From fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81 Mon Sep 17 00:00:00 2001
From: James Procter <j.procter@dundee.ac.uk>
Date: Mon, 22 May 2023 09:52:01 +0100
Subject: [PATCH] JAL-1551 spotless

---
 src/jalview/analysis/AlignmentSorter.java          |    4 +-
 src/jalview/analysis/AlignmentUtils.java           |   13 +-
 src/jalview/analysis/AnnotationSorter.java         |   19 +-
 src/jalview/analysis/TreeModel.java                |    9 +-
 src/jalview/appletgui/TreeCanvas.java              |   13 +-
 src/jalview/bin/Cache.java                         |    9 +-
 src/jalview/datamodel/Alignment.java               |   12 +-
 src/jalview/datamodel/AlignmentAnnotation.java     |   12 +-
 src/jalview/datamodel/ColumnSelection.java         |    4 +-
 src/jalview/datamodel/ContactMatrixI.java          |   35 +-
 src/jalview/datamodel/ContactRange.java            |    5 +-
 .../datamodel/SeqDistanceContactMatrix.java        |   29 +-
 src/jalview/gui/AnnotationLabels.java              |   13 +-
 src/jalview/gui/OverviewCanvas.java                |    5 +-
 src/jalview/gui/QuitHandler.java                   |    3 +-
 src/jalview/gui/TreeCanvas.java                    |  122 +-
 src/jalview/gui/TreePanel.java                     |   14 +-
 src/jalview/gui/WebserviceInfo.java                |    4 +-
 src/jalview/io/BackupFiles.java                    |    3 +-
 src/jalview/io/FileParse.java                      |    4 +-
 src/jalview/io/PContactPredictionFile.java         |   20 +-
 src/jalview/io/StockholmFile.java                  |   11 +-
 src/jalview/io/vamsas/Tree.java                    |    3 +-
 src/jalview/project/Jalview2XML.java               |   66 +-
 .../renderer/AnnotationRendererFactory.java        |    8 +-
 src/jalview/renderer/ContactMapRenderer.java       |   24 +-
 src/jalview/renderer/OverviewResColourFinder.java  |    1 +
 .../renderer/api/AnnotationRowRendererI.java       |    7 +-
 .../renderer/seqfeatures/FeatureRenderer.java      |    2 +-
 src/jalview/viewmodel/AlignmentViewport.java       |    1 -
 src/jalview/xml/binding/embl/EntrySetType.java     |   76 +-
 src/jalview/xml/binding/embl/EntryType.java        | 4399 ++++----
 src/jalview/xml/binding/embl/ObjectFactory.java    |  296 +-
 src/jalview/xml/binding/embl/ROOT.java             |  108 +-
 src/jalview/xml/binding/embl/XrefType.java         |  155 +-
 src/jalview/xml/binding/jalview/AlcodonFrame.java  |  456 +-
 src/jalview/xml/binding/jalview/Annotation.java    | 1395 +--
 .../binding/jalview/AnnotationColourScheme.java    |  429 +-
 .../xml/binding/jalview/AnnotationElement.java     |  314 +-
 src/jalview/xml/binding/jalview/DoubleMatrix.java  |  293 +-
 src/jalview/xml/binding/jalview/DoubleVector.java  |   80 +-
 src/jalview/xml/binding/jalview/Feature.java       |  555 +-
 .../xml/binding/jalview/FeatureMatcher.java        |  226 +-
 .../xml/binding/jalview/FeatureMatcherSet.java     |  257 +-
 src/jalview/xml/binding/jalview/FilterBy.java      |   61 +-
 src/jalview/xml/binding/jalview/JalviewModel.java  |11896 ++++++++++----------
 .../xml/binding/jalview/JalviewUserColours.java    |  971 +-
 src/jalview/xml/binding/jalview/MapListType.java   |  444 +-
 src/jalview/xml/binding/jalview/Mapping.java       |  166 +-
 src/jalview/xml/binding/jalview/MatrixType.java    |  534 +-
 src/jalview/xml/binding/jalview/NoValueColour.java |   61 +-
 src/jalview/xml/binding/jalview/ObjectFactory.java | 1042 +-
 src/jalview/xml/binding/jalview/PcaDataType.java   |  169 +-
 src/jalview/xml/binding/jalview/Pdbentry.java      |  351 +-
 src/jalview/xml/binding/jalview/Property.java      |  107 +-
