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="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <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" />
+     *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
* - * @param value - * allowed object is {@link Integer } * */ - public void setPidThreshold(Integer value) - { - this.pidThreshold = value; - } - - /** - * Gets the value of the consensusSecondaryStructureThreshold property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getConsensusSecondaryStructureThreshold() - { - return consensusSecondaryStructureThreshold; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "annotationColours", + "hiddenColumns", + "calcIdParam", + "overview", + "secStrProvider" + }) + 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; + @XmlElement(namespace = "www.jalview.org") + protected JalviewModel.Viewport.Overview overview; + @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org") + protected List secStrProvider; + @XmlAttribute(name = "bgColour") + protected String bgColour; + @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; + /** + * whether a new group has conservation displayed by default + * + */ + @XmlAttribute(name = "showGroupConservation") + protected Boolean showGroupConservation; + /** + * whether a new group has consensus displayed by default + * + */ + @XmlAttribute(name = "showGroupConsensus") + protected Boolean showGroupConsensus; + /** + * whether a new group has secondary structure consensus displayed by default + * + */ + @XmlAttribute(name = "showGroupSecStrConsensus") + protected Boolean showGroupSecStrConsensus; + @XmlAttribute(name = "startRes") + protected Integer startRes; + @XmlAttribute(name = "startSeq") + protected Integer startSeq; + @XmlAttribute(name = "charWidth") + protected Integer charWidth; + @XmlAttribute(name = "charHeight") + protected Integer charHeight; + @XmlAttribute(name = "fontName") + protected String fontName; + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + @XmlAttribute(name = "idWidth") + protected Integer idWidth; + @XmlAttribute(name = "idWidthManuallyAdjusted") + protected Boolean idWidthManuallyAdjusted; + @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; + /** + * unique id used by jalview to + * synchronize + * between stored and + * instantiated views + * + */ + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + /** + * The viewport id of this viewport's + * (cdna/protein) coding complement, if any + * + */ + @XmlAttribute(name = "complementId") + protected String complementId; + @XmlAttribute(name = "showComplementFeatures") + protected Boolean showComplementFeatures; + @XmlAttribute(name = "showComplementFeaturesOnTop") + protected Boolean showComplementFeaturesOnTop; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + @XmlAttribute(name = "conservationSelected") + protected Boolean conservationSelected; + /** + * Conservation shading increment + * + */ + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + @XmlAttribute(name = "pidSelected") + protected Boolean pidSelected; + /** + * Percent Identity Threshold + * + */ + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + /** + * Secondary structure consensus shading - since 2.11.4 + * + */ + @XmlAttribute(name = "secstrSelected") + protected Boolean secstrSelected; + /** + * Secondary structure consensus increment + * + */ + @XmlAttribute(name = "secstrThreshold") + protected Integer secstrThreshold; + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; - /** - * Sets the value of the consensusSecondaryStructureThreshold property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setConsensusSecondaryStructureThreshold(Integer value) - { - this.consensusSecondaryStructureThreshold = value; - } - - - /** - * Gets the value of the title property. - * - * @return possible object is {@link String } - * - */ - public String getTitle() - { - return title; - } + /** + * Gets the value of the annotationColours property. + * + * @return + * possible object is + * {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() { + return annotationColours; + } - /** - * Sets the value of the title property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setTitle(String value) - { - this.title = value; - } + /** + * 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 showFullId property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowFullId() - { - return showFullId; - } + /** + * 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 } + *

+ * + * + * @return + * The value of the hiddenColumns property. + */ + public List getHiddenColumns() { + if (hiddenColumns == null) { + hiddenColumns = new ArrayList(); + } + return this.hiddenColumns; + } - /** - * 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 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 } + *

+ * + * + * @return + * The value of the calcIdParam property. + */ + public List getCalcIdParam() { + if (calcIdParam == null) { + calcIdParam = new ArrayList(); + } + return this.calcIdParam; + } - /** - * Gets the value of the rightAlignIds property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isRightAlignIds() - { - return rightAlignIds; - } + /** + * Gets the value of the overview property. + * + * @return + * possible object is + * {@link JalviewModel.Viewport.Overview } + * + */ + public JalviewModel.Viewport.Overview getOverview() { + return overview; + } - /** - * Sets the value of the rightAlignIds property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setRightAlignIds(Boolean value) - { - this.rightAlignIds = value; - } + /** + * Sets the value of the overview property. + * + * @param value + * allowed object is + * {@link JalviewModel.Viewport.Overview } + * + */ + public void setOverview(JalviewModel.Viewport.Overview value) { + this.overview = value; + } - /** - * Gets the value of the showText property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowText() - { - return showText; - } + /** + * Gets the value of the secStrProvider 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 secStrProvider property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link String } + *

