From c1d8867e99833bcb9019aaebddfabb99dd852f66 Mon Sep 17 00:00:00 2001 From: James Procter Date: Fri, 1 Sep 2023 16:10:33 +0100 Subject: [PATCH] JAL-4124 matrix is saved in dataset, with forward references made from alignments --- schemas/vamsas.xsd | 3 +- src/jalview/datamodel/Alignment.java | 2 +- src/jalview/project/Jalview2XML.java | 129 +- src/jalview/renderer/ContactMapRenderer.java | 4 + src/jalview/xml/binding/jalview/AlcodonFrame.java | 154 +- src/jalview/xml/binding/jalview/Annotation.java | 158 +- .../binding/jalview/AnnotationColourScheme.java | 42 +- .../xml/binding/jalview/AnnotationElement.java | 54 +- src/jalview/xml/binding/jalview/DoubleMatrix.java | 52 +- src/jalview/xml/binding/jalview/DoubleVector.java | 44 +- src/jalview/xml/binding/jalview/Feature.java | 104 +- .../xml/binding/jalview/FeatureMatcher.java | 50 +- .../xml/binding/jalview/FeatureMatcherSet.java | 96 +- src/jalview/xml/binding/jalview/FilterBy.java | 29 +- src/jalview/xml/binding/jalview/JalviewModel.java | 2066 ++++++++++---------- .../xml/binding/jalview/JalviewUserColours.java | 210 +- src/jalview/xml/binding/jalview/MapListType.java | 146 +- .../xml/binding/jalview/MapOnAMatrixType.java | 50 +- src/jalview/xml/binding/jalview/Mapping.java | 50 +- src/jalview/xml/binding/jalview/MatrixType.java | 86 +- src/jalview/xml/binding/jalview/NoValueColour.java | 29 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 114 +- src/jalview/xml/binding/jalview/PcaDataType.java | 36 +- src/jalview/xml/binding/jalview/Pdbentry.java | 96 +- src/jalview/xml/binding/jalview/Property.java | 30 +- src/jalview/xml/binding/jalview/Sequence.java | 114 +- src/jalview/xml/binding/jalview/SequenceSet.java | 168 +- src/jalview/xml/binding/jalview/SequenceType.java | 38 +- src/jalview/xml/binding/jalview/ThresholdType.java | 29 +- src/jalview/xml/binding/jalview/VAMSAS.java | 58 +- .../binding/jalview/WebServiceParameterSet.java | 52 +- src/jalview/xml/binding/jalview/package-info.java | 6 +- 32 files changed, 2184 insertions(+), 2115 deletions(-) diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 38152fd..364bfbe 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -23,7 +23,6 @@ xjc schemas/jalview.xsd -d src -p jalview.xml.binding.jalview Note this also generates code for included schemas --> - - Matrices referred to by this set of sequences. diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 514a326..cfd6aee 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -2057,7 +2057,7 @@ public class Alignment implements AlignmentI, AutoCloseable if (cm == null && _aa.sequenceRef != null) { cm = _aa.sequenceRef.getContactMatrixFor(_aa); - if (cm == null) + if (cm == null && _aa.sequenceRef.getDatasetSequence()!=null) { // TODO fix up this logic and unify with getContactListFor cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa); diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index f8be544..627aba3 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -272,7 +272,7 @@ public class Jalview2XML Map incompleteSeqs = null; - List frefedSequence = null; + List frefedSequence = null; boolean raiseGUI = true; // whether errors are raised in dialog boxes or not @@ -293,6 +293,7 @@ public class Jalview2XML */ private Map contactMatrices = new HashMap<>(); private Map contactMatrixRefs = new HashMap<>(); + private List xmlMatrices= new ArrayList<>(); /** * A helper method for safely using the value of an optional attribute that @@ -390,18 +391,17 @@ public class Jalview2XML } /** - * base class for resolving forward references to sequences by their ID + * base class for resolving forward references to an as-yet unmarshalled object referenced by already unmarshalled objects * * @author jprocter * */ - abstract class SeqFref - { + abstract class forwardRef { String sref; String type; - public SeqFref(String _sref, String type) + public forwardRef(String _sref, String type) { sref = _sref; this.type = type; @@ -412,6 +412,28 @@ public class Jalview2XML return sref; } + public abstract boolean isResolvable(); + /** + * @return true if the forward reference was fully resolved + */ + abstract boolean resolve(); + + @Override + public String toString() + { + return type + " reference to " + sref; + } + } + /** + * resolve forward references to sequences by their ID + * @author jprocter + */ + abstract class SeqFref extends forwardRef + { + public SeqFref(String _sref, String type) + { + super(_sref, type); + } public SequenceI getSrefSeq() { return seqRefIds.get(sref); @@ -434,17 +456,6 @@ public class