 src/jalview/xml/binding/jalview/Sequence.java      |  503 +-
 src/jalview/xml/binding/jalview/SequenceSet.java   |  482 +-
 src/jalview/xml/binding/jalview/SequenceType.java  |  226 +-
 src/jalview/xml/binding/jalview/ThresholdType.java |   31 +-
 src/jalview/xml/binding/jalview/VAMSAS.java        |  139 +-
 .../binding/jalview/WebServiceParameterSet.java    |  300 +-
 src/jalview/xml/binding/jalview/package-info.java  |    4 +-
 src/jalview/xml/binding/uniprot/CitationType.java  |  916 +-
 src/jalview/xml/binding/uniprot/CofactorType.java  |  173 +-
 src/jalview/xml/binding/uniprot/CommentType.java   | 2817 ++---
 .../xml/binding/uniprot/ConsortiumType.java        |   63 +-
 .../xml/binding/uniprot/DbReferenceType.java       |  288 +-
 src/jalview/xml/binding/uniprot/Entry.java         | 1098 +-
 src/jalview/xml/binding/uniprot/EventType.java     |   59 +-
 src/jalview/xml/binding/uniprot/EvidenceType.java  |  225 +-
 .../xml/binding/uniprot/EvidencedStringType.java   |  172 +-
 src/jalview/xml/binding/uniprot/FeatureType.java   |  478 +-
 .../xml/binding/uniprot/GeneLocationType.java      |  188 +-
 src/jalview/xml/binding/uniprot/GeneNameType.java  |  176 +-
 src/jalview/xml/binding/uniprot/GeneType.java      |   80 +-
 .../xml/binding/uniprot/ImportedFromType.java      |   66 +-
 .../xml/binding/uniprot/InteractantType.java       |  156 +-
 src/jalview/xml/binding/uniprot/IsoformType.java   |  519 +-
 src/jalview/xml/binding/uniprot/KeywordType.java   |  172 +-
 src/jalview/xml/binding/uniprot/LocationType.java  |  225 +-
 src/jalview/xml/binding/uniprot/MoleculeType.java  |  111 +-
 src/jalview/xml/binding/uniprot/NameListType.java  |   83 +-
 src/jalview/xml/binding/uniprot/ObjectFactory.java | 1037 +-
 .../xml/binding/uniprot/OrganismNameType.java      |  111 +-
 src/jalview/xml/binding/uniprot/OrganismType.java  |  350 +-
 src/jalview/xml/binding/uniprot/PersonType.java    |   59 +-
 .../binding/uniprot/PhysiologicalReactionType.java |  172 +-
 src/jalview/xml/binding/uniprot/PositionType.java  |  179 +-
 src/jalview/xml/binding/uniprot/PropertyType.java  |  107 +-
 .../xml/binding/uniprot/ProteinExistenceType.java  |   63 +-
 src/jalview/xml/binding/uniprot/ProteinType.java   | 1746 +--
 src/jalview/xml/binding/uniprot/ReactionType.java  |  187 +-
 src/jalview/xml/binding/uniprot/ReferenceType.java |  292 +-
 src/jalview/xml/binding/uniprot/SequenceType.java  |  396 +-
 .../xml/binding/uniprot/SourceDataType.java        |  671 +-
 src/jalview/xml/binding/uniprot/SourceType.java    |  113 +-
 src/jalview/xml/binding/uniprot/StatusType.java    |  120 +-
 .../binding/uniprot/SubcellularLocationType.java   |  205 +-
 src/jalview/xml/binding/uniprot/Uniprot.java       |  123 +-
 src/jalview/xml/binding/uniprot/package-info.java  |    4 +-
 src/mc_view/PDBChain.java                          |    4 +-
 test/jalview/analysis/AlignmentUtilsTests.java     |    3 +-
 .../analysis/AverageDistanceEngineTest.java        |  116 +-
 test/jalview/datamodel/AlignmentTest.java          |    5 +-
 test/jalview/datamodel/ContactRangeTest.java       |    5 +-
 test/jalview/gui/AlignmentPanelTest.java           |   16 +-
 .../StructureChooserQuerySourceTest.java           |    6 +-
 test/jalview/io/CrossRef2xmlTests.java             |    4 +-
 test/jalview/io/StockholmFileTest.java             |   13 +-
 test/jalview/project/Jalview2xmlTests.java         |   10 +-
 test/jalview/renderer/OverviewRendererTest.java    |    4 +-
 .../renderer/OverviewResColourFinderTest.java      |    9 +-
 .../seqfeatures/FeatureColourFinderTest.java       |    3 +-
 113 files changed, 21052 insertions(+), 20147 deletions(-)

diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java
index 0f3edfd..b02d49c 100755
--- a/src/jalview/analysis/AlignmentSorter.java
+++ b/src/jalview/analysis/AlignmentSorter.java
@@ -548,7 +548,9 @@ public class AlignmentSorter
 
     if ((left == null) && (right == null))
     {
-      if (!(node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder()) && (node.element() != null))
+      if (!(node instanceof SequenceNode
+              && ((SequenceNode) node).isPlaceholder())
+              && (node.element() != null))
       {
         if (node.element() instanceof SequenceI)
         {
diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java
index 0906872..201f88b 100644
--- a/src/jalview/analysis/AlignmentUtils.java
+++ b/src/jalview/analysis/AlignmentUtils.java
@@ -184,10 +184,10 @@ public class AlignmentUtils
       // TODO use Character.toLowerCase to avoid creating String objects?
       char[] upstream = new String(ds
               .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1))
-              .toLowerCase(Locale.ROOT).toCharArray();
+                      .toLowerCase(Locale.ROOT).toCharArray();
       char[] downstream = new String(
               ds.getSequence(s_end - 1, s_end + dstream_ds))
-              .toLowerCase(Locale.ROOT).toCharArray();
+                      .toLowerCase(Locale.ROOT).toCharArray();
       char[] coreseq = s.getSequence();
       char[] nseq = new char[offset + upstream.length + downstream.length
               + coreseq.length];
@@ -1471,19 +1471,20 @@ public class AlignmentUtils
          */
         final Iterable<AlignmentAnnotation> matchedAlignmentAnnotations = al
                 .findAnnotations(seq, dsann.getCalcId(), dsann.label);
-        boolean found=false;
+        boolean found = false;
         if (matchedAlignmentAnnotations != null)
         {
-          for (AlignmentAnnotation matched:matchedAlignmentAnnotations)
+          for (AlignmentAnnotation matched : matchedAlignmentAnnotations)
           {
             if (dsann.description.equals(matched.description))
             {
-              found=true;
+              found = true;
               break;
             }
           }
         }
-        if (!found) {
+        if (!found)
+        {
           result.add(dsann);
           if (labelForCalcId != null)
           {
diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java
index 0f0cf68..1f2e78f 100644
--- a/src/jalview/analysis/AnnotationSorter.java
+++ b/src/jalview/analysis/AnnotationSorter.java
@@ -157,12 +157,13 @@ public class AnnotationSorter
         return showAutocalcAbove ? 1 : -1;
       }
       int computedOrder = compareSequences(o1, o2);
-      if (computedOrder==0) {
+      if (computedOrder == 0)
+      {
         computedOrder = compareLabels(o1, o2);
       }
-      if (computedOrder==0)
+      if (computedOrder == 0)
       {
-        computedOrder = compareDescriptions(o1,o2);
+        computedOrder = compareDescriptions(o1, o2);
       }
       return computedOrder;
     }
@@ -365,18 +366,19 @@ public class AnnotationSorter
     }
     String label1 = o1.label;
     String label2 = o2.label;
-    return compareString(label1,label2);
+    return compareString(label1, label2);
   }
 
   /**
-   * Non-case-sensitive comparison of annotation descriptions. Returns zero if either
-   * argument is null.
+   * Non-case-sensitive comparison of annotation descriptions. Returns zero if
+   * either argument is null.
    * 
    * @param o1
    * @param o2
    * @return
    */
-  private int compareDescriptions(AlignmentAnnotation o1, AlignmentAnnotation o2)
+  private int compareDescriptions(AlignmentAnnotation o1,
+          AlignmentAnnotation o2)
   {
     if (o1 == null || o2 == null)
     {
@@ -384,8 +386,9 @@ public class AnnotationSorter
     }
     String label1 = o1.description;
     String label2 = o2.description;
-    return compareString(label1,label2);
+    return compareString(label1, label2);
   }
+
   private int compareString(String label1, String label2)
   {
     if (label1 == null && label2 == null)
diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index dd56424..6260067 100644
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -80,7 +80,7 @@ public class TreeModel
   public TreeModel(SequenceI[] seqs, AlignmentView odata,
           NewickFile treefile)
   {
-    this(seqs,  treefile.getTree(), treefile.HasDistances(),
+    this(seqs, treefile.getTree(), treefile.HasDistances(),
             treefile.HasBootstrap(), treefile.HasRootDistance());
     seqData = odata;
 
