From: James Procter Date: Wed, 15 Mar 2023 10:54:19 +0000 (+0000) Subject: JAL-4134 JAL-3855 store/restore groups, tree and threshold used to cluster a PAE... X-Git-Tag: Release_2_11_3_0~15^2^2~17 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=a81e74154d35e10958b58c3c9411aa9ee21880a6 JAL-4134 JAL-3855 store/restore groups, tree and threshold used to cluster a PAE matrix --- diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index 5fd2bab..abfabb1 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -219,12 +219,7 @@ - - - - - - + @@ -312,13 +307,48 @@ - - - - - - - + + + + serialised representation of matrix as one or + more sets of comma separated values + + + + + Comma separated series of BigIntegers formed from + bitsets defining partitions on the rows/columns of the matrix + + + + + + tree computed for this + + + + + + + + + + + + + + + + + diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java index 4e2076d..9eabb10 100644 --- a/src/jalview/datamodel/ContactMatrixI.java +++ b/src/jalview/datamodel/ContactMatrixI.java @@ -1,6 +1,8 @@ package jalview.datamodel; +import java.util.Arrays; import java.util.BitSet; +import java.util.List; public interface ContactMatrixI { @@ -37,4 +39,31 @@ public interface ContactMatrixI return colbitset; } + default List getGroups() { + return Arrays.asList(); + } + + default boolean hasTree() { + return false; + } + + /** + * Newick representation of clustered matrix + * @return null unless hasTree is true + */ + default String getNewick() { + return null; + } + + default String getTreeMethod() { + return null; + } + + default boolean hasCutHeight() { + return false; + } + + default double getCutHeight() { + return 0; + } } diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 14803df..36c87ce 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -45,6 +45,7 @@ import java.net.MalformedURLException; import java.net.URL; import java.util.ArrayList; import java.util.Arrays; +import java.util.BitSet; import java.util.Collections; import java.util.Enumeration; import java.util.GregorianCalendar; @@ -2307,7 +2308,28 @@ public class Jalview2XML xmlmat.setType(cm.getType()); xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); - xmlmat.setValue(ContactMatrix.contactToFloatString(cm)); + // consider using an opaque to/from -> allow instance to control its representation ? + xmlmat.setElements(ContactMatrix.contactToFloatString(cm)); + if (cm.hasGroups()) + { + for (BitSet gp: cm.getGroups()) + { + BigInteger val = new BigInteger(gp.toByteArray()); + xmlmat.getGroups().add(val.toString()); + } + } + if (cm.hasTree()) + { + // provenance object for tree ? + xmlmat.getNewick().add(cm.getNewick()); + xmlmat.setTreeMethod(cm.getTreeMethod()); + } + if (cm.hasCutHeight()) + { + xmlmat.setCutHeight(cm.getCutHeight()); + } + + // set/get properties an.getContactmatrix().add(xmlmat); } } @@ -2342,10 +2364,9 @@ public class Jalview2XML { for (String pr : annotation.getProperties()) { - jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property(); + jalview.xml.binding.jalview.Property prop = new jalview.xml.binding.jalview.Property(); prop.setName(pr); prop.setValue(annotation.getProperty(pr)); - // an.addProperty(prop); an.getProperty().add(prop); } } @@ -3920,7 +3941,7 @@ public class Jalview2XML jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { - for (Annotation.Property prop : annotation.getProperty()) + for (jalview.xml.binding.jalview.Property prop : annotation.getProperty()) { jaa.setProperty(prop.getName(), prop.getValue()); } @@ -3941,12 +3962,36 @@ public class Jalview2XML else { float[][] elements = ContactMatrix - .fromFloatStringToContacts(xmlmat.getValue(), + .fromFloatStringToContacts(xmlmat.getElements(), xmlmat.getCols().intValue(), xmlmat.getRows().intValue()); PAEContactMatrix newpae = new PAEContactMatrix( jaa.sequenceRef, elements); + List newgroups=new ArrayList(); + if (xmlmat.getGroups().size()>0) + { + for (String sgroup:xmlmat.getGroups()) + { + try { + BigInteger group = new BigInteger(sgroup); + newgroups.add(BitSet.valueOf(group.toByteArray())); + } catch (NumberFormatException nfe) + { + Console.error("Problem parsing groups for a contact matrix (\""+sgroup+"\"",nfe); + } + } + } + String nwk=xmlmat.getNewick().size()>0 ? xmlmat.getNewick().get(0):null; + if (xmlmat.getNewick().size()>1) + { + Console.log.info( + "Ignoring additional clusterings for contact matrix"); + } + + String treeMethod = xmlmat.getTreeMethod(); + double thresh = xmlmat.getCutHeight()!=null ? xmlmat.getCutHeight() : 0; + newpae.restoreGroups(newgroups, treeMethod, nwk, thresh); jaa.sequenceRef.addContactListFor(jaa, newpae); } } diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java index db3addc..87ccab6 100644 --- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java @@ -228,9 +228,11 @@ public class PAEContactMatrix implements ContactMatrixI @Override public String getAnnotLabel() { - StringBuilder label = new StringBuilder("pAE Matrix"); + StringBuilder label = new StringBuilder("PAE Matrix"); if (this.getReferenceSeq() != null) + { label.append(":").append(this.getReferenceSeq().getDisplayId(false)); + } return label.toString(); } @@ -264,12 +266,15 @@ public class PAEContactMatrix implements ContactMatrixI { return newick; } + boolean abs; + double thresh; + String treeType=null; public void makeGroups(float thresh,boolean abs) { AverageDistanceEngine clusterer = new AverageDistanceEngine(null, null, this); double height = clusterer.findHeight(clusterer.getTopNode()); newick = new jalview.io.NewickFile(clusterer.getTopNode(),false,true).print(); - + treeType = "UPGMA"; Console.trace("Newick string\n"+newick); List nodegroups; @@ -285,7 +290,8 @@ public class PAEContactMatrix implements ContactMatrixI nodegroups = new ArrayList(); nodegroups.add(clusterer.getTopNode()); } - + this.abs=abs; + this.thresh=thresh; groups = new ArrayList<>(); for (BinaryNode root:nodegroups) { @@ -309,4 +315,28 @@ public class PAEContactMatrix implements ContactMatrixI } return ContactMatrixI.super.getGroupsFor(column); } + + public void restoreGroups(List newgroups, String treeMethod, + String tree, double thresh2) + { + treeType=treeMethod; + groups = newgroups; + thresh=thresh2; + newick =tree; + + } + @Override + public boolean hasCutHeight() { + return groups!=null && thresh!=0; + } + @Override + public double getCutHeight() + { + return thresh; + } + @Override + public String getTreeMethod() + { + return treeType; + } } diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java index d72dd8d..5e1b3ea 100644 --- a/src/jalview/xml/binding/embl/EntrySetType.java +++ b/src/jalview/xml/binding/embl/EntrySetType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.02.22 at 10:08:57 PM GMT +// Generated on: 2023.03.09 at 07:45:03 AM GMT // diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java index f744eb5..84a1ab3 100644 --- a/src/jalview/xml/binding/embl/EntryType.java +++ b/src/jalview/xml/binding/embl/EntryType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.02.22 at 10:08:57 PM GMT +// Generated on: 2023.03.09 at 07:45:03 AM GMT // diff --git a/src/jalview/xml/binding/embl/ObjectFactory.java b/src/jalview/xml/binding/embl/ObjectFactory.java index 4a5bf19..234c721 100644 --- a/src/jalview/xml/binding/embl/ObjectFactory.java +++ b/src/jalview/xml/binding/embl/ObjectFactory.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.02.22 at 10:08:57 PM GMT +// Generated on: 2023.03.09 at 07:45:03 AM GMT // diff --git a/src/jalview/xml/binding/embl/ROOT.java b/src/jalview/xml/binding/embl/ROOT.java index 6d98c82..76cb42d 100644 --- a/src/jalview/xml/binding/embl/ROOT.java +++ b/src/jalview/xml/binding/embl/ROOT.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.02.22 at 10:08:57 PM GMT +// Generated on: 2023.03.09 at 07:45:03 AM GMT // diff --git a/src/jalview/xml/binding/embl/XrefType.java b/src/jalview/xml/binding/embl/XrefType.java index a53c82b..56a9539 100644 --- a/src/jalview/xml/binding/embl/XrefType.java +++ b/src/jalview/xml/binding/embl/XrefType.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.02.22 at 10:08:57 PM GMT +// Generated on: 2023.03.09 at 07:45:03 AM GMT // diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 53bc217..cdc21a5 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.02.22 at 10:08:57 PM GMT +// Generated on: 2023.03.09 at 07:45:02 AM GMT // diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index 8df1313..ba54d37 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -2,7 +2,7 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.02.22 at 10:08:57 PM GMT +// Generated on: 2023.03.09 at 07:45:02 AM GMT // @@ -43,16 +43,7 @@ import javax.xml.bind.annotation.XmlType; * </complexType> * </element> * <element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" 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" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> + * <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" /> @@ -96,7 +87,7 @@ public class Annotation { protected String description; protected Annotation.ThresholdLine thresholdLine; protected List contactmatrix; - protected List property; + protected List property; @XmlAttribute(name = "graph", required = true) protected boolean graph; @XmlAttribute(name = "graphType") @@ -280,13 +271,13 @@ public class Annotation { * *