Jalview2XML } return sq; } - - /** - * @return true if the forward reference was fully resolved - */ - abstract boolean resolve(); - - @Override - public String toString() - { - return type + " reference to " + sref; - } } /** @@ -507,15 +518,42 @@ public class Jalview2XML }; return fref; } + + public forwardRef newMatrixFref(final String matRef, + final jalview.util.MapList mapping, final AlignmentAnnotation jaa) + { + forwardRef fref = new forwardRef(matRef, + "Matrix Reference for sequence and annotation") + { + + @Override + boolean resolve() + { + ContactMatrixI cm = contactMatrixRefs.get(matRef); + PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef, + mapping, cm); + + jaa.sequenceRef.addContactListFor(jaa, newpae); + return true; + } + + @Override + public boolean isResolvable() + { + return (contactMatrixRefs.get(matRef) != null); + } + }; + return fref; + } public void resolveFrefedSequences() { - Iterator nextFref = frefedSequence.iterator(); + Iterator nextFref = frefedSequence.iterator(); int toresolve = frefedSequence.size(); int unresolved = 0, failedtoresolve = 0; while (nextFref.hasNext()) { - SeqFref ref = nextFref.next(); + forwardRef ref = nextFref.next(); if (ref.isResolvable()) { try @@ -1761,6 +1799,20 @@ public class Jalview2XML // jms.addViewport(view); object.getViewport().add(view); } + + + if (storeDS) + { + // store matrices referenced by any views or annotation in this dataset + if (xmlMatrices!=null && xmlMatrices.size()>0) + { + Console.debug("Adding "+xmlMatrices.size()+" matrices to dataset."); + vamsasSet.getMatrix().addAll(xmlMatrices); + xmlMatrices.clear(); + } + } + + // object.setJalviewModelSequence(jms); // object.getVamsasModel().addSequenceSet(vamsasSet); object.getVamsasModel().getSequenceSet().add(vamsasSet); @@ -2464,10 +2516,13 @@ public class Jalview2XML { xmlmat.setCutHeight(cm.getCutHeight()); } - xmlmat.setId(cmId = makeHashCode(cm, null)); + xmlmat.setId(cmId = "m"+contactMatrices.size()+System.currentTimeMillis()); + Console.trace("Matrix data stored :"+cmId); contactMatrices.put(cm, cmId); contactMatrixRefs.put(cmId, cm); - root.getMatrices().add(xmlmat); + xmlMatrices.add(xmlmat); + } else { + Console.trace("Existing Matrix stored :"+cmId); } // now store mapping @@ -3534,9 +3589,9 @@ public class Jalview2XML // //////////////////////////////// // LOAD MATRICES (IF ANY) - if (vamsasSet.getMatrices()!=null && vamsasSet.getMatrices().size()>0) + if (vamsasSet.getMatrix()!=null && vamsasSet.getMatrix().size()>0) { - importMatrixData(vamsasSet.getMatrices()); + importMatrixData(vamsasSet.getMatrix()); } // //////////////////////////////// @@ -4356,17 +4411,7 @@ public class Jalview2XML private void restoreMatrixFor(SequenceI sequenceRef, AlignmentAnnotation jaa, MapOnAMatrixType xmlmatmapping) - { - MatrixType xmlmat; - - // locate matrix data in project XML and import - ContactMatrixI cm = contactMatrixRefs.get(xmlmatmapping.getMatrix()); - if (cm == null) - { - Console.error("Cannot restore mapping to matrix " - + xmlmatmapping.getMatrix() + " - not found in project."); - } - + { // restore mapping data to matrix data jalview.util.MapList mapping = null; if (xmlmatmapping.getMapping() != null) @@ -4393,10 +4438,22 @@ public class Jalview2XML mapping = new jalview.util.MapList(fr, fto, m.getMapFromUnit().intValue(), m.getMapToUnit().intValue()); } - PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef, mapping, - cm); + + // locate matrix data in project XML and import + ContactMatrixI cm = contactMatrixRefs.get(xmlmatmapping.getMatrix()); + if (cm == null) + { + frefedSequence + .add(newMatrixFref(xmlmatmapping.getMatrix(), mapping, jaa)); + } + else + { + // create the PAEMatrix now + PAEContactMatrix newpae = new PAEContactMatrix(jaa.sequenceRef, + mapping, cm); - jaa.sequenceRef.addContactListFor(jaa, newpae); + jaa.sequenceRef.addContactListFor(jaa, newpae); + } return; } diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java index 0471145..c5d4b14 100644 --- a/src/jalview/renderer/ContactMapRenderer.java +++ b/src/jalview/renderer/ContactMapRenderer.java @@ -119,6 +119,10 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI int column; int aaMax = aa_annotations.length - 1; ContactMatrixI cm = viewport.getContactMatrix(_aa); + if (cm==null) + { + return; + } while (x < eRes - sRes) { column = sRes + x; diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 9d356a0..c241422 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -20,43 +20,43 @@ import javax.xml.bind.annotation.XmlType; /** - *