+ * + * + * @return + * The value of the secStrProvider property. + */ + public List getSecStrProvider() { + if (secStrProvider == null) { + secStrProvider = new ArrayList(); + } + return this.secStrProvider; + } - /** - * 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 bgColour property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getBgColour() { + return bgColour; + } - /** - * Gets the value of the showColourText property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowColourText() - { - return showColourText; - } + /** + * Sets the value of the bgColour property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setBgColour(String value) { + this.bgColour = value; + } - /** - * 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 title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } - /** - * 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 title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } - /** - * 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 showFullId property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowFullId() { + return showFullId; + } - /** - * Gets the value of the showBoxes property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowBoxes() - { - return showBoxes; - } + /** + * Sets the value of the showFullId property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowFullId(Boolean value) { + this.showFullId = value; + } - /** - * 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 rightAlignIds property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isRightAlignIds() { + return rightAlignIds; + } - /** - * Gets the value of the wrapAlignment property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isWrapAlignment() - { - return wrapAlignment; - } + /** + * Sets the value of the rightAlignIds property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setRightAlignIds(Boolean value) { + this.rightAlignIds = value; + } - /** - * 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 showText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowText() { + return showText; + } - /** - * Gets the value of the renderGaps property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isRenderGaps() - { - return renderGaps; - } + /** + * Sets the value of the showText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowText(Boolean value) { + this.showText = value; + } - /** - * 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 showColourText property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowColourText() { + return showColourText; + } - /** - * Gets the value of the showSequenceFeatures property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowSequenceFeatures() - { - return showSequenceFeatures; - } + /** + * Sets the value of the showColourText property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowColourText(Boolean value) { + this.showColourText = value; + } - /** - * 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 showUnconserved property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowUnconserved() { + if (showUnconserved == null) { + return false; + } else { + return showUnconserved; + } + } - /** - * Gets the value of the showNPfeatureTooltip property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowNPfeatureTooltip() - { - return showNPfeatureTooltip; - } + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) { + this.showUnconserved = value; + } - /** - * 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 showBoxes property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowBoxes() { + return showBoxes; + } - /** - * Gets the value of the showDbRefTooltip property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowDbRefTooltip() - { - return showDbRefTooltip; - } + /** + * 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; + } + + /** + * whether a new group has conservation displayed by default + * + * @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 } + * + * @see #isShowGroupConservation() + */ + public void setShowGroupConservation(Boolean value) { + this.showGroupConservation = value; + } + + /** + * whether a new group has consensus displayed by default + * + * @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 } + * + * @see #isShowGroupConsensus() + */ + public void setShowGroupConsensus(Boolean value) { + this.showGroupConsensus = value; + } - /** - * Sets the value of the showDbRefTooltip property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowDbRefTooltip(Boolean value) - { - this.showDbRefTooltip = value; - } + /** + * whether a new group has secondary structure consensus displayed by default + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowGroupSecStrConsensus() { + if (showGroupSecStrConsensus == null) { + return false; + } else { + return showGroupSecStrConsensus; + } + } - /** - * 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 showGroupSecStrConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + * @see #isShowGroupSecStrConsensus() + */ + public void setShowGroupSecStrConsensus(Boolean value) { + this.showGroupSecStrConsensus = value; + } - /** - * 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 startRes property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStartRes() { + return startRes; + } - /** - * 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 startRes property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStartRes(Integer value) { + this.startRes = value; + } - /** - * 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 startSeq property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getStartSeq() { + return startSeq; + } - /** - * Gets the value of the showAnnotation property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowAnnotation() - { - return showAnnotation; - } + /** + * Sets the value of the startSeq property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setStartSeq(Integer value) { + this.startSeq = value; + } - /** - * 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 charWidth property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getCharWidth() { + return charWidth; + } - /** - * 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 charWidth property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setCharWidth(Integer value) { + this.charWidth = value; + } - /** - * 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 charHeight property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getCharHeight() { + return charHeight; + } - /** - * 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 charHeight property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setCharHeight(Integer value) { + this.charHeight = value; + } - /** - * 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 fontName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getFontName() { + return fontName; + } - /** - * 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 fontName property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setFontName(String value) { + this.fontName = value; + } - /** - * 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 showGroupSSConsensus property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isShowGroupSSConsensus() - { - if (showGroupSSConsensus == null) - { - return false; - } - else - { - return showGroupSSConsensus; - } - } - - /** - * Sets the value of the showGroupSSConsensus property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowGroupSSConsensus(Boolean value) - { - this.showGroupSSConsensus = value; - } + /** + * Gets the value of the fontSize property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontSize() { + return fontSize; + } - /** - * 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 fontSize property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontSize(Integer value) { + this.fontSize = value; + } - /** - * 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 fontStyle property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getFontStyle() { + return fontStyle; + } - /** - * 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 fontStyle property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setFontStyle(Integer value) { + this.fontStyle = value; + } - /** - * 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 idWidth property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getIdWidth() { + return idWidth; + } - /** - * 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 idWidth property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setIdWidth(Integer value) { + this.idWidth = value; + } - /** - * 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 idWidthManuallyAdjusted property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isIdWidthManuallyAdjusted() { + return idWidthManuallyAdjusted; + } - /** - * 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 idWidthManuallyAdjusted property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIdWidthManuallyAdjusted(Boolean value) { + this.idWidthManuallyAdjusted = value; + } - /** - * 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 scaleProteinAsCdna property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isScaleProteinAsCdna() { + if (scaleProteinAsCdna == null) { + return true; + } else { + return scaleProteinAsCdna; + } + } - /** - * Gets the value of the startRes property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getStartRes() - { - return startRes; - } + /** + * Sets the value of the scaleProteinAsCdna property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setScaleProteinAsCdna(Boolean value) { + this.scaleProteinAsCdna = value; + } - /** - * 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 viewName property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getViewName() { + return viewName; + } - /** - * Gets the value of the startSeq property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getStartSeq() - { - return startSeq; - } + /** + * 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 startSeq property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setStartSeq(Integer value) - { - this.startSeq = value; - } + /** + * 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 charWidth property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getCharWidth() - { - return charWidth; - } + /** + * Gets the value of the gatheredViews property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isGatheredViews() { + return gatheredViews; + } - /** - * Sets the value of the charWidth property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setCharWidth(Integer value) - { - this.charWidth = value; - } + /** + * 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 charHeight property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getCharHeight() - { - return charHeight; - } + /** + * Gets the value of the textCol1 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol1() { + return textCol1; + } - /** - * Sets the value of the charHeight property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setCharHeight(Integer value) - { - this.charHeight = value; - } + /** + * 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 fontName property. - * - * @return possible object is {@link String } - * - */ - public String getFontName() - { - return fontName; - } + /** + * Gets the value of the textCol2 property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextCol2() { + return textCol2; + } - /** - * Sets the value of the fontName property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setFontName(String value) - { - this.fontName = value; - } + /** + * 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 fontSize property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getFontSize() - { - return fontSize; - } + /** + * Gets the value of the textColThreshold property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getTextColThreshold() { + return textColThreshold; + } - /** - * Sets the value of the fontSize property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setFontSize(Integer value) - { - this.fontSize = value; - } + /** + * 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 fontStyle property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getFontStyle() - { - return fontStyle; - } + /** + * unique id used by jalview to + * synchronize + * between stored and + * instantiated views + * + * @return + * possible object is + * {@link String } + * + */ + public String getId() { + return id; + } - /** - * Sets the value of the fontStyle property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setFontStyle(Integer value) - { - this.fontStyle = value; - } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getId() + */ + public void setId(String value) { + this.id = value; + } - /** - * Gets the value of the idWidth property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getIdWidth() - { - return idWidth; - } + /** + * The viewport id of this viewport's + * (cdna/protein) coding complement, if any + * + * @return + * possible object is + * {@link String } + * + */ + public String getComplementId() { + return complementId; + } - /** - * Sets the value of the idWidth property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setIdWidth(Integer value) - { - this.idWidth = value; - } + /** + * Sets the value of the complementId property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getComplementId() + */ + public void setComplementId(String value) { + this.complementId = value; + } - /** - * Gets the value of the idWidthManuallyAdjusted property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isIdWidthManuallyAdjusted() - { - return idWidthManuallyAdjusted; - } + /** + * Gets the value of the showComplementFeatures property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowComplementFeatures() { + if (showComplementFeatures == null) { + return false; + } else { + return showComplementFeatures; + } + } - /** - * Sets the value of the idWidthManuallyAdjusted property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setIdWidthManuallyAdjusted(Boolean value) - { - this.idWidthManuallyAdjusted = value; - } + /** + * Sets the value of the showComplementFeatures property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowComplementFeatures(Boolean value) { + this.showComplementFeatures = 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; - } - } + /** + * Gets the value of the showComplementFeaturesOnTop property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowComplementFeaturesOnTop() { + if (showComplementFeaturesOnTop == null) { + return false; + } else { + return showComplementFeaturesOnTop; + } + } - /** - * Sets the value of the scaleProteinAsCdna property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setScaleProteinAsCdna(Boolean value) - { - this.scaleProteinAsCdna = value; - } + /** + * Sets the value of the showComplementFeaturesOnTop property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowComplementFeaturesOnTop(Boolean value) { + this.showComplementFeaturesOnTop = value; + } - /** - * Gets the value of the viewName property. - * - * @return possible object is {@link String } - * - */ - public String getViewName() - { - return viewName; - } + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } - /** - * Sets the value of the viewName property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setViewName(String value) - { - this.viewName = value; - } + /** + * 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 sequenceSetId property. - * - * @return possible object is {@link String } - * - */ - public String getSequenceSetId() - { - return sequenceSetId; - } + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } - /** - * Sets the value of the sequenceSetId property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setSequenceSetId(String value) - { - this.sequenceSetId = value; - } + /** + * 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 gatheredViews property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isGatheredViews() - { - return gatheredViews; - } + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } - /** - * Sets the value of the gatheredViews property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setGatheredViews(Boolean value) - { - this.gatheredViews = value; - } + /** + * 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 textCol1 property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getTextCol1() - { - return textCol1; - } + /** + * 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; + } - /** - * 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 conservationSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isConservationSelected() { + return conservationSelected; + } - /** - * Gets the value of the textCol2 property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getTextCol2() - { - return textCol2; - } + /** + * Sets the value of the conservationSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setConservationSelected(Boolean value) { + this.conservationSelected = value; + } - /** - * Sets the value of the textCol2 property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setTextCol2(Integer value) - { - this.textCol2 = value; - } + /** + * Conservation shading increment + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getConsThreshold() { + return consThreshold; + } - /** - * Gets the value of the textColThreshold property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getTextColThreshold() - { - return textColThreshold; - } + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + * @see #getConsThreshold() + */ + public void setConsThreshold(Integer value) { + this.consThreshold = value; + } - /** - * 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 pidSelected property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isPidSelected() { + return pidSelected; + } - /** - * Gets the value of the id property. - * - * @return possible object is {@link String } - * - */ - public String getId() - { - return id; - } + /** + * Sets the value of the pidSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setPidSelected(Boolean value) { + this.pidSelected = value; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setId(String value) - { - this.id = value; - } + /** + * Percent Identity Threshold + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getPidThreshold() { + return pidThreshold; + } - /** - * Gets the value of the complementId property. - * - * @return possible object is {@link String } - * - */ - public String getComplementId() - { - return complementId; - } + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + * @see #getPidThreshold() + */ + public void setPidThreshold(Integer value) { + this.pidThreshold = value; + } - /** - * Sets the value of the complementId property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setComplementId(String value) - { - this.complementId = value; - } + /** + * Secondary structure consensus shading - since 2.11.4 + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isSecstrSelected() { + if (secstrSelected == null) { + return false; + } else { + return secstrSelected; + } + } - /** - * Gets the value of the showComplementFeatures property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isShowComplementFeatures() - { - if (showComplementFeatures == null) - { - return false; - } - else - { - return showComplementFeatures; - } - } + /** + * Sets the value of the secstrSelected property. + * + * @param value + * allowed object is + * {@link Boolean } + * + * @see #isSecstrSelected() + */ + public void setSecstrSelected(Boolean value) { + this.secstrSelected = value; + } - /** - * Sets the value of the showComplementFeatures property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowComplementFeatures(Boolean value) - { - this.showComplementFeatures = value; - } + /** + * Secondary structure consensus increment + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getSecstrThreshold() { + return secstrThreshold; + } - /** - * Gets the value of the showComplementFeaturesOnTop property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isShowComplementFeaturesOnTop() - { - if (showComplementFeaturesOnTop == null) - { - return false; - } - else - { - return showComplementFeaturesOnTop; - } - } + /** + * Sets the value of the secstrThreshold property. + * + * @param value + * allowed object is + * {@link Integer } + * + * @see #getSecstrThreshold() + */ + public void setSecstrThreshold(Integer value) { + this.secstrThreshold = value; + } - /** - * Sets the value of the showComplementFeaturesOnTop property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowComplementFeaturesOnTop(Boolean value) - { - this.showComplementFeaturesOnTop = 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; + } + } - /** - * Gets the value of the width property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getWidth() - { - return width; - } + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) { + this.showConsensusHistogram = value; + } - /** - * 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 showSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isShowSequenceLogo() { + if (showSequenceLogo == null) { + return false; + } else { + return showSequenceLogo; + } + } - /** - * Gets the value of the height property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getHeight() - { - return height; - } + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) { + this.showSequenceLogo = value; + } - /** - * 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 normaliseSequenceLogo property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() { + if (normaliseSequenceLogo == null) { + return false; + } else { + return normaliseSequenceLogo; + } + } - /** - * Gets the value of the xpos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getXpos() - { - return xpos; - } + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) { + this.normaliseSequenceLogo = value; + } - /** - * 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 ignoreGapsinConsensus property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() { + if (ignoreGapsinConsensus == null) { + return true; + } else { + return ignoreGapsinConsensus; + } + } - /** - * Gets the value of the ypos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getYpos() - { - return ypos; - } + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) { + this.ignoreGapsinConsensus = value; + } - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setYpos(Integer value) - { - this.ypos = value; - } - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;extension - * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt; - * &lt;attribute name="calcId" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="needsUpdate" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" - * /&gt; &lt;attribute name="autoUpdate" use="required" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/extension&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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) + /** + *