* Objects of the following type(s) are allowed in the list - * {@link Annotation.Property } + * {@link Property } * * */ - public List getProperty() { + public List getProperty() { if (property == null) { - property = new ArrayList(); + property = new ArrayList(); } return this.property; } @@ -713,84 +704,6 @@ public class Annotation { * <complexType> * <complexContent> * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * - * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Property { - - @XmlAttribute(name = "name") - protected String name; - @XmlAttribute(name = "value") - protected String value; - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
      *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
      *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index fe0f49d..ccd6222 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index 4d34ce2..72a3e73 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index 8ab2f67..c304ff8 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index 5c34abf..2a8d1eb 100644
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index 41771fd..09701ba 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index 94c26e0..2e41fe0 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index ea26bed..faf4182 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java
index e13905d..e4ea645 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index cbe06b4..0bf4211 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index f383f52..c5177ba 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
index 752b37d..22242eb 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index b1dbda2..a147ab4 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java
index f201c32..fcf9958 100644
--- a/src/jalview/xml/binding/jalview/MatrixType.java
+++ b/src/jalview/xml/binding/jalview/MatrixType.java
@@ -2,18 +2,20 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
+import java.util.ArrayList;
+import java.util.List;
 import javax.xml.bind.annotation.XmlAccessType;
 import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
-import javax.xml.bind.annotation.XmlValue;
 