@@ -94,7 +94,7 @@ public class TreeModel
    */
   public TreeModel(TreeBuilder tree)
   {
-    this(tree.getSequences(),  tree.getTopNode(), tree.hasDistances(),
+    this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
             tree.hasBootstrap(), tree.hasRootDistance());
     seqData = tree.getOriginalData();
   }
@@ -141,7 +141,7 @@ public class TreeModel
     while (i < leaves.size())
     {
       // TODO - decide if we get rid of the polymorphism here ?
-      j = (SequenceNode)leaves.elementAt(i++);
+      j = (SequenceNode) leaves.elementAt(i++);
       realnam = j.getName();
       nam = null;
 
@@ -311,8 +311,7 @@ public class TreeModel
    * 
    * @return Vector of leaf nodes on binary tree
    */
-  Vector<BinaryNode> findLeaves(BinaryNode nd,
-          Vector<BinaryNode> leaves)
+  Vector<BinaryNode> findLeaves(BinaryNode nd, Vector<BinaryNode> leaves)
   {
     if (nd == null)
     {
diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 8c3e39a..f965ff4 100755
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -131,7 +131,7 @@ public class TreeCanvas extends Panel
     {
       BinaryNode lf = leaves.elementAt(i);
 
-      if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
+      if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
       {
         has_placeholders = true;
       }
@@ -211,9 +211,10 @@ public class TreeCanvas extends Panel
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && node instanceof SequenceNode && ((SequenceNode) node).isPlaceholder())
-              ? (PLACEHOLDER + node.getName())
-              : node.getName();
+      String name = (markPlaceholders && node instanceof SequenceNode
+              && ((SequenceNode) node).isPlaceholder())
+                      ? (PLACEHOLDER + node.getName())
+                      : node.getName();
       FontMetrics fm = g.getFontMetrics(font);
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = fm.getHeight();
@@ -385,8 +386,8 @@ public class TreeCanvas extends Panel
     }
     else
     {
-      pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width,
-              offx, offy);
+      pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx,
+              offy);
       pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width,
               offx, offy);
     }
diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index f4c8854..6b33fea 100755
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -1436,11 +1436,10 @@ public class Cache
                 if (customProxySet &&
                 // we have a username but no password for the scheme being
                 // requested
-                        (protocol.equalsIgnoreCase("http")
-                                && (httpUser != null
-                                        && httpUser.length() > 0
-                                        && (httpPassword == null
-                                                || httpPassword.length == 0)))
+                (protocol.equalsIgnoreCase("http")
+                        && (httpUser != null && httpUser.length() > 0
+                                && (httpPassword == null
+                                        || httpPassword.length == 0)))
                         || (protocol.equalsIgnoreCase("https")
                                 && (httpsUser != null
                                         && httpsUser.length() > 0
diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java
index 517a6dd..4d3d578 100755
--- a/src/jalview/datamodel/Alignment.java
+++ b/src/jalview/datamodel/Alignment.java
@@ -2050,14 +2050,14 @@ public class Alignment implements AlignmentI, AutoCloseable
   public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa)
   {
     ContactMatrixI cm = cmholder.getContactMatrixFor(_aa);
-    if (cm==null && _aa.groupRef!=null)
+    if (cm == null && _aa.groupRef != null)
     {
       cm = _aa.groupRef.getContactMatrixFor(_aa);
     }
-    if (cm==null && _aa.sequenceRef!=null)
+    if (cm == null && _aa.sequenceRef != null)
     {
       cm = _aa.sequenceRef.getContactMatrixFor(_aa);
-      if (cm==null)
+      if (cm == null)
       {
         // TODO fix up this logic and unify with getContactListFor
         cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa);
@@ -2080,10 +2080,12 @@ public class Alignment implements AlignmentI, AutoCloseable
       if (spos >= _aa.sequenceRef.getStart()
               && spos <= 1 + _aa.sequenceRef.getEnd())
       {
-        cl = _aa.sequenceRef.getContactListFor(_aa, spos-_aa.sequenceRef.getStart());
+        cl = _aa.sequenceRef.getContactListFor(_aa,
+                spos - _aa.sequenceRef.getStart());
         if (cl == null && _aa.sequenceRef.getDatasetSequence() != null)
         {
-          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos-_aa.sequenceRef.getStart());
+          _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa,
+                  spos - _aa.sequenceRef.getStart());
         }
       }
     }
diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java
index 4861dfd..b5987f4 100755
--- a/src/jalview/datamodel/AlignmentAnnotation.java
+++ b/src/jalview/datamodel/AlignmentAnnotation.java
@@ -568,12 +568,12 @@ public class AlignmentAnnotation
                       : annotations[index + offset].displayCharacter == null
                               || annotations[index
                                       + offset].displayCharacter
-                                      .length() == 0
-                                              ? annotations[index
-                                                      + offset].secondaryStructure
-                                              : annotations[index
-                                                      + offset].displayCharacter
-                                                      .charAt(0));
+                                              .length() == 0
+                                                      ? annotations[index
+                                                              + offset].secondaryStructure
+                                                      : annotations[index
+                                                              + offset].displayCharacter
+                                                                      .charAt(0));
     }
 