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 { - return false; + + /** + * handle for the calculation which uses + * this parameter set + * + */ + @XmlAttribute(name = "calcId", required = true) + protected String calcId; + /** + * should the calculation be performed + * immediately after loading in order to refresh results + * + */ + @XmlAttribute(name = "needsUpdate") + protected Boolean needsUpdate; + /** + * should the calculation be automatically + * performed on edits + * + */ + @XmlAttribute(name = "autoUpdate", required = true) + protected boolean autoUpdate; + + /** + * handle for the calculation which uses + * this parameter set + * + * @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 } + * + * @see #getCalcId() + */ + public void setCalcId(String value) { + this.calcId = value; + } + + /** + * should the calculation be performed + * immediately after loading in order to refresh results + * + * @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 } + * + * @see #isNeedsUpdate() + */ + public void setNeedsUpdate(Boolean value) { + this.needsUpdate = value; + } + + /** + * should the calculation be automatically + * performed on edits + * + */ + public boolean isAutoUpdate() { + return autoUpdate; + } + + /** + * Sets the value of the autoUpdate property. + * + */ + public void setAutoUpdate(boolean value) { + this.autoUpdate = value; + } + } - 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; - } - } - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attribute name="start" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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; - } + /** + *

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; + } - } + } - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup - * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute - * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="residueColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;attribute name="hiddenColour" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Overview - { - - @XmlAttribute(name = "showHidden") - protected Boolean showHidden; - - @XmlAttribute(name = "residueColour") - protected Integer residueColour; - - @XmlAttribute(name = "gapColour") - protected Integer gapColour; - - @XmlAttribute(name = "hiddenColour") - protected Integer hiddenColour; - - @XmlAttribute(name = "title") - protected String title; - - @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 showHidden property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowHidden() - { - return showHidden; - } - - /** - * Sets the value of the showHidden property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowHidden(Boolean value) - { - this.showHidden = value; - } - - /** - * Gets the value of the residueColour property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getResidueColour() - { - return residueColour; - } - - /** - * Sets the value of the residueColour property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setResidueColour(Integer value) - { - this.residueColour = value; - } - - /** - * Gets the value of the gapColour property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getGapColour() - { - return gapColour; - } - - /** - * Sets the value of the gapColour property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setGapColour(Integer value) - { - this.gapColour = value; - } - - /** - * Gets the value of the hiddenColour property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getHiddenColour() - { - return hiddenColour; - } - - /** - * Sets the value of the hiddenColour property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setHiddenColour(Integer value) - { - this.hiddenColour = 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 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">
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Overview { + + @XmlAttribute(name = "showHidden") + protected Boolean showHidden; + @XmlAttribute(name = "residueColour") + protected Integer residueColour; + @XmlAttribute(name = "gapColour") + protected Integer gapColour; + @XmlAttribute(name = "hiddenColour") + protected Integer hiddenColour; + @XmlAttribute(name = "title") + protected String title; + @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 showHidden property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowHidden() { + return showHidden; + } + + /** + * Sets the value of the showHidden property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowHidden(Boolean value) { + this.showHidden = value; + } + + /** + * Gets the value of the residueColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getResidueColour() { + return residueColour; + } + + /** + * Sets the value of the residueColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setResidueColour(Integer value) { + this.residueColour = value; + } + + /** + * Gets the value of the gapColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getGapColour() { + return gapColour; + } + + /** + * Sets the value of the gapColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGapColour(Integer value) { + this.gapColour = value; + } + + /** + * Gets the value of the hiddenColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHiddenColour() { + return hiddenColour; + } + + /** + * Sets the value of the hiddenColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHiddenColour(Integer value) { + this.hiddenColour = 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 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; + } + + } - } + } } diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index ea2c6ac..5a97ac8 100644 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -15,585 +16,622 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for JalviewUserColours complex type. + *

Java class for JalviewUserColours complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="JalviewUserColours"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="Version" - * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; - * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="attributeName" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute - * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="RGB" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="noValueColour" - * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt; - * &lt;attribute name="threshType" - * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute - * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" - * /&gt; &lt;attribute name="min" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="autoScale" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="filter" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="matcherSet" - * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt; - * &lt;/sequence&gt; &lt;attribute name="featureType" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attribute name="schemeName" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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. - * - * <p> 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 - * <CODE>set</CODE> method for the colour property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getColour().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the filter property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getFilter().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="attributeName" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute - * name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="RGB" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="noValueColour" - * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt; - * &lt;attribute name="threshType" - * type="{www.jalview.org/colours}ThresholdType" /&gt; &lt;attribute - * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; - * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" - * /&gt; &lt;attribute name="min" - * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute - * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" - * /&gt; &lt;attribute name="autoScale" - * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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; +@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = { + "version", + "colour", + "filter" +}) +public class JalviewUserColours { /** - * Gets the value of the attributeName property. - * - * <p> 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 - * <CODE>set</CODE> method for the attributeName property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAttributeName().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link String } - * + * Jalview colour scheme document version. * */ - 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; - } + @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 noValueColour property. - * - * @return possible object is {@link NoValueColour } + * Jalview colour scheme document version. * + * @return + * possible object is + * {@link String } + * */ - public NoValueColour getNoValueColour() - { - if (noValueColour == null) - { - return NoValueColour.MIN; - } - else - { - return noValueColour; - } + public String getVersion() { + return version; } /** - * Sets the value of the noValueColour property. + * Sets the value of the version property. * * @param value - * allowed object is {@link NoValueColour } - * + * allowed object is + * {@link String } + * + * @see #getVersion() */ - public void setNoValueColour(NoValueColour value) - { - this.noValueColour = value; + public void setVersion(String value) { + this.version = value; } /** - * Gets the value of the threshType property. + * Gets the value of the colour property. * - * @return possible object is {@link ThresholdType } + *

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.

* - */ - public ThresholdType getThreshType() - { - return threshType; - } - - /** - * Sets the value of the threshType property. + *

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

+ * 
+     * getColour().add(newItem);
+     *
* - * @param value - * allowed object is {@link ThresholdType } * - */ - public void setThreshType(ThresholdType value) - { - this.threshType = value; - } - - /** - * Gets the value of the threshold property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewUserColours.Colour } + *

* - * @return possible object is {@link Float } * + * @return + * The value of the colour property. */ - public Float getThreshold() - { - return threshold; + public List getColour() { + if (colour == null) { + colour = new ArrayList(); + } + return this.colour; } /** - * Sets the value of the threshold property. + * Gets the value of the filter property. * - * @param value - * allowed object is {@link Float } + *

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.

* - */ - public void setThreshold(Float value) - { - this.threshold = value; - } - - /** - * Gets the value of the max property. + *

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

+ * 
+     * getFilter().add(newItem);
+     *
* - * @return possible object is {@link Float } * - */ - public Float getMax() - { - return max; - } - - /** - * Sets the value of the max property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewUserColours.Filter } + *

* - * @param value - * allowed object is {@link Float } * + * @return + * The value of the filter property. */ - public void setMax(Float value) - { - this.max = value; + public List getFilter() { + if (filter == null) { + filter = new ArrayList(); + } + return this.filter; } /** - * Gets the value of the min property. - * - * @return possible object is {@link Float } + * Gets the value of the schemeName property. * + * @return + * possible object is + * {@link String } + * */ - public Float getMin() - { - return min; + public String getSchemeName() { + return schemeName; } /** - * Sets the value of the min property. + * Sets the value of the schemeName property. * * @param value - * allowed object is {@link Float } - * + * allowed object is + * {@link String } + * */ - public void setMin(Float value) - { - this.min = value; + public void setSchemeName(String value) { + this.schemeName = 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. + *

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>
+     *
* - * @param value - * allowed object is {@link Boolean } * */ - public void setColourByLabel(Boolean value) - { - this.colourByLabel = value; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { + "attributeName" + }) + public static class Colour { + + /** + * name of feature attribute to colour by, or attribute and sub-attribute + * + */ + @XmlElement(namespace = "") + protected List attributeName; + /** + * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme + * + */ + @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; + + /** + * name of feature attribute to colour by, or attribute and sub-attribute + * + * 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 } + *

+ * + * + * @return + * The value of the attributeName property. + */ + public List getAttributeName() { + if (attributeName == null) { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme + * + * @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 } + * + * @see #getName() + */ + 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; + } - /** - * 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; - } - - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="matcherSet" - * type="{www.jalview.org/colours}FeatureMatcherSet"/&gt; - * &lt;/sequence&gt; &lt;attribute name="featureType" - * use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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. + *

Java class for anonymous complex type

. * - * @param value - * allowed object is {@link FeatureMatcherSet } + *

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

* - */ - public void setMatcherSet(FeatureMatcherSet value) - { - this.matcherSet = value; - } - - /** - * Gets the value of the featureType property. + * 
+     * <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>
+     *
* - * @return possible object is {@link String } * */ - public String getFeatureType() - { - return featureType; - } + @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; + } - /** - * 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 index 644e6fe..f25dcf5 100644 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -17,291 +18,357 @@ 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 * - * This effectively represents a java.util.MapList object - * + *