 
 /**
@@ -23,14 +25,22 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  * 
  * <complexType name="MatrixType">
- *   <simpleContent>
- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
- *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *   <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" />
- *     </extension>
- *   </simpleContent>
+ *       <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" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
  * </complexType>
  * 

  * 
@@ -38,67 +48,140 @@ import javax.xml.bind.annotation.XmlValue;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "MatrixType", propOrder = {
-    "value"
+    "elements",
+    "groups",
+    "newick",
+    "property"
 })
 public class MatrixType {
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "id")
-    protected String id;
+    @XmlElement(required = true)
+    protected String elements;
+    protected List groups;
+    protected List newick;
+    protected List property;
     @XmlAttribute(name = "type", required = true)
     protected String type;
     @XmlAttribute(name = "rows", required = true)
     protected BigInteger rows;
     @XmlAttribute(name = "cols", required = true)
     protected BigInteger cols;
+    @XmlAttribute(name = "treeMethod")
+    protected String treeMethod;
+    @XmlAttribute(name = "cutHeight")
+    protected Double cutHeight;
+    @XmlAttribute(name = "id")
+    protected String id;
 
     /**
-     * Gets the value of the value property.
+     * Gets the value of the elements property.
      * 
      * @return
      *     possible object is
      *     {@link String }
      *     
      */
-    public String getValue() {
-        return value;
+    public String getElements() {
+        return elements;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the elements property.
      * 
      * @param value
      *     allowed object is
      *     {@link String }
      *     
      */
-    public void setValue(String value) {
-        this.value = value;
+    public void setElements(String value) {
+        this.elements = value;
     }
 
     /**
-     * Gets the value of the id property.
+     * Gets the value of the groups property.
+     * 
+     * 

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

+     * For example, to add a new item, do as follows:
+     * 
+     *    getGroups().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getId() {
-        return id;
+    public List getGroups() {
+        if (groups == null) {
+            groups = new ArrayList();
+        }
+        return this.groups;
     }
 
     /**
-     * Sets the value of the id property.
+     * Gets the value of the newick property.
+     * 
+     * 

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

+     * For example, to add a new item, do as follows:
+     * 
+     *    getNewick().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
      */
-    public void setId(String value) {
-        this.id = value;
+    public List getNewick() {
+        if (newick == null) {
+            newick = new ArrayList();
+        }
+        return this.newick;
+    }
+
+    /**
+     * Gets the value of the property property.
+     * 
+     * 