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. * - * 

- * <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>
- *
+ * <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> * * */ @@ -74,20 +74,20 @@ public class AlcodonFrame { /** * 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 set method for the alcodon property. + * 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 } * @@ -103,20 +103,20 @@ public class AlcodonFrame { /** * 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 set method for the alcodMap property. + * 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 } * @@ -131,22 +131,22 @@ public class AlcodonFrame { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -225,21 +225,21 @@ public class AlcodonFrame { * (indicating a gapped column with no translated peptide). * * - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index dc485c5..bb20751 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -19,53 +19,53 @@ import javax.xml.bind.annotation.XmlType; /** - *

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. * - * 

- * <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>
- *
+ * <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> * * */ @@ -126,20 +126,20 @@ public class Annotation { /** * 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 set method for the annotationElement property. + * 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 } * @@ -227,20 +227,20 @@ public class Annotation { /** * 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 set method for the contactmatrix property. + * 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 } * @@ -256,20 +256,20 @@ public class Annotation { /** * 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 set method for the property property. + * 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 } * @@ -696,21 +696,21 @@ public class Annotation { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index 5bfa180..5f2f7d0 100644 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -15,26 +15,26 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java index cdb697e..eaddc5a 100644 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -16,32 +16,32 @@ import javax.xml.bind.annotation.XmlType; /** - *

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. * - * 

- * <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>
- *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java index c96d6fa..f2d3fe2 100644 --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -18,25 +18,25 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -61,20 +61,20 @@ public class DoubleMatrix { /** * 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 set method for the row property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index 12dd58d..b7d7d87 100644 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -17,21 +17,21 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -47,20 +47,20 @@ public class DoubleVector { /** * 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 set method for the v property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index 70c35dc..7b25d44 100644 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -17,38 +17,38 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -77,20 +77,20 @@ public class Feature { /** * 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 set method for the otherData property. + * 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 } * @@ -257,21 +257,21 @@ public class Feature { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index b560eb9..d83131c 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -18,24 +18,24 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -59,20 +59,20 @@ public class FeatureMatcher { /** * 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 set method for the attributeName property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index cb6375a..f182816 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -20,33 +20,33 @@ import javax.xml.bind.annotation.XmlType; /** * A feature match condition, which may be simple or compound * - *