Java class for mapListType complex type

. * - * <p>Java class for mapListType complex type. + *

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

* - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType name="mapListType"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="mapListFrom" - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="end" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt; - * &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attribute name="start" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute - * name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attribute name="mapFromUnit" use="required" - * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt; - * &lt;attribute name="mapToUnit" use="required" - * type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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. - * - * <p> 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 - * <CODE>set</CODE> method for the mapListFrom property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getMapListFrom().add(newItem); </pre> - * - * - * <p> 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. - * - * <p> 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 - * <CODE>set</CODE> method for the mapListTo property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getMapListTo().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="end" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class MapListFrom - { +@XmlType(name = "mapListType", propOrder = { + "mapListFrom", + "mapListTo" +}) +@XmlSeeAlso({ + Mapping.class +}) +public class MapListType { - @XmlAttribute(name = "start", required = true) - protected int start; - - @XmlAttribute(name = "end", required = true) - protected int end; + /** + * a region from start to end inclusive + * + */ + protected List mapListFrom; + /** + * a region from start to end inclusive + * + */ + protected List mapListTo; + /** + * number of dictionary symbol widths involved in + * each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). + * This is optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + */ + @XmlAttribute(name = "mapFromUnit", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger mapFromUnit; + /** + * number of dictionary symbol widths involved in + * each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). + * This is optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. + * + */ + @XmlAttribute(name = "mapToUnit", required = true) + @XmlSchemaType(name = "positiveInteger") + protected BigInteger mapToUnit; /** - * Gets the value of the start property. + * a region from start to end inclusive + * + * 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 } + *

+ * + * + * @return + * The value of the mapListFrom property. */ - public int getStart() - { - return start; + public List getMapListFrom() { + if (mapListFrom == null) { + mapListFrom = new ArrayList(); + } + return this.mapListFrom; } /** - * Sets the value of the start property. + * a region from start to end inclusive + * + * 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 } + *

+ * + * + * @return + * The value of the mapListTo property. */ - public void setStart(int value) - { - this.start = value; + public List getMapListTo() { + if (mapListTo == null) { + mapListTo = new ArrayList(); + } + return this.mapListTo; } /** - * Gets the value of the end property. + * number of dictionary symbol widths involved in + * each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). + * This is optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. * + * @return + * possible object is + * {@link BigInteger } + * */ - public int getEnd() - { - return end; + public BigInteger getMapFromUnit() { + return mapFromUnit; } /** - * Sets the value of the end property. + * Sets the value of the mapFromUnit property. * + * @param value + * allowed object is + * {@link BigInteger } + * + * @see #getMapFromUnit() */ - public void setEnd(int value) - { - this.end = value; + public void setMapFromUnit(BigInteger value) { + this.mapFromUnit = value; } - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" - * /&gt; &lt;attribute name="end" use="required" - * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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. + * number of dictionary symbol widths involved in + * each + * mapped position on this sequence (for example, 3 for a dna + * sequence exon + * region that is being mapped to a protein sequence). + * This is optional, + * since the unit can be usually be inferred from the + * dictionary type of + * each sequence involved in the mapping. * + * @return + * possible object is + * {@link BigInteger } + * */ - public int getStart() - { - return start; + public BigInteger getMapToUnit() { + return mapToUnit; } /** - * Sets the value of the start property. + * Sets the value of the mapToUnit property. * + * @param value + * allowed object is + * {@link BigInteger } + * + * @see #getMapToUnit() */ - public void setStart(int value) - { - this.start = value; + public void setMapToUnit(BigInteger value) { + this.mapToUnit = value; } + /** - * Gets the value of the end property. + *

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>
+     *
+ * * */ - public int getEnd() - { - return end; + @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; + } + } + /** - * Sets the value of the end property. + *

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>
+     *
+ * * */ - public void setEnd(int value) - { - this.end = value; - } + @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/MapOnAMatrixType.java b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java index de9132a..ece5d33 100644 --- a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java +++ b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -14,139 +15,162 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; + /** - * Defines a mapping from the local frame to a matrix and its associated data - * specified by MatrixType - * + * Defines a mapping from the local frame to a matrix + * and its associated data specified by MatrixType * - * <p>Java class for MapOnAMatrixType complex type. + *

Java class for MapOnAMatrixType complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="MapOnAMatrixType"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="property" - * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="mapping" - * type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="matrix" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <complexType name="MapOnAMatrixType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="matrix" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "MapOnAMatrixType", propOrder = { "property", "mapping" }) -public class MapOnAMatrixType -{ - - protected List property; - - protected MapListType mapping; - - @XmlAttribute(name = "matrix", required = true) - protected String matrix; +@XmlType(name = "MapOnAMatrixType", propOrder = { + "property", + "mapping" +}) +public class MapOnAMatrixType { - @XmlAttribute(name = "id") - protected String id; + protected List property; + /** + * mapping from the matrix row and column positions + * to + * associated reference frame + * + */ + protected MapListType mapping; + /** + * reference to the matrix type this Map refers to + * + */ + @XmlAttribute(name = "matrix", required = true) + protected String matrix; + @XmlAttribute(name = "id") + protected String id; - /** - * Gets the value of the property property. - * - * <p> 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 - * <CODE>set</CODE> method for the property property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getProperty().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link Property } - * - * - */ - public List getProperty() - { - if (property == null) - { - property = new ArrayList(); + /** + * 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 Property } + *

+ * + * + * @return + * The value of the property property. + */ + public List getProperty() { + if (property == null) { + property = new ArrayList(); + } + return this.property; } - return this.property; - } - /** - * Gets the value of the mapping property. - * - * @return possible object is {@link MapListType } - * - */ - public MapListType getMapping() - { - return mapping; - } + /** + * mapping from the matrix row and column positions + * to + * associated reference frame + * + * @return + * possible object is + * {@link MapListType } + * + */ + public MapListType getMapping() { + return mapping; + } - /** - * Sets the value of the mapping property. - * - * @param value - * allowed object is {@link MapListType } - * - */ - public void setMapping(MapListType value) - { - this.mapping = value; - } + /** + * Sets the value of the mapping property. + * + * @param value + * allowed object is + * {@link MapListType } + * + * @see #getMapping() + */ + public void setMapping(MapListType value) { + this.mapping = value; + } - /** - * Gets the value of the matrix property. - * - * @return possible object is {@link String } - * - */ - public String getMatrix() - { - return matrix; - } + /** + * reference to the matrix type this Map refers to + * + * @return + * possible object is + * {@link String } + * + */ + public String getMatrix() { + return matrix; + } - /** - * Sets the value of the matrix property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setMatrix(String value) - { - this.matrix = value; - } + /** + * Sets the value of the matrix property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getMatrix() + */ + public void setMatrix(String value) { + this.matrix = value; + } - /** - * Gets the value of the id property. - * - * @return possible object is {@link String } - * - */ - public String getId() - { - return id; - } + /** + * 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; - } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } } diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index e53c4f7..4f28ae3 100644 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -14,115 +15,133 @@ 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). * - * 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

. * - * <p>Java class for anonymous complex type. + *

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

* - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;extension - * base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt; - * &lt;sequence&gt; &lt;choice minOccurs="0"&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt; &lt;element - * name="dseqFor"&gt; &lt;simpleType&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}string"&gt; - * &lt;/restriction&gt; &lt;/simpleType&gt; - * &lt;/element&gt; &lt;/choice&gt; &lt;/sequence&gt; - * &lt;attribute name="mappingType" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/extension&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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>
+ *       <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </extension>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "", propOrder = { "sequence", "dseqFor" }) +@XmlType(name = "", propOrder = { + "sequence", + "dseqFor" +}) @XmlRootElement(name = "Mapping") -public class Mapping extends MapListType +public class Mapping + extends MapListType { - @XmlElement(name = "Sequence") - protected Sequence sequence; - - protected String dseqFor; - - @XmlAttribute(name = "mappingType") - protected String mappingType; + @XmlElement(name = "Sequence") + protected Sequence sequence; + protected String dseqFor; + /** + * Biotype of the mapping e.g. CdsToPeptide + * + */ + @XmlAttribute(name = "mappingType") + protected String mappingType; - /** - * Gets the value of the sequence property. - * - * @return possible object is {@link Sequence } - * - */ - public Sequence getSequence() - { - return sequence; - } + /** + * 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; - } + /** + * 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; - } + /** + * 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; - } + /** + * Sets the value of the dseqFor property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDseqFor(String value) { + this.dseqFor = value; + } - /** - * Gets the value of the mappingType property. - * - * @return possible object is {@link String } - * - */ - public String getMappingType() - { - return mappingType; - } + /** + * Biotype of the mapping e.g. CdsToPeptide + * + * @return + * possible object is + * {@link String } + * + */ + public String getMappingType() { + return mappingType; + } - /** - * Sets the value of the mappingType property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setMappingType(String value) - { - this.mappingType = value; - } + /** + * Sets the value of the mappingType property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getMappingType() + */ + public void setMappingType(String value) { + this.mappingType = value; + } } diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java index 65e65f6..714b3f3 100644 --- a/src/jalview/xml/binding/jalview/MatrixType.java +++ b/src/jalview/xml/binding/jalview/MatrixType.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -16,313 +17,350 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - * Represents matrix data imported to Jalview, and the results of any derived - * calculations (independent of a particular view on the matrix). + * Represents matrix data imported to Jalview, and the + * results of any derived calculations (independent of a particular + * view + * on the matrix). * + *