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

+     * For example, to add a new item, do as follows:
+     * 
+     *    getProperty().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Property }
+     * 
+     * 
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
     }
 
     /**
@@ -173,4 +256,76 @@ public class MatrixType {
         this.cols = value;
     }
 
+    /**
+     * Gets the value of the treeMethod property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getTreeMethod() {
+        return treeMethod;
+    }
+
+    /**
+     * Sets the value of the treeMethod property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTreeMethod(String value) {
+        this.treeMethod = value;
+    }
+
+    /**
+     * Gets the value of the cutHeight property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Double }
+     *     
+     */
+    public Double getCutHeight() {
+        return cutHeight;
+    }
+
+    /**
+     * Sets the value of the cutHeight property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Double }
+     *     
+     */
+    public void setCutHeight(Double value) {
+        this.cutHeight = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
 }
diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
index dd1357d..935adc5 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index ea5428a..3a2f81b 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
@@ -283,11 +283,11 @@ public class ObjectFactory {
     }
 
     /**
-     * Create an instance of {@link Annotation.Property }
+     * Create an instance of {@link jalview.xml.binding.jalview.Property }
      * 
      */
-    public Annotation.Property createAnnotationProperty() {
-        return new Annotation.Property();
+    public jalview.xml.binding.jalview.Property createProperty() {
+        return new jalview.xml.binding.jalview.Property();
     }
 
     /**
diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
index a510399..3d19c58 100644
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index 8c3a499..544b568 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index 09fdcb5..5851659 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index f50e4cb..f96550a 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java
index 0a360ed..62c04c8 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index f717f2e..304d653 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index 0983075..0571f85 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index 9baa3bc..21b35d7 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index 5bb7db6..a8e5b9f 100644
--- a/src/jalview/xml/binding/jalview/package-info.java
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:57 PM GMT 
+// Generated on: 2023.03.09 at 07:45:02 AM GMT 
 //
 