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

- * <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>
- *
+ * <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> * * */ @@ -112,22 +112,22 @@ public class FeatureMatcherSet { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -145,20 +145,20 @@ public class FeatureMatcherSet { /** * 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 set method for the matcherSet property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index 3982b52..2db2173 100644 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -14,19 +14,18 @@ import javax.xml.bind.annotation.XmlType; /** - *

Java class for FilterBy. + * <p>Java class for FilterBy. * - *

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

- * 

- * <simpleType name="FilterBy">
- *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *     <enumeration value="byLabel"/>
- *     <enumeration value="byScore"/>
- *     <enumeration value="byAttribute"/>
- *   </restriction>
- * </simpleType>
- *
+ * <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> * */ @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours") diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 2b4b89e..4e0857d 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -24,359 +24,359 @@ import javax.xml.datatype.XMLGregorianCalendar; /** - *

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

- * <complexType name="JalviewModel">
- *   <complexContent>
- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       <sequence>
- *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- *         <sequence>
- *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <extension base="{www.jalview.org}pdbentry">
- *                             <sequence>
- *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- *                                 <complexType>
- *                                   <simpleContent>
- *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
- *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
- *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     </extension>
- *                                   </simpleContent>
- *                                 </complexType>
- *                               </element>
- *                             </sequence>
- *                           </extension>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <sequence>
- *                               <element name="secondaryStructure" maxOccurs="unbounded">
- *                                 <complexType>
- *                                   <complexContent>
- *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     </restriction>
- *                                   </complexContent>
- *                                 </complexType>
- *                               </element>
- *                             </sequence>
- *                             <attGroup ref="{www.jalview.org}swingwindow"/>
- *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                   </sequence>
- *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                   </sequence>
- *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           </extension>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <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>
- *                   </sequence>
- *                   <attGroup ref="{www.jalview.org}swingwindow"/>
- *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="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="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}SimilarityParams"/>
- *                   <attGroup ref="{www.jalview.org}swingwindow"/>
- *                   <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>
- *
+ * <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="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> * * */ @@ -491,20 +491,20 @@ public class JalviewModel { /** * 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 set method for the jSeq property. + * 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 } * @@ -520,20 +520,20 @@ public class JalviewModel { /** * 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 set method for the jGroup property. + * 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 } * @@ -549,20 +549,20 @@ public class JalviewModel { /** * 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 set method for the viewport property. + * 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 } * @@ -578,20 +578,20 @@ public class JalviewModel { /** * 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 set method for the userColours property. + * 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 } * @@ -607,20 +607,20 @@ public class JalviewModel { /** * 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 set method for the tree property. + * 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 } * @@ -636,20 +636,20 @@ public class JalviewModel { /** * 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 set method for the pcaViewer property. + * 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 } * @@ -688,54 +688,54 @@ public class JalviewModel { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -754,20 +754,20 @@ public class JalviewModel { /** * 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 set method for the setting property. + * 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 } * @@ -783,20 +783,20 @@ public class JalviewModel { /** * 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 set method for the group property. + * 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 } * @@ -811,20 +811,20 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ @@ -881,34 +881,34 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ @@ -951,20 +951,20 @@ public class JalviewModel { /** * 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 set method for the attributeName property. + * 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 } * @@ -1283,41 +1283,41 @@ public class JalviewModel { /** - *