Java class for MatrixType complex type

. * - * <p>Java class for MatrixType complex type. + *

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

* - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType name="MatrixType"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="elements" - * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element - * name="groups" type="{http://www.w3.org/2001/XMLSchema}string" - * maxOccurs="unbounded" minOccurs="0"/&gt; &lt;element name="newick" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="property" - * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute - * name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="rows" use="required" - * type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; &lt;attribute - * name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" - * /&gt; &lt;attribute name="treeMethod" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" /&gt; - * &lt;attribute name="id" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <complexType name="MatrixType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="elements" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         <element name="groups" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="rows" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *       <attribute name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *       <attribute name="treeMethod" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" />
+ *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType( - name = "MatrixType", - propOrder = - { "elements", "groups", "newick", "property" }) -public class MatrixType -{ - - @XmlElement(required = true) - protected String elements; - - protected List groups; - - protected List newick; - - protected List property; +@XmlType(name = "MatrixType", propOrder = { + "elements", + "groups", + "newick", + "property" +}) +public class MatrixType { - @XmlAttribute(name = "type", required = true) - protected String type; + /** + * serialised representation of matrix as one or + * more sets of comma separated values + * + */ + @XmlElement(required = true) + protected String elements; + /** + * Comma separated series of longs formed from + * bitsets defining partitions on the rows/columns of the matrix + * + */ + protected List groups; + /** + * tree computed for this + * + */ + protected List newick; + protected List property; + @XmlAttribute(name = "type", required = true) + protected String type; + @XmlAttribute(name = "rows", required = true) + protected BigInteger rows; + @XmlAttribute(name = "cols", required = true) + protected BigInteger cols; + @XmlAttribute(name = "treeMethod") + protected String treeMethod; + @XmlAttribute(name = "cutHeight") + protected Double cutHeight; + @XmlAttribute(name = "id", required = true) + protected String id; - @XmlAttribute(name = "rows", required = true) - protected BigInteger rows; - - @XmlAttribute(name = "cols", required = true) - protected BigInteger cols; - - @XmlAttribute(name = "treeMethod") - protected String treeMethod; - - @XmlAttribute(name = "cutHeight") - protected Double cutHeight; - - @XmlAttribute(name = "id", required = true) - protected String id; - - /** - * Gets the value of the elements property. - * - * @return possible object is {@link String } - * - */ - public String getElements() - { - return elements; - } + /** + * serialised representation of matrix as one or + * more sets of comma separated values + * + * @return + * possible object is + * {@link String } + * + */ + public String getElements() { + return elements; + } - /** - * Sets the value of the elements property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setElements(String value) - { - this.elements = value; - } + /** + * Sets the value of the elements property. + * + * @param value + * allowed object is + * {@link String } + * + * @see #getElements() + */ + public void setElements(String value) { + this.elements = value; + } - /** - * Gets the value of the groups property. - * - * <p> 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 - * <CODE>set</CODE> method for the groups property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getGroups().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getGroups() - { - if (groups == null) - { - groups = new ArrayList(); + /** + * Comma separated series of longs formed from + * bitsets defining partitions on the rows/columns of the matrix + * + * Gets the value of the groups 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 groups property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link String } + *

+ * + * + * @return + * The value of the groups property. + */ + public List getGroups() { + if (groups == null) { + groups = new ArrayList(); + } + return this.groups; } - return this.groups; - } - /** - * Gets the value of the newick property. - * - * <p> 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 - * <CODE>set</CODE> method for the newick property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getNewick().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getNewick() - { - if (newick == null) - { - newick = new ArrayList(); + /** + * tree computed for this + * + * Gets the value of the newick 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 newick property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link String } + *

+ * + * + * @return + * The value of the newick property. + */ + public List getNewick() { + if (newick == null) { + newick = new ArrayList(); + } + return this.newick; } - return this.newick; - } - /** - * Gets the value of the property property. - * - * <p> 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 - * <CODE>set</CODE> method for the property property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getProperty().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link Property } - * - * - */ - public List getProperty() - { - if (property == null) - { - property = new ArrayList(); + /** + * 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 Property } + *

+ * + * + * @return + * The value of the property property. + */ + public List getProperty() { + if (property == null) { + property = new ArrayList(); + } + return this.property; } - return this.property; - } - /** - * Gets the value of the type property. - * - * @return possible object is {@link String } - * - */ - public String getType() - { - return type; - } + /** + * 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; - } + /** + * 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 rows property. - * - * @return possible object is {@link BigInteger } - * - */ - public BigInteger getRows() - { - return rows; - } + /** + * Gets the value of the rows property. + * + * @return + * possible object is + * {@link BigInteger } + * + */ + public BigInteger getRows() { + return rows; + } - /** - * Sets the value of the rows property. - * - * @param value - * allowed object is {@link BigInteger } - * - */ - public void setRows(BigInteger value) - { - this.rows = value; - } + /** + * Sets the value of the rows property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setRows(BigInteger value) { + this.rows = value; + } - /** - * Gets the value of the cols property. - * - * @return possible object is {@link BigInteger } - * - */ - public BigInteger getCols() - { - return cols; - } + /** + * Gets the value of the cols property. + * + * @return + * possible object is + * {@link BigInteger } + * + */ + public BigInteger getCols() { + return cols; + } - /** - * Sets the value of the cols property. - * - * @param value - * allowed object is {@link BigInteger } - * - */ - public void setCols(BigInteger value) - { - this.cols = value; - } + /** + * Sets the value of the cols property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setCols(BigInteger value) { + this.cols = value; + } - /** - * Gets the value of the treeMethod property. - * - * @return possible object is {@link String } - * - */ - public String getTreeMethod() - { - return treeMethod; - } + /** + * Gets the value of the treeMethod property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTreeMethod() { + return treeMethod; + } - /** - * Sets the value of the treeMethod property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setTreeMethod(String value) - { - this.treeMethod = value; - } + /** + * Sets the value of the treeMethod property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTreeMethod(String value) { + this.treeMethod = value; + } - /** - * Gets the value of the cutHeight property. - * - * @return possible object is {@link Double } - * - */ - public Double getCutHeight() - { - return cutHeight; - } + /** + * Gets the value of the cutHeight property. + * + * @return + * possible object is + * {@link Double } + * + */ + public Double getCutHeight() { + return cutHeight; + } - /** - * Sets the value of the cutHeight property. - * - * @param value - * allowed object is {@link Double } - * - */ - public void setCutHeight(Double value) - { - this.cutHeight = value; - } + /** + * Sets the value of the cutHeight property. + * + * @param value + * allowed object is + * {@link Double } + * + */ + public void setCutHeight(Double value) { + this.cutHeight = value; + } - /** - * Gets the value of the id property. - * - * @return possible object is {@link String } - * - */ - public String getId() - { - return id; - } + /** + * 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; - } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setId(String value) { + this.id = value; + } } diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index 98dfe8a..5fe4041 100644 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@ -1,60 +1,78 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 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; + /** - * <p>Java class for NoValueColour. + * Graduated feature colour if no score (or attribute) value + * + *

Java class for NoValueColour

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. <pre> &lt;simpleType - * name="NoValueColour"&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration - * value="None"/&gt; &lt;enumeration value="Min"/&gt; - * &lt;enumeration value="Max"/&gt; &lt;/restriction&gt; - * &lt;/simpleType&gt; </pre> + *