 @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java
index a7381a1..15940c7 100644
--- a/src/jalview/xml/binding/uniprot/CitationType.java
+++ b/src/jalview/xml/binding/uniprot/CitationType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java
index 693e586..f2ecd0c 100644
--- a/src/jalview/xml/binding/uniprot/CofactorType.java
+++ b/src/jalview/xml/binding/uniprot/CofactorType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java
index 72ca25c..7ce7ebc 100644
--- a/src/jalview/xml/binding/uniprot/CommentType.java
+++ b/src/jalview/xml/binding/uniprot/CommentType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java
index a2db65a..022099d 100644
--- a/src/jalview/xml/binding/uniprot/ConsortiumType.java
+++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java
index d3c111e..b623d2c 100644
--- a/src/jalview/xml/binding/uniprot/DbReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java
index 7c485d5..74efb7c 100644
--- a/src/jalview/xml/binding/uniprot/Entry.java
+++ b/src/jalview/xml/binding/uniprot/Entry.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java
index ed97121..f8d37c5 100644
--- a/src/jalview/xml/binding/uniprot/EventType.java
+++ b/src/jalview/xml/binding/uniprot/EventType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java
index 4e99255..afe1b60 100644
--- a/src/jalview/xml/binding/uniprot/EvidenceType.java
+++ b/src/jalview/xml/binding/uniprot/EvidenceType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
index caa9d94..78ed315 100644
--- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java
+++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java
index ca03a54..0632ac3 100644
--- a/src/jalview/xml/binding/uniprot/FeatureType.java
+++ b/src/jalview/xml/binding/uniprot/FeatureType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java
index 998d1b9..1094851 100644
--- a/src/jalview/xml/binding/uniprot/GeneLocationType.java
+++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java
index dc03075..6547333 100644
--- a/src/jalview/xml/binding/uniprot/GeneNameType.java
+++ b/src/jalview/xml/binding/uniprot/GeneNameType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java
index d419e09..0dbe520 100644
--- a/src/jalview/xml/binding/uniprot/GeneType.java
+++ b/src/jalview/xml/binding/uniprot/GeneType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java
index 1dacab8..4c493d5 100644
--- a/src/jalview/xml/binding/uniprot/ImportedFromType.java
+++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java
index d579506..038f37f 100644
--- a/src/jalview/xml/binding/uniprot/InteractantType.java
+++ b/src/jalview/xml/binding/uniprot/InteractantType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java
index 69b251e..b3aa4e8 100644
--- a/src/jalview/xml/binding/uniprot/IsoformType.java
+++ b/src/jalview/xml/binding/uniprot/IsoformType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java
index 5497e6d..7f3c265 100644
--- a/src/jalview/xml/binding/uniprot/KeywordType.java
+++ b/src/jalview/xml/binding/uniprot/KeywordType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java
index 78a388b..38c1665 100644
--- a/src/jalview/xml/binding/uniprot/LocationType.java
+++ b/src/jalview/xml/binding/uniprot/LocationType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java
index e734c27..285b8d3 100644
--- a/src/jalview/xml/binding/uniprot/MoleculeType.java
+++ b/src/jalview/xml/binding/uniprot/MoleculeType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java
index c638af7..eddabb2 100644
--- a/src/jalview/xml/binding/uniprot/NameListType.java
+++ b/src/jalview/xml/binding/uniprot/NameListType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java
index 0459e04..d18fdcd 100644
--- a/src/jalview/xml/binding/uniprot/ObjectFactory.java
+++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java
index 312c0ee..06a0470 100644
--- a/src/jalview/xml/binding/uniprot/OrganismNameType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java
index 55774e3..80171d4 100644
--- a/src/jalview/xml/binding/uniprot/OrganismType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java
index 2b130f2..63ea683 100644
--- a/src/jalview/xml/binding/uniprot/PersonType.java
+++ b/src/jalview/xml/binding/uniprot/PersonType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
index 445f99f..f5a126a 100644
--- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
+++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java
index 05b6afc..33c194e 100644
--- a/src/jalview/xml/binding/uniprot/PositionType.java
+++ b/src/jalview/xml/binding/uniprot/PositionType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java
index c9324b0..45f654f 100644
--- a/src/jalview/xml/binding/uniprot/PropertyType.java
+++ b/src/jalview/xml/binding/uniprot/PropertyType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
index f7f989a..7cdaabd 100644
--- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java
index 5f1a018..9edfb71 100644
--- a/src/jalview/xml/binding/uniprot/ProteinType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java
index 806a8f7..933a013 100644
--- a/src/jalview/xml/binding/uniprot/ReactionType.java
+++ b/src/jalview/xml/binding/uniprot/ReactionType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java
index e00e9a7..8315a1c 100644
--- a/src/jalview/xml/binding/uniprot/ReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/ReferenceType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java
index e747820..fbd840b 100644
--- a/src/jalview/xml/binding/uniprot/SequenceType.java
+++ b/src/jalview/xml/binding/uniprot/SequenceType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java
index 9598976..ef8f052 100644
--- a/src/jalview/xml/binding/uniprot/SourceDataType.java
+++ b/src/jalview/xml/binding/uniprot/SourceDataType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java
index 755ca21..711afca 100644
--- a/src/jalview/xml/binding/uniprot/SourceType.java
+++ b/src/jalview/xml/binding/uniprot/SourceType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java
index 63c281d..dc8f920 100644
--- a/src/jalview/xml/binding/uniprot/StatusType.java
+++ b/src/jalview/xml/binding/uniprot/StatusType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
index bebbd62..27ea148 100644
--- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
+++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java
index 1de89de..a7bc828 100644
--- a/src/jalview/xml/binding/uniprot/Uniprot.java
+++ b/src/jalview/xml/binding/uniprot/Uniprot.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 
diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java
index 560368d..3f8b048 100644
--- a/src/jalview/xml/binding/uniprot/package-info.java
+++ b/src/jalview/xml/binding/uniprot/package-info.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.02.22 at 10:08:58 PM GMT 
+// Generated on: 2023.03.09 at 07:45:04 AM GMT 
 //
 
 @javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 510b21d..0ab9dcb 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -1567,7 +1567,7 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
     float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
     assertEquals(vals[3][4],paevals[3][4]);
-    
+    dummyMat.makeGroups(0.5f, false);
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
     File tfile = File.createTempFile("testStoreAndRecoverPAEmatrix",
@@ -1598,6 +1598,11 @@ public class Jalview2xmlTests extends Jalview2xmlBase
         Assert.assertEquals(oldCM.getContactAt(j), newCM.getContactAt(j));
       }
     }
+    Assert.assertEquals(dummyMat.hasGroups(), restoredMat.hasGroups());
+    Assert.assertEquals(dummyMat.getGroups(), restoredMat.getGroups());
+    Assert.assertEquals(dummyMat.hasTree(), restoredMat.hasTree());
+    Assert.assertEquals(dummyMat.getNewick(), restoredMat.getNewick());
+    
     
   }