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. * - * 

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
+ * <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> * * */ @@ -1374,20 +1374,20 @@ public class JalviewModel { /** * 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 set method for the seq property. + * 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 } * @@ -1900,80 +1900,80 @@ public class JalviewModel { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -2010,20 +2010,20 @@ public class JalviewModel { /** * 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 set method for the features property. + * 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 } * @@ -2039,20 +2039,20 @@ public class JalviewModel { /** * 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 set method for the pdbids property. + * 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 } * @@ -2068,20 +2068,20 @@ public class JalviewModel { /** * 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 set method for the hiddenSequences property. + * 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 } * @@ -2097,20 +2097,20 @@ public class JalviewModel { /** * 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 set method for the rnaViewer property. + * 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 } * @@ -2253,35 +2253,35 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ @@ -2299,20 +2299,20 @@ public class JalviewModel { /** * 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 set method for the structureState property. + * 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 } * @@ -2327,25 +2327,25 @@ public class JalviewModel { /** - *

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. * - * 

-             * <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>
-             *
+ * <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> * * */ @@ -2660,37 +2660,37 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ @@ -2722,20 +2722,20 @@ public class JalviewModel { /** * 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 set method for the secondaryStructure property. + * 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 } * @@ -2942,22 +2942,22 @@ public class JalviewModel { /** - *

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. * - * 

-             * <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>
-             *
+ * <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> * * */ @@ -3078,69 +3078,69 @@ public class JalviewModel { /** - *

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. * - * 

-     * <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}SimilarityParams"/>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <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>
-     *
+ * <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> * * */ @@ -3202,20 +3202,20 @@ public class JalviewModel { /** * 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 set method for the sequencePoint property. + * 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 } * @@ -3231,20 +3231,20 @@ public class JalviewModel { /** * 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 set method for the axis property. + * 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 } * @@ -3739,19 +3739,19 @@ public class JalviewModel { /** - *

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. * - * 

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         *
+ * <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> * * */ @@ -3842,19 +3842,19 @@ public class JalviewModel { /** - *

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. * - * 

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         *
+ * <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> * * */ @@ -3945,19 +3945,19 @@ public class JalviewModel { /** - *

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. * - * 

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         *
+ * <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> * * */ @@ -4048,20 +4048,20 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ @@ -4180,36 +4180,36 @@ public class JalviewModel { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -4730,22 +4730,22 @@ public class JalviewModel { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -4812,102 +4812,102 @@ public class JalviewModel { /** - *

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. * - * 

-     * <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>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="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="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>
-     *
+ * <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="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> * * */ @@ -5057,20 +5057,20 @@ public class JalviewModel { /** * 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 set method for the hiddenColumns property. + * 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 } * @@ -5086,20 +5086,20 @@ public class JalviewModel { /** * 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 set method for the calcIdParam property. + * 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 } * @@ -6366,21 +6366,21 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ @@ -6469,20 +6469,20 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ @@ -6547,24 +6547,24 @@ public class JalviewModel { /** - *

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. * - * 

-         * <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>
-         *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index 703178c..1c0af33 100644 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -18,55 +18,55 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -114,20 +114,20 @@ public class JalviewUserColours { /** * 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 set method for the colour property. + * 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 } * @@ -143,20 +143,20 @@ public class JalviewUserColours { /** * 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 set method for the filter property. + * 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 } * @@ -195,31 +195,31 @@ public class JalviewUserColours { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -255,20 +255,20 @@ 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 set method for the attributeName property. + * 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 } * @@ -529,22 +529,22 @@ public class JalviewUserColours { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index ac05ff5..2bac782 100644 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -25,42 +25,42 @@ import javax.xml.bind.annotation.XmlType; * 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. * - * 

- * <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>
- *
+ * <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> * * */ @@ -86,20 +86,20 @@ public class MapListType { /** * 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 set method for the mapListFrom property. + * 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 } * @@ -115,20 +115,20 @@ public class MapListType { /** * 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 set method for the mapListTo property. + * 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 } * @@ -191,20 +191,20 @@ public class MapListType { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ @@ -253,20 +253,20 @@ public class MapListType { /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java index d94f60e..47460a3 100644 --- a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java +++ b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -21,24 +21,24 @@ import javax.xml.bind.annotation.XmlType; * and its associated data specified by MatrixType * * - *