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; - } +public enum NoValueColour { + + @XmlEnumValue("None") + NONE("None"), + @XmlEnumValue("Min") + MIN("Min"), + @XmlEnumValue("Max") + MAX("Max"); + private final String value; + + NoValueColour(String v) { + value = v; + } + + /** + * Gets the value associated to the enum constant. + * + * @return + * The value linked to the enum. + */ + public String value() { + return value; + } + + /** + * Gets the enum associated to the value passed as parameter. + * + * @param v + * The value to get the enum from. + * @return + * The enum which corresponds to the value, if it exists. + * @throws IllegalArgumentException + * If no value matches in the enum declaration. + */ + public static NoValueColour fromValue(String v) { + for (NoValueColour c: NoValueColour.values()) { + if (c.value.equals(v)) { + return c; + } + } + throw new IllegalArgumentException(v); } - throw new IllegalArgumentException(v); - } } diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index 27d9e41..b86ebdb 100644 --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.JAXBElement; @@ -12,587 +13,512 @@ 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. - * <p>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. + * 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"); - - private final static QName _JalviewUserColours_QNAME = new QName( - "www.jalview.org/colours", "JalviewUserColours"); - - private final static QName _WebServiceParameterSet_QNAME = new QName( - "www.jalview.org/xml/wsparamset", "WebServiceParameterSet"); - - /** - * 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 MapListType } - * - */ - public MapListType createMapListType() - { - return new MapListType(); - } - - /** - * Create an instance of {@link Sequence } - * - */ - public Sequence createSequence() - { - return new Sequence(); - } - - /** - * Create an instance of {@link AlcodonFrame } - * - */ - public AlcodonFrame createAlcodonFrame() - { - return new AlcodonFrame(); - } - - /** - * 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.PcaViewer } - * - */ - public JalviewModel.PcaViewer createJalviewModelPcaViewer() - { - return new JalviewModel.PcaViewer(); - } - - /** - * 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 PcaDataType } - * - */ - public PcaDataType createPcaDataType() - { - return new PcaDataType(); - } - - /** - * Create an instance of {@link DoubleVector } - * - */ - public DoubleVector createDoubleVector() - { - return new DoubleVector(); - } - - /** - * Create an instance of {@link DoubleMatrix } - * - */ - public DoubleMatrix createDoubleMatrix() - { - return new DoubleMatrix(); - } - - /** - * 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 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 Annotation.ThresholdLine } - * - */ - public Annotation.ThresholdLine createAnnotationThresholdLine() - { - return new Annotation.ThresholdLine(); - } - - /** - * Create an instance of {@link MapOnAMatrixType } - * - */ - public MapOnAMatrixType createMapOnAMatrixType() - { - return new MapOnAMatrixType(); - } - - /** - * Create an instance of {@link jalview.xml.binding.jalview.Property } - * - */ - public jalview.xml.binding.jalview.Property createProperty() - { - return new jalview.xml.binding.jalview.Property(); - } - - /** - * Create an instance of {@link SequenceSet.SequenceSetProperties } - * - */ - public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() - { - return new SequenceSet.SequenceSetProperties(); - } - - /** - * Create an instance of {@link MatrixType } - * - */ - public MatrixType createMatrixType() - { - return new MatrixType(); - } - - /** - * 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.PcaViewer.SequencePoint } - * - */ - public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() - { - return new JalviewModel.PcaViewer.SequencePoint(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer.Axis } - * - */ - public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() - { - return new JalviewModel.PcaViewer.Axis(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin } - * - */ - public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() - { - return new JalviewModel.PcaViewer.SeqPointMin(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax } - * - */ - public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() - { - return new JalviewModel.PcaViewer.SeqPointMax(); - } - - /** - * 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.Viewport.Overview } - * - */ - public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() - { - return new JalviewModel.Viewport.Overview(); - } - - /** - * 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 >} - * - * @param value - * Java instance representing xml element's value. - * @return the new 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); - } - - /** - * Create an instance of {@link JAXBElement - * }{@code <}{@link JalviewUserColours }{@code >} - * - * @param value - * Java instance representing xml element's value. - * @return the new instance of {@link JAXBElement - * }{@code <}{@link JalviewUserColours }{@code >} - */ - @XmlElementDecl( - namespace = "www.jalview.org/colours", - name = "JalviewUserColours") - public JAXBElement createJalviewUserColours( - JalviewUserColours value) - { - return new JAXBElement(_JalviewUserColours_QNAME, - JalviewUserColours.class, null, value); - } - - /** - * Create an instance of {@link JAXBElement - * }{@code <}{@link WebServiceParameterSet }{@code >} - * - * @param value - * Java instance representing xml element's value. - * @return the new instance of {@link JAXBElement - * }{@code <}{@link WebServiceParameterSet }{@code >} - */ - @XmlElementDecl( - namespace = "www.jalview.org/xml/wsparamset", - name = "WebServiceParameterSet") - public JAXBElement createWebServiceParameterSet( - WebServiceParameterSet value) - { - return new JAXBElement( - _WebServiceParameterSet_QNAME, WebServiceParameterSet.class, - null, value); - } +public class ObjectFactory { + + private static final QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel"); + private static final QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours"); + private static final QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet"); + + /** + * 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 MapListType } + * + */ + public MapListType createMapListType() { + return new MapListType(); + } + + /** + * Create an instance of {@link Sequence } + * + */ + public Sequence createSequence() { + return new Sequence(); + } + + /** + * Create an instance of {@link AlcodonFrame } + * + */ + public AlcodonFrame createAlcodonFrame() { + return new AlcodonFrame(); + } + + /** + * 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.PcaViewer } + * + */ + public JalviewModel.PcaViewer createJalviewModelPcaViewer() { + return new JalviewModel.PcaViewer(); + } + + /** + * 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 PcaDataType } + * + */ + public PcaDataType createPcaDataType() { + return new PcaDataType(); + } + + /** + * Create an instance of {@link DoubleVector } + * + */ + public DoubleVector createDoubleVector() { + return new DoubleVector(); + } + + /** + * Create an instance of {@link DoubleMatrix } + * + */ + public DoubleMatrix createDoubleMatrix() { + return new DoubleMatrix(); + } + + /** + * 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 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 Annotation.ThresholdLine } + * + */ + public Annotation.ThresholdLine createAnnotationThresholdLine() { + return new Annotation.ThresholdLine(); + } + + /** + * Create an instance of {@link MapOnAMatrixType } + * + */ + public MapOnAMatrixType createMapOnAMatrixType() { + return new MapOnAMatrixType(); + } + + /** + * Create an instance of {@link jalview.xml.binding.jalview.Property } + * + */ + public jalview.xml.binding.jalview.Property createProperty() { + return new jalview.xml.binding.jalview.Property(); + } + + /** + * Create an instance of {@link SequenceSet.SequenceSetProperties } + * + */ + public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() { + return new SequenceSet.SequenceSetProperties(); + } + + /** + * Create an instance of {@link MatrixType } + * + */ + public MatrixType createMatrixType() { + return new MatrixType(); + } + + /** + * 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.PcaViewer.SequencePoint } + * + */ + public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() { + return new JalviewModel.PcaViewer.SequencePoint(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer.Axis } + * + */ + public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() { + return new JalviewModel.PcaViewer.Axis(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin } + * + */ + public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() { + return new JalviewModel.PcaViewer.SeqPointMin(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax } + * + */ + public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() { + return new JalviewModel.PcaViewer.SeqPointMax(); + } + + /** + * 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.Viewport.Overview } + * + */ + public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() { + return new JalviewModel.Viewport.Overview(); + } + + /** + * 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 >} + * + * @param value + * Java instance representing xml element's value. + * @return + * the new 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); + } + + /** + * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >} + * + * @param value + * Java instance representing xml element's value. + * @return + * the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >} + */ + @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours") + public JAXBElement createJalviewUserColours(JalviewUserColours value) { + return new JAXBElement(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value); + } + + /** + * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >} + * + * @param value + * Java instance representing xml element's value. + * @return + * the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >} + */ + @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet") + public JAXBElement createWebServiceParameterSet(WebServiceParameterSet value) { + return new JAXBElement(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value); + } } diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index d33d47c..a0dd653 100644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -12,114 +13,115 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - * * The results of a PCA calculation * + *

Java class for PcaDataType complex type

. * - * <p>Java class for PcaDataType complex type. + *

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

* - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType name="PcaDataType"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="pairwiseMatrix" - * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;element - * name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt; - * &lt;element name="eigenMatrix" - * type="{www.jalview.org}DoubleMatrix"/&gt; &lt;/sequence&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <complexType name="PcaDataType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *         <element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *         <element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType( - name = "PcaDataType", - namespace = "www.jalview.org", - propOrder = - { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" }) -public class PcaDataType -{ - - @XmlElement(required = true) - protected DoubleMatrix pairwiseMatrix; - - @XmlElement(required = true) - protected DoubleMatrix tridiagonalMatrix; +@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = { + "pairwiseMatrix", + "tridiagonalMatrix", + "eigenMatrix" +}) +public class PcaDataType { - @XmlElement(required = true) - protected DoubleMatrix eigenMatrix; + @XmlElement(required = true) + protected DoubleMatrix pairwiseMatrix; + @XmlElement(required = true) + protected DoubleMatrix tridiagonalMatrix; + @XmlElement(required = true) + protected DoubleMatrix eigenMatrix; - /** - * Gets the value of the pairwiseMatrix property. - * - * @return possible object is {@link DoubleMatrix } - * - */ - public DoubleMatrix getPairwiseMatrix() - { - return pairwiseMatrix; - } + /** + * Gets the value of the pairwiseMatrix property. + * + * @return + * possible object is + * {@link DoubleMatrix } + * + */ + public DoubleMatrix getPairwiseMatrix() { + return pairwiseMatrix; + } - /** - * Sets the value of the pairwiseMatrix property. - * - * @param value - * allowed object is {@link DoubleMatrix } - * - */ - public void setPairwiseMatrix(DoubleMatrix value) - { - this.pairwiseMatrix = value; - } + /** + * Sets the value of the pairwiseMatrix property. + * + * @param value + * allowed object is + * {@link DoubleMatrix } + * + */ + public void setPairwiseMatrix(DoubleMatrix value) { + this.pairwiseMatrix = value; + } - /** - * Gets the value of the tridiagonalMatrix property. - * - * @return possible object is {@link DoubleMatrix } - * - */ - public DoubleMatrix getTridiagonalMatrix() - { - return tridiagonalMatrix; - } + /** + * Gets the value of the tridiagonalMatrix property. + * + * @return + * possible object is + * {@link DoubleMatrix } + * + */ + public DoubleMatrix getTridiagonalMatrix() { + return tridiagonalMatrix; + } - /** - * Sets the value of the tridiagonalMatrix property. - * - * @param value - * allowed object is {@link DoubleMatrix } - * - */ - public void setTridiagonalMatrix(DoubleMatrix value) - { - this.tridiagonalMatrix = value; - } + /** + * Sets the value of the tridiagonalMatrix property. + * + * @param value + * allowed object is + * {@link DoubleMatrix } + * + */ + public void setTridiagonalMatrix(DoubleMatrix value) { + this.tridiagonalMatrix = value; + } - /** - * Gets the value of the eigenMatrix property. - * - * @return possible object is {@link DoubleMatrix } - * - */ - public DoubleMatrix getEigenMatrix() - { - return eigenMatrix; - } + /** + * Gets the value of the eigenMatrix property. + * + * @return + * possible object is + * {@link DoubleMatrix } + * + */ + public DoubleMatrix getEigenMatrix() { + return eigenMatrix; + } - /** - * Sets the value of the eigenMatrix property. - * - * @param value - * allowed object is {@link DoubleMatrix } - * - */ - public void setEigenMatrix(DoubleMatrix value) - { - this.eigenMatrix = value; - } + /** + * Sets the value of the eigenMatrix property. + * + * @param value + * allowed object is + * {@link DoubleMatrix } + * + */ + public void setEigenMatrix(DoubleMatrix value) { + this.eigenMatrix = value; + } } diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index f53b801..1093e94 100644 --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -15,223 +16,235 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlSeeAlso; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for pdbentry complex type. + *

Java class for pdbentry complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="pdbentry"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;element name="property" - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="value" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attribute name="id" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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. - * - * <p> 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 - * <CODE>set</CODE> method for the property property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getProperty().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="value" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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; +@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 name property. + * 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 } + *