     @Override
diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java
index 6ee324f..3c2d166 100644
--- a/src/jalview/datamodel/ColumnSelection.java
+++ b/src/jalview/datamodel/ColumnSelection.java
@@ -586,8 +586,8 @@ public class ColumnSelection
           int cpos = ann_row.sequenceRef.findPosition(column) - 1;
           ContactListI clist = ann_row.sequenceRef
                   .getContactListFor(ann_row, cpos);
-          for (int row = column + 8,
-                  rowEnd = clist.getContactHeight(); row < rowEnd; row++)
+          for (int row = column + 8, rowEnd = clist
+                  .getContactHeight(); row < rowEnd; row++)
           {
             if (filterParams
                     .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD
diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java
index 3510ed1..1d7391b 100644
--- a/src/jalview/datamodel/ContactMatrixI.java
+++ b/src/jalview/datamodel/ContactMatrixI.java
@@ -33,41 +33,51 @@ public interface ContactMatrixI
   int getWidth();
 
   int getHeight();
-  
-  default boolean hasGroups() {
+
+  default boolean hasGroups()
+  {
     return false;
   }
-  default BitSet getGroupsFor(int column) {
-    BitSet colbitset  = new BitSet();
+
+  default BitSet getGroupsFor(int column)
+  {
+    BitSet colbitset = new BitSet();
     colbitset.set(column);
     return colbitset;
   }
 
-  default List<BitSet> getGroups() {
+  default List<BitSet> getGroups()
+  {
     return Arrays.asList();
   }
 
-  default boolean hasTree() {
+  default boolean hasTree()
+  {
     return false;
   }
 
   /**
    * Newick representation of clustered matrix
+   * 
    * @return null unless hasTree is true
    */
-  default String getNewick() {
+  default String getNewick()
+  {
     return null;
   }
 
-  default String getTreeMethod() {
+  default String getTreeMethod()
+  {
     return null;
   }
 
-  default boolean hasCutHeight() {
+  default boolean hasCutHeight()
+  {
     return false;
   }
 
-  default double getCutHeight() {
+  default double getCutHeight()
+  {
     return 0;
   }
 
@@ -75,5 +85,8 @@ public interface ContactMatrixI
 
   void setColorForGroup(BitSet bs, Color color);
 
-  default Color getColourForGroup(BitSet bs) { return Color.white;};
+  default Color getColourForGroup(BitSet bs)
+  {
+    return Color.white;
+  };
 }
diff --git a/src/jalview/datamodel/ContactRange.java b/src/jalview/datamodel/ContactRange.java
index 5de8b04..fe66aa5 100644
--- a/src/jalview/datamodel/ContactRange.java
+++ b/src/jalview/datamodel/ContactRange.java
@@ -1,6 +1,5 @@
 package jalview.datamodel;
 
-
 /**
  * bean for max/min positions for a given range
  * 
@@ -31,8 +30,8 @@ public class ContactRange
    * @param maxPos
    * @param max
    */
-  public void update(int from_column, int to_column, int minPos,
-          double min, int maxPos, double max, double mean)
+  public void update(int from_column, int to_column, int minPos, double min,
+          int maxPos, double max, double mean)
   {
     this.from_column = from_column;
     this.to_column = to_column;
diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java
index e37a5b2..a915bb0 100644
--- a/src/jalview/datamodel/SeqDistanceContactMatrix.java
+++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java
@@ -124,40 +124,47 @@ public class SeqDistanceContactMatrix implements ContactMatrixI
   {
     return width;
   }
-  private List<BitSet> groups=null;
+
+  private List<BitSet> groups = null;
+
   @Override
   public void updateGroups(List<BitSet> colGroups)
   {
     groups = colGroups;
   }
+
   @Override
   public boolean hasGroups()
   {
-    return groups!=null;
+    return groups != null;
   }
+
   @Override
   public List<BitSet> getGroups()
   {
     return groups;
-  }  
+  }
 