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

- * <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>
- *
+ * <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> * * */ @@ -59,20 +59,20 @@ public class MapOnAMatrixType { /** * 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 set method for the property property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index c7b1386..f32c611 100644 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -26,30 +26,30 @@ import javax.xml.bind.annotation.XmlType; * 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. * - * 

- * <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>
- *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java index aac0c43..01629b0 100644 --- a/src/jalview/xml/binding/jalview/MatrixType.java +++ b/src/jalview/xml/binding/jalview/MatrixType.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -25,30 +25,30 @@ import javax.xml.bind.annotation.XmlType; * 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. * - * 

- * <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>
- *
+ * <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> * * */ @@ -106,20 +106,20 @@ public class MatrixType { /** * 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 set method for the groups property. + * 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 } * @@ -135,20 +135,20 @@ public class MatrixType { /** * 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 set method for the newick property. + * 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 } * @@ -164,20 +164,20 @@ public class MatrixType { /** * 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 set method for the property property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java index f626036..5b329a9 100644 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -14,19 +14,18 @@ import javax.xml.bind.annotation.XmlType; /** - *

Java class for NoValueColour. + * <p>Java class for NoValueColour. * - *

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

- * 

- * <simpleType name="NoValueColour">
- *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *     <enumeration value="None"/>
- *     <enumeration value="Min"/>
- *     <enumeration value="Max"/>
- *   </restriction>
- * </simpleType>
- *
+ * <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> * */ @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours") diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java index bb6c7be..26269ec 100644 --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -18,7 +18,7 @@ import javax.xml.namespace.QName; * This object contains factory methods for each * Java content interface and Java element interface * generated in the jalview.xml.binding.jalview package. - *

An ObjectFactory allows you to programatically + * <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 @@ -31,9 +31,9 @@ import javax.xml.namespace.QName; @XmlRegistry public class ObjectFactory { - private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet"); 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 @@ -43,14 +43,6 @@ public class ObjectFactory { } /** - * Create an instance of {@link AlcodonFrame } - * - */ - public AlcodonFrame createAlcodonFrame() { - return new AlcodonFrame(); - } - - /** * Create an instance of {@link MapListType } * */ @@ -67,6 +59,14 @@ public class ObjectFactory { } /** + * Create an instance of {@link AlcodonFrame } + * + */ + public AlcodonFrame createAlcodonFrame() { + return new AlcodonFrame(); + } + + /** * Create an instance of {@link Annotation } * */ @@ -171,14 +171,6 @@ public class ObjectFactory { } /** - * Create an instance of {@link DoubleMatrix } - * - */ - public DoubleMatrix createDoubleMatrix() { - return new DoubleMatrix(); - } - - /** * Create an instance of {@link AnnotationColourScheme } * */ @@ -203,27 +195,11 @@ public class ObjectFactory { } /** - * 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 } + * Create an instance of {@link DoubleMatrix } * */ - public AnnotationElement createAnnotationElement() { - return new AnnotationElement(); + public DoubleMatrix createDoubleMatrix() { + return new DoubleMatrix(); } /** @@ -267,6 +243,30 @@ public class ObjectFactory { } /** + * 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 } * */ @@ -483,17 +483,12 @@ public class ObjectFactory { } /** - * Create an 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); - } - - /** - * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}} + * 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) { @@ -501,12 +496,29 @@ public class ObjectFactory { } /** - * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}} + * 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 e4952bd..a4b2dbe 100644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -19,23 +19,23 @@ 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. * - * 

- * <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>
- *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java index 5c7a219..6fabea0 100644 --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -18,33 +18,33 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -68,20 +68,20 @@ public class Pdbentry { /** * 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 set method for the property property. + * 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 } * @@ -168,20 +168,20 @@ public class Pdbentry { /** - *

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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/Property.java b/src/jalview/xml/binding/jalview/Property.java index 095d48b..4c85bc3 100644 --- a/src/jalview/xml/binding/jalview/Property.java +++ b/src/jalview/xml/binding/jalview/Property.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -15,20 +15,20 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index a9ed23d..76b4f1a 100644 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -19,38 +19,38 @@ import javax.xml.bind.annotation.XmlType; /** - *