+ * * - * @return possible object is {@link String } + * @return + * The value of the property 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 getName() - { - return name; + public String getId() { + return id; } /** - * Sets the value of the name property. + * Sets the value of the id property. * * @param value - * allowed object is {@link String } + * 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 void setName(String value) - { - this.name = value; + public String getType() { + return type; } /** - * Gets the value of the value property. + * Sets the value of the type property. * - * @return possible object is {@link String } + * @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 getValue() - { - return value; + public String getFile() { + return file; } /** - * Sets the value of the value property. + * Sets the value of the file property. * * @param value - * allowed object is {@link String } - * + * allowed object is + * {@link String } + * */ - public void setValue(String value) - { - this.value = value; + 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/Property.java b/src/jalview/xml/binding/jalview/Property.java index 5e00f95..f6da4ad 100644 --- a/src/jalview/xml/binding/jalview/Property.java +++ b/src/jalview/xml/binding/jalview/Property.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -12,78 +13,80 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for property complex type. + *

Java class for property complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="property"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="value" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <complexType name="property">
+ *   <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 = "property") -public class Property -{ - - @XmlAttribute(name = "name") - protected String name; +public class Property { - @XmlAttribute(name = "value") - protected String value; + @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; - } + /** + * 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; - } + /** + * 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; - } + /** + * 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; - } + /** + * 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 index 9f61a22..fc07dbb 100644 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -16,325 +17,363 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for anonymous complex type. + *

Java class for anonymous complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;extension - * base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt; - * &lt;sequence&gt; &lt;element name="DBRef" maxOccurs="unbounded" - * minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="source" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="accessionId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" - * /&gt; &lt;attribute name="canonical" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; - * &lt;/sequence&gt; &lt;attribute name="dsseqid" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/extension&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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" />
+ *                 <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </extension>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "", propOrder = { "dbRef" }) +@XmlType(name = "", propOrder = { + "dbRef" +}) @XmlRootElement(name = "Sequence") -public class Sequence extends SequenceType +public class Sequence + extends SequenceType { - @XmlElement(name = "DBRef") - protected List dbRef; - - @XmlAttribute(name = "dsseqid") - protected String dsseqid; - - @XmlAttribute(name = "biotype") - protected String biotype; - - /** - * Gets the value of the dbRef property. - * - * <p> 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 - * <CODE>set</CODE> method for the dbRef property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getDBRef().add(newItem); </pre> - * - * - * <p> 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; - } - - /** - * Gets the value of the biotype property. - * - * @return possible object is {@link String } - * - */ - public String getBiotype() - { - return biotype; - } - - /** - * Sets the value of the biotype property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setBiotype(String value) - { - this.biotype = value; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt; - * &lt;/sequence&gt; &lt;attribute name="source" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="accessionId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" - * default="false" /&gt; &lt;attribute name="canonical" - * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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; - - @XmlAttribute(name = "locus") - protected Boolean locus; - - @XmlAttribute(name = "canonical") - protected Boolean canonical; - + @XmlElement(name = "DBRef") + protected List dbRef; /** - * 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 } + * dataset sequence id for this sequence. Will be + * created as union of sequences. * */ - public void setMapping(Mapping value) - { - this.mapping = value; - } - + @XmlAttribute(name = "dsseqid") + protected String dsseqid; /** - * Gets the value of the source property. - * - * @return possible object is {@link String } + * Biotype of the sequence (if known) * */ - public String getSource() - { - return source; - } + @XmlAttribute(name = "biotype") + protected String biotype; /** - * Sets the value of the source property. + * Gets the value of the dbRef property. * - * @param value - * allowed object is {@link String } + *

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.

* - */ - public void setSource(String value) - { - this.source = value; - } - - /** - * Gets the value of the version property. + *

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

+ * 
+     * getDBRef().add(newItem);
+     *
* - * @return possible object is {@link String } * - */ - public String getVersion() - { - return version; - } - - /** - * Sets the value of the version property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link Sequence.DBRef } + *

* - * @param value - * allowed object is {@link String } * + * @return + * The value of the dbRef property. */ - public void setVersion(String value) - { - this.version = value; + public List getDBRef() { + if (dbRef == null) { + dbRef = new ArrayList(); + } + return this.dbRef; } /** - * Gets the value of the accessionId property. - * - * @return possible object is {@link String } + * dataset sequence id for this sequence. Will be + * created as union of sequences. * + * @return + * possible object is + * {@link String } + * */ - public String getAccessionId() - { - return accessionId; + public String getDsseqid() { + return dsseqid; } /** - * Sets the value of the accessionId property. + * Sets the value of the dsseqid property. * * @param value - * allowed object is {@link String } - * + * allowed object is + * {@link String } + * + * @see #getDsseqid() */ - public void setAccessionId(String value) - { - this.accessionId = value; + public void setDsseqid(String value) { + this.dsseqid = value; } /** - * Gets the value of the locus property. - * - * @return possible object is {@link Boolean } + * Biotype of the sequence (if known) * + * @return + * possible object is + * {@link String } + * */ - public boolean isLocus() - { - if (locus == null) - { - return false; - } - else - { - return locus; - } + public String getBiotype() { + return biotype; } /** - * Sets the value of the locus property. + * Sets the value of the biotype property. * * @param value - * allowed object is {@link Boolean } - * + * allowed object is + * {@link String } + * + * @see #getBiotype() */ - public void setLocus(Boolean value) - { - this.locus = value; + public void setBiotype(String value) { + this.biotype = value; } + /** - * Gets the value of the canonical property. + *

Java class for anonymous complex type

. * - * @return possible object is {@link Boolean } + *

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

* - */ - public boolean isCanonical() - { - if (canonical == null) - { - return false; - } - else - { - return canonical; - } - } - - /** - * Sets the value of the canonical property. + * 
+     * <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" />
+     *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     *
* - * @param value - * allowed object is {@link Boolean } * */ - public void setCanonical(Boolean value) - { - this.canonical = value; - } + @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; + /** + * true for gene locus mapping, source=species, + * version=assembly, accession=chromosome + * + */ + @XmlAttribute(name = "locus") + protected Boolean locus; + /** + * true for the representative accession for + * databases where multiple accessions map to the same entry + * (eg. Uniprot) + * + */ + @XmlAttribute(name = "canonical") + protected Boolean canonical; + + /** + * 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; + } + + /** + * true for gene locus mapping, source=species, + * version=assembly, accession=chromosome + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isLocus() { + if (locus == null) { + return false; + } else { + return locus; + } + } + + /** + * Sets the value of the locus property. + * + * @param value + * allowed object is + * {@link Boolean } + * + * @see #isLocus() + */ + public void setLocus(Boolean value) { + this.locus = value; + } + + /** + * true for the representative accession for + * databases where multiple accessions map to the same entry + * (eg. Uniprot) + * + * @return + * possible object is + * {@link Boolean } + * + */ + public boolean isCanonical() { + if (canonical == null) { + return false; + } else { + return canonical; + } + } + + /** + * Sets the value of the canonical property. + * + * @param value + * allowed object is + * {@link Boolean } + * + * @see #isCanonical() + */ + public void setCanonical(Boolean value) { + this.canonical = value; + } - } + } } diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index c45fe81..db9aea9 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -16,319 +17,363 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for anonymous complex type. + *

Java class for anonymous complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="sequenceSetProperties" - * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="value" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; &lt;/element&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element name="Matrix" - * type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute - * name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" - * /&gt; &lt;attribute name="datasetId" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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"/>
+ *         <element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" 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", - "matrix" }) +@XmlType(name = "", propOrder = { + "sequence", + "annotation", + "sequenceSetProperties", + "alcodonFrame", + "matrix" +}) @XmlRootElement(name = "SequenceSet") -public class SequenceSet -{ - - @XmlElement(name = "Sequence") - protected List sequence; - - @XmlElement(name = "Annotation") - protected List annotation; - - protected List sequenceSetProperties; +public class SequenceSet { - @XmlElement(name = "AlcodonFrame") - protected List alcodonFrame; - - @XmlElement(name = "Matrix") - protected List matrix; - - @XmlAttribute(name = "gapChar", required = true) - protected String gapChar; - - @XmlAttribute(name = "datasetId") - protected String datasetId; + @XmlElement(name = "Sequence") + protected List sequence; + @XmlElement(name = "Annotation") + protected List annotation; + protected List sequenceSetProperties; + @XmlElement(name = "AlcodonFrame") + protected List alcodonFrame; + /** + * Matrices referred to by this set of sequences. + * + */ + @XmlElement(name = "Matrix") + protected List matrix; + @XmlAttribute(name = "gapChar", required = true) + protected String gapChar; + /** + * reference to set where jalview will gather the + * dataset sequences for all sequences in the set. + * + */ + @XmlAttribute(name = "datasetId") + protected String datasetId; - /** - * Gets the value of the sequence property. - * - * <p> 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 - * <CODE>set</CODE> method for the sequence property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getSequence().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link Sequence } - * - * - */ - public List getSequence() - { - if (sequence == null) - { - sequence = new ArrayList(); + /** + * 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 } + *

+ * + * + * @return + * The value of the sequence property. + */ + public List getSequence() { + if (sequence == null) { + sequence = new ArrayList(); + } + return this.sequence; } - return this.sequence; - } - /** - * Gets the value of the annotation property. - * - * <p> 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 - * <CODE>set</CODE> method for the annotation property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAnnotation().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link Annotation } - * - * - */ - public List getAnnotation() - { - if (annotation == null) - { - annotation = new ArrayList(); + /** + * 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 } + *

+ * + * + * @return + * The value of the annotation property. + */ + public List getAnnotation() { + if (annotation == null) { + annotation = new ArrayList(); + } + return this.annotation; } - return this.annotation; - } - /** - * Gets the value of the sequenceSetProperties property. - * - * <p> 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 - * <CODE>set</CODE> method for the sequenceSetProperties property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getSequenceSetProperties().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link SequenceSet.SequenceSetProperties } - * - * - */ - public List getSequenceSetProperties() - { - if (sequenceSetProperties == null) - { - sequenceSetProperties = new ArrayList(); + /** + * 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 } + *

+ * + * + * @return + * The value of the sequenceSetProperties property. + */ + public List getSequenceSetProperties() { + if (sequenceSetProperties == null) { + sequenceSetProperties = new ArrayList(); + } + return this.sequenceSetProperties; } - return this.sequenceSetProperties; - } - /** - * Gets the value of the alcodonFrame property. - * - * <p> 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 - * <CODE>set</CODE> method for the alcodonFrame property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getAlcodonFrame().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link AlcodonFrame } - * - * - */ - public List getAlcodonFrame() - { - if (alcodonFrame == null) - { - alcodonFrame = new ArrayList(); + /** + * 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 } + *

+ * + * + * @return + * The value of the alcodonFrame property. + */ + public List getAlcodonFrame() { + if (alcodonFrame == null) { + alcodonFrame = new ArrayList(); + } + return this.alcodonFrame; } - return this.alcodonFrame; - } - /** - * Gets the value of the matrix property. - * - * <p> 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 - * <CODE>set</CODE> method for the matrix property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getMatrix().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link MatrixType } - * - * - */ - public List getMatrix() - { - if (matrix == null) - { - matrix = new ArrayList(); + /** + * Matrices referred to by this set of sequences. + * + * Gets the value of the matrix 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 matrix property.