-  HashMap<BitSet,Color> colorMap = new HashMap<>();
-  @Override 
+  HashMap<BitSet, Color> colorMap = new HashMap<>();
+
+  @Override
   public Color getColourForGroup(BitSet bs)
   {
-    if (bs==null) {
+    if (bs == null)
+    {
       return Color.white;
     }
-    Color groupCol=colorMap.get(bs);
-    if (groupCol==null)
+    Color groupCol = colorMap.get(bs);
+    if (groupCol == null)
     {
       return Color.white;
     }
     return groupCol;
   }
-  @Override 
-  public void setColorForGroup(BitSet bs,Color color)
+
+  @Override
+  public void setColorForGroup(BitSet bs, Color color)
   {
-    colorMap.put(bs,color);
+    colorMap.put(bs, color);
   }
 }
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 52a6066..7462bc8 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -422,13 +422,14 @@ public class AnnotationLabels extends JPanel
         consclipbrd.addActionListener(this);
         pop.add(consclipbrd);
       }
-       if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
+      if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP
               && PAEContactMatrix.PAEMATRIX
                       .equals(aa[selectedRow].getCalcId()))
       {
         final PAEContactMatrix cm = (PAEContactMatrix) av
                 .getContactMatrix(aa[selectedRow]);
-        if (cm!=null && cm.getNewick()!=null && cm.getNewick().length()>0)
+        if (cm != null && cm.getNewick() != null
+                && cm.getNewick().length() > 0)
         {
           item = new JMenuItem("Show Tree for Matrix");
           item.addActionListener(new ActionListener()
@@ -438,7 +439,7 @@ public class AnnotationLabels extends JPanel
             public void actionPerformed(ActionEvent e)
             {
 
-                ap.alignFrame.showContactMapTree(aa[selectedRow],cm);
+              ap.alignFrame.showContactMapTree(aa[selectedRow], cm);
 
             }
           });
@@ -1123,7 +1124,8 @@ public class AnnotationLabels extends JPanel
         }
         olY = y;
         // look ahead to next annotation
-        for (nexAA=i+1; nexAA<aa.length && !aa[nexAA].visible; nexAA++)
+        for (nexAA = i + 1; nexAA < aa.length
+                && !aa[nexAA].visible; nexAA++)
           ;
         y += aa[i].height;
         if (clip)
@@ -1273,7 +1275,8 @@ public class AnnotationLabels extends JPanel
         {
           if (vertBar)
           {
-            g.drawLine(width-3, y + offset-fontHeight, width-3, (int)(y - 1.5*aa[i].height-offset-fontHeight));
+            g.drawLine(width - 3, y + offset - fontHeight, width - 3,
+                    (int) (y - 1.5 * aa[i].height - offset - fontHeight));
             // g.drawLine(20, y + offset, x - 20, y + offset);
 
           }
diff --git a/src/jalview/gui/OverviewCanvas.java b/src/jalview/gui/OverviewCanvas.java
index 99dba3d..0827208 100644
--- a/src/jalview/gui/OverviewCanvas.java
+++ b/src/jalview/gui/OverviewCanvas.java
@@ -95,8 +95,9 @@ public class OverviewCanvas extends JPanel
             OVERVIEW_DEFAULT_GAP);
     Color hiddenCol = Cache.getDefaultColour(Preferences.HIDDEN_COLOUR,
             OVERVIEW_DEFAULT_HIDDEN);
-    Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE : OVERVIEW_DEFAULT_RESIDUE;
-    
+    Color residueCol = useLegacy ? OVERVIEW_DEFAULT_LEGACY_RESIDUE
+            : OVERVIEW_DEFAULT_RESIDUE;
+
     cf = new OverviewResColourFinder(gapCol, residueCol, hiddenCol);
 
     setSize(od.getWidth(), od.getHeight());
diff --git a/src/jalview/gui/QuitHandler.java b/src/jalview/gui/QuitHandler.java
index 9a44306..79723cf 100644
--- a/src/jalview/gui/QuitHandler.java
+++ b/src/jalview/gui/QuitHandler.java
@@ -169,7 +169,8 @@ public class QuitHandler
       qd.showDialogOnTopAsync(
               new StringBuilder(
                       MessageManager.getString("label.quit_jalview"))
-                      .append("\n").append(messageString).toString(),
+                              .append("\n").append(messageString)
+                              .toString(),
               MessageManager.getString("action.quit"),
               JOptionPane.YES_NO_OPTION, JOptionPane.QUESTION_MESSAGE, null,
               new Object[]
diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 29826f0..3a055ae 100755
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -189,7 +189,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
       BinaryNode lf = leaves.elementAt(i);
 
-      if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder())
+      if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder())
       {
         has_placeholders = true;
       }
@@ -285,9 +285,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         g.drawString(nodeLabel, xstart + 2, ypos - 2);
       }
 