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. * - * 

- * <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>
- *
+ * <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> * * */ @@ -73,20 +73,20 @@ public class Sequence /** * 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 set method for the dbRef property. + * 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 } * @@ -149,26 +149,26 @@ public class Sequence /** - *

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. * - * 

-     * <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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index 78df533..ce80b9c 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -19,36 +19,36 @@ import javax.xml.bind.annotation.XmlType; /** - *

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. * - * 

- * <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="Matrices" 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>
- *
+ * <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> * * */ @@ -58,7 +58,7 @@ import javax.xml.bind.annotation.XmlType; "annotation", "sequenceSetProperties", "alcodonFrame", - "matrices" + "matrix" }) @XmlRootElement(name = "SequenceSet") public class SequenceSet { @@ -70,8 +70,8 @@ public class SequenceSet { protected List sequenceSetProperties; @XmlElement(name = "AlcodonFrame") protected List alcodonFrame; - @XmlElement(name = "Matrices") - protected List matrices; + @XmlElement(name = "Matrix") + protected List matrix; @XmlAttribute(name = "gapChar", required = true) protected String gapChar; @XmlAttribute(name = "datasetId") @@ -80,20 +80,20 @@ public class SequenceSet { /** * 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 set method for the sequence property. + * 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 } * @@ -109,20 +109,20 @@ public class SequenceSet { /** * 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 set method for the annotation property. + * 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 } * @@ -138,20 +138,20 @@ public class SequenceSet { /** * 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 set method for the sequenceSetProperties property. + * 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 } * @@ -167,20 +167,20 @@ public class SequenceSet { /** * 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 set method for the alcodonFrame property. + * 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 } * @@ -194,32 +194,32 @@ public class SequenceSet { } /** - * Gets the value of the matrices property. + * 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 set method for the matrices property. + * 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: - * 

-     *    getMatrices().add(newItem);
-     *
+ * <pre> + * getMatrix().add(newItem); + * </pre> * * - *

+ * <p> * Objects of the following type(s) are allowed in the list * {@link MatrixType } * * */ - public List getMatrices() { - if (matrices == null) { - matrices = new ArrayList(); + public List getMatrix() { + if (matrix == null) { + matrix = new ArrayList(); } - return this.matrices; + return this.matrix; } /** @@ -272,20 +272,20 @@ public class SequenceSet { /** - *

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>
-     *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index 3d3e616..dbcefe8 100644 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -16,24 +16,24 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java index 0a9aa13..a467506 100644 --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -13,19 +13,18 @@ import javax.xml.bind.annotation.XmlType; /** - *

Java class for ThresholdType. + * <p>Java class for ThresholdType. * - *

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

- * 

- * <simpleType name="ThresholdType">
- *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *     <enumeration value="NONE"/>
- *     <enumeration value="ABOVE"/>
- *     <enumeration value="BELOW"/>
- *   </restriction>
- * </simpleType>
- *
+ * <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> * */ @XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours") diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java index a56f957..f1eab2b 100644 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -17,22 +17,22 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -51,20 +51,20 @@ public class VAMSAS { /** * 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 set method for the tree property. + * 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 } * @@ -80,20 +80,20 @@ public class VAMSAS { /** * 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 set method for the sequenceSet property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index d067e81..577c9a4 100644 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @@ -20,25 +20,25 @@ import javax.xml.bind.annotation.XmlType; /** - *

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

- * <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>
- *
+ * <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> * * */ @@ -117,20 +117,20 @@ public class WebServiceParameterSet { /** * 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 set method for the serviceURL property. + * 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 } * diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index 817f533..21a46db 100644 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@ -1,8 +1,8 @@ // -// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 -// See http://java.sun.com/xml/jaxb +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.08.28 at 01:52:46 PM BST +// Generated on: 2023.09.01 at 02:16:11 PM BST // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) -- 1.7.10.2