+ * + *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link MatrixType } + *

+ * + * + * @return + * The value of the matrix property. + */ + public List getMatrix() { + if (matrix == null) { + matrix = new ArrayList(); + } + return this.matrix; } - return this.matrix; - } - - /** - * 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; - } - - /** - * <p>Java class for anonymous complex type. - * - * <p>The following schema fragment specifies the expected content - * contained within this class. - * - * <pre> &lt;complexType&gt; &lt;complexContent&gt; - * &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute - * name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;attribute name="value" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> - * - * - */ - @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 } + * Gets the value of the gapChar property. * + * @return + * possible object is + * {@link String } + * */ - public String getKey() - { - return key; + public String getGapChar() { + return gapChar; } /** - * Sets the value of the key property. + * Sets the value of the gapChar property. * * @param value - * allowed object is {@link String } - * + * allowed object is + * {@link String } + * */ - public void setKey(String value) - { - this.key = value; + public void setGapChar(String value) { + this.gapChar = value; } /** - * Gets the value of the value property. - * - * @return possible object is {@link String } + * reference to set where jalview will gather the + * dataset sequences for all sequences in the set. * + * @return + * possible object is + * {@link String } + * */ - public String getValue() - { - return value; + public String getDatasetId() { + return datasetId; } /** - * Sets the value of the value property. + * Sets the value of the datasetId property. * * @param value - * allowed object is {@link String } - * + * allowed object is + * {@link String } + * + * @see #getDatasetId() */ - public void setValue(String value) - { - this.value = value; + 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 index 4409e5b..2bbbdc3 100644 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -13,132 +14,140 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlSeeAlso; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for SequenceType complex type. + *

Java class for SequenceType complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="SequenceType"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="sequence" - * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; - * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;attribute name="id" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute - * name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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; - } +@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 index a417840..c213d18 100644 --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@ -1,42 +1,49 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlEnum; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for ThresholdType. + * Whether filter has a threshold, and if so is it + * above or below + * + *

Java class for ThresholdType

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. <pre> &lt;simpleType - * name="ThresholdType"&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}string"&gt; &lt;enumeration - * value="NONE"/&gt; &lt;enumeration value="ABOVE"/&gt; - * &lt;enumeration value="BELOW"/&gt; &lt;/restriction&gt; - * &lt;/simpleType&gt; </pre> + *

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 -{ +public enum ThresholdType { - NONE, ABOVE, BELOW; + NONE, + ABOVE, + BELOW; - public String value() - { - return name(); - } + public String value() { + return name(); + } - public static ThresholdType fromValue(String v) - { - return valueOf(v); - } + 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 index a3fb1e9..beacdce 100644 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -14,85 +15,101 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for VAMSAS complex type. + *

Java class for VAMSAS complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="VAMSAS"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="Tree" - * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;element - * ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" - * minOccurs="0"/&gt; &lt;/sequence&gt; &lt;/restriction&gt; - * &lt;/complexContent&gt; &lt;/complexType&gt; </pre> + * 
+ * <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; +@XmlType(name = "VAMSAS", propOrder = { + "tree", + "sequenceSet" +}) +public class VAMSAS { - @XmlElement(name = "SequenceSet") - protected List sequenceSet; + @XmlElement(name = "Tree") + protected List tree; + @XmlElement(name = "SequenceSet") + protected List sequenceSet; - /** - * Gets the value of the tree property. - * - * <p> 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 - * <CODE>set</CODE> method for the tree property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getTree().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getTree() - { - if (tree == null) - { - tree = new ArrayList(); + /** + * 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 } + *

+ * + * + * @return + * The value of the tree property. + */ + public List getTree() { + if (tree == null) { + tree = new ArrayList(); + } + return this.tree; } - return this.tree; - } - /** - * Gets the value of the sequenceSet property. - * - * <p> 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 - * <CODE>set</CODE> method for the sequenceSet property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getSequenceSet().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link SequenceSet } - * - * - */ - public List getSequenceSet() - { - if (sequenceSet == null) - { - sequenceSet = new ArrayList(); + /** + * 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 } + *

+ * + * + * @return + * The value of the sequenceSet property. + */ + public List getSequenceSet() { + if (sequenceSet == null) { + sequenceSet = new ArrayList(); + } + return this.sequenceSet; } - return this.sequenceSet; - } } diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index a8e663c..29732de 100644 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@ -1,10 +1,11 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // + package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -17,173 +18,226 @@ import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlSeeAlso; import javax.xml.bind.annotation.XmlType; + /** - * <p>Java class for WebServiceParameterSet complex type. + *

Java class for WebServiceParameterSet complex type

. * - * <p>The following schema fragment specifies the expected content - * contained within this class. + *

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

* - * <pre> &lt;complexType name="WebServiceParameterSet"&gt; - * &lt;complexContent&gt; &lt;restriction - * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;sequence&gt; &lt;element name="Version" - * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; - * &lt;element name="description" - * type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; - * &lt;element name="serviceURL" - * type="{http://www.w3.org/2001/XMLSchema}anyURI" - * maxOccurs="unbounded"/&gt; &lt;element name="parameters" - * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; - * &lt;/sequence&gt; &lt;attribute name="name" use="required" - * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; &lt;/complexContent&gt; - * &lt;/complexType&gt; </pre> + * 
+ * <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" }) +@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. - * - * <p> 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 - * <CODE>set</CODE> method for the serviceURL property. - * - * <p> For example, to add a new item, do as follows: <pre> - * getServiceURL().add(newItem); </pre> - * - * - * <p> Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getServiceURL() - { - if (serviceURL == null) - { - serviceURL = new ArrayList(); + jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class +}) +public class WebServiceParameterSet { + + /** + * A Jalview Web Service Parameter Set container + * version number. + * Version 1 created for storing Jaba user presets. + * + */ + @XmlElement(name = "Version", namespace = "") + protected String version; + /** + * Short description - as utf8 encoded text. This is + * usually displayed + * in the body of an HTML capable tooltip, so HTML tags may be embedded + * using standard UTF8 encoding. + * + */ + @XmlElement(namespace = "") + protected String description; + /** + * URL for which the parameter set is valid. Jalview will use it to + * match up parameter sets to service instances that can parse the + * parameter set payload. + * + */ + @XmlElement(namespace = "", required = true) + @XmlSchemaType(name = "anyURI") + protected List serviceURL; + /** + * UTF8 encoded string to be processed into a specific web services' + * parameter set. Note - newlines may be important to the structure + * of this file. + * + */ + @XmlElement(namespace = "", required = true) + protected String parameters; + /** + * The short name for the parameter set. This will be shown amongst the + * other presets for the web service. + * + */ + @XmlAttribute(name = "name", required = true) + protected String name; + + /** + * A Jalview Web Service Parameter Set container + * version number. + * Version 1 created for storing Jaba user presets. + * + * @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 } + * + * @see #getVersion() + */ + public void setVersion(String value) { + this.version = value; + } + + /** + * Short description - as utf8 encoded text. This is + * usually displayed + * in the body of an HTML capable tooltip, so HTML tags may be embedded + * using standard UTF8 encoding. + * + * @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 } + * + * @see #getDescription() + */ + public void setDescription(String value) { + this.description = value; + } + + /** + * URL for which the parameter set is valid. Jalview will use it to + * match up parameter sets to service instances that can parse the + * parameter set payload. + * + * 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 } + *

+ * + * + * @return + * The value of the serviceURL property. + */ + public List getServiceURL() { + if (serviceURL == null) { + serviceURL = new ArrayList(); + } + return this.serviceURL; + } + + /** + * UTF8 encoded string to be processed into a specific web services' + * parameter set. Note - newlines may be important to the structure + * of this file. + * + * @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 } + * + * @see #getParameters() + */ + public void setParameters(String value) { + this.parameters = value; + } + + /** + * The short name for the parameter set. This will be shown amongst the + * other presets for the web service. + * + * @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 } + * + * @see #getName() + */ + public void setName(String value) { + this.name = value; } - 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 index 3ebfa3e..496652f 100644 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@ -1,11 +1,9 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.9 // See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.11.01 at 07:03:09 PM GMT +// Generated on: 2024.07.25 at 02:29:22 PM BST // -@javax.xml.bind.annotation.XmlSchema( - namespace = "www.vamsas.ac.uk/jalview/version2", - elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) +@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