-      String name = (markPlaceholders && ((node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder())))
-              ? (PLACEHOLDER + node.getName())
-              : node.getName();
+      String name = (markPlaceholders && ((node instanceof SequenceNode
+              && ((SequenceNode) node).isPlaceholder())))
+                      ? (PLACEHOLDER + node.getName())
+                      : node.getName();
 
       int charWidth = fm.stringWidth(name) + 3;
       int charHeight = font.getSize();
@@ -354,8 +355,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       int ystart = (node.left() == null ? 0
               : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
       int yend = (node.right() == null ? 0
-              : (int) (((BinaryNode) node.right()).ycount * chunk))
-              + offy;
+              : (int) (((BinaryNode) node.right()).ycount * chunk)) + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
       nodeHash.put(node, pos);
@@ -826,14 +826,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     else
     {
       Vector<BinaryNode> leaves = tree.findLeaves(highlightNode);
-      if (tp.isColumnWise()) {
-        markColumnsFor(getAssociatedPanels(), leaves, Color.red);
-      } else {
-      for (int i = 0; i < leaves.size(); i++)
+      if (tp.isColumnWise())
       {
-        SequenceI seq = (SequenceI) leaves.elementAt(i).element();
-        treeSelectionChanged(seq);
+        markColumnsFor(getAssociatedPanels(), leaves, Color.red);
       }
+      else
+      {
+        for (int i = 0; i < leaves.size(); i++)
+        {
+          SequenceI seq = (SequenceI) leaves.elementAt(i).element();
+          treeSelectionChanged(seq);
+        }
       }
       av.sendSelection();
     }
@@ -998,7 +1001,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
   {
     AlignmentPanel[] aps = getAssociatedPanels();
     List<BitSet> colGroups = new ArrayList<>();
-    Map<BitSet,Color> colors=new HashMap();
+    Map<BitSet, Color> colors = new HashMap();
     for (int i = 0; i < groups.size(); i++)
     {
       Color col = new Color((int) (Math.random() * 255),
@@ -1006,10 +1009,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       setColor(groups.get(i), col.brighter());
 
       Vector<BinaryNode> l = tree.findLeaves(groups.get(i));
-      if (!tp.isColumnWise()) {
+      if (!tp.isColumnWise())
+      {
         createSeqGroupFor(aps, l, col);
-      } else {
-        BitSet gp=createColumnGroupFor(l,col);
+      }
+      else
+      {
+        BitSet gp = createColumnGroupFor(l, col);
 
         colGroups.add(gp);
         colors.put(gp, col);
@@ -1018,12 +1024,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     if (tp.isColumnWise())
     {
       AlignmentAnnotation aa = tp.getAssocAnnotation();
-      if (aa!=null) {
+      if (aa != null)
+      {
         ContactMatrixI cm = av.getContactMatrix(aa);
-        if (cm!=null)
+        if (cm != null)
         {
           cm.updateGroups(colGroups);
-          for (BitSet gp:colors.keySet())
+          for (BitSet gp : colors.keySet())
           {
             cm.setColorForGroup(gp, colors.get(gp));
           }
@@ -1058,46 +1065,50 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     {
       return false;
     }
-    if (av==null||av.getAlignment()==null)
+    if (av == null || av.getAlignment() == null)
     {
       // alignment is closed
       return false;
     }
     ColumnSelection cs = av.getColumnSelection();
-    
+
     HiddenColumns hc = av.getAlignment().getHiddenColumns();
     int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
             : colm;
 
     if (!av.hasHiddenColumns())
     {
-      return cs.contains(offp-1);
+      return cs.contains(offp - 1);
     }
-    if (hc.isVisible(offp-1))
+    if (hc.isVisible(offp - 1))
     {
-      return cs.contains(offp-1);
-//      return cs.contains(hc.absoluteToVisibleColumn(offp));
+      return cs.contains(offp - 1);
+      // return cs.contains(hc.absoluteToVisibleColumn(offp));
     }
     return false;
   }
-  
-  private BitSet createColumnGroupFor(Vector<BinaryNode> l,
-          Color col)
+
+  private BitSet createColumnGroupFor(Vector<BinaryNode> l, Color col)
   {
-    BitSet gp=new BitSet();
-    for (BinaryNode bn:l)
+    BitSet gp = new BitSet();
+    for (BinaryNode bn : l)
     {
-      int colm=-1;
-      if (bn.element()!=null && bn.element()instanceof Integer)
-      { colm = (Integer)bn.element();
-      } else {
-        // parse out from nodename
-      try {
-        colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
-      } catch (Exception e)
+      int colm = -1;
+      if (bn.element() != null && bn.element() instanceof Integer)
       {
-        continue;
+        colm = (Integer) bn.element();
       }
+      else
+      {
+        // parse out from nodename
+        try
+        {
+          colm = Integer.parseInt(
+                  bn.getName().substring(bn.getName().indexOf("c") + 1));
+        } catch (Exception e)
+        {
+          continue;
+        }
       }
       gp.set(colm);
     }
@@ -1108,17 +1119,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
           Color col)
   {
     SequenceI rseq = tp.assocAnnotation.sequenceRef;
-    if (av==null||av.getAlignment()==null)
+    if (av == null || av.getAlignment() == null)
     {
       // alignment is closed
       return;
     }
 
-    for (BinaryNode bn:l)
+    for (BinaryNode bn : l)
     {
-      int colm=-1;
-      try {
-        colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1));
+      int colm = -1;
+      try
+      {
+        colm = Integer.parseInt(
+                bn.getName().substring(bn.getName().indexOf("c") + 1));
       } catch (Exception e)
       {
         continue;
@@ -1126,19 +1139,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       ColumnSelection cs = av.getColumnSelection();
       HiddenColumns hc = av.getAlignment().getHiddenColumns();
       {
-        int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()+colm) : colm;
-        
-        if (!av.hasHiddenColumns() || hc.isVisible(offp-1))
-        { 
-          if (cs.contains(offp-1))
+        int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm)
+                : colm;
+
+        if (!av.hasHiddenColumns() || hc.isVisible(offp - 1))
+        {
+          if (cs.contains(offp - 1))
           {
-            cs.removeElement(offp-1);
-          } else {
-            cs.addElement(offp-1);
+            cs.removeElement(offp - 1);
+          }
+          else
+          {
+            cs.addElement(offp - 1);
           }
         }
       }
-    } 
+    }
   }
 
   public void createSeqGroupFor(AlignmentPanel[] aps, Vector<BinaryNode> l,
diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 30e4305..0e1fd42 100755
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -136,20 +136,24 @@ public class TreePanel extends GTreePanel
           AlignmentAnnotation aa, String title)
   {
     super();
-    columnWise=true;
+    columnWise = true;
     assocAnnotation = aa;
     this.setFrameIcon(null);
     this.treeTitle = title;
     initTreePanel(alignPanel, null, null, fin, null);
   }
-  
-  boolean columnWise=false;
-  AlignmentAnnotation assocAnnotation=null;
+
+  boolean columnWise = false;
+
+  AlignmentAnnotation assocAnnotation = null;
+
   public boolean isColumnWise()
   {
     return columnWise;
   }
-  public AlignmentAnnotation getAssocAnnotation() {
+
+  public AlignmentAnnotation getAssocAnnotation()
+  {
     return assocAnnotation;
   }
 
diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java
index 4aac062..7eeee9a 100644
--- a/src/jalview/gui/WebserviceInfo.java
+++ b/src/jalview/gui/WebserviceInfo.java
@@ -626,8 +626,8 @@ public class WebserviceInfo extends GWebserviceInfo
               true, false);
       ((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport()
               .getComponent(0))
-              .setText(ensureHtmlTagged(
-                      txt + getHtmlFragment(text, false, true)));
+                      .setText(ensureHtmlTagged(
+                              txt + getHtmlFragment(text, false, true)));
     }
     else
     {
diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java
index bec584f..c67c307 100644
--- a/src/jalview/io/BackupFiles.java
+++ b/src/jalview/io/BackupFiles.java
@@ -234,7 +234,8 @@ public class BackupFiles
     classInit();
     if (file.getParentFile() == null)
     {
-      // filename probably in pwd represented with no parent -- fix it before it's a problem
+      // filename probably in pwd represented with no parent -- fix it before
+      // it's a problem
       file = file.getAbsoluteFile();
     }
     this.file = file;
diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java
index d3a6ba9..8d3283d 100755
--- a/src/jalview/io/FileParse.java
+++ b/src/jalview/io/FileParse.java
@@ -343,8 +343,8 @@ public class FileParse
     }
     String encoding = _conn.getContentEncoding();
     String contentType = _conn.getContentType();
-    boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType) || contentType.endsWith("gzip")
-            || "gzip".equals(encoding);
+    boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType)
+            || contentType.endsWith("gzip") || "gzip".equals(encoding);
     Exception e = null;
     InputStream inputStream = _conn.getInputStream();
     if (isgzipped)
diff --git a/src/jalview/io/PContactPredictionFile.java b/src/jalview/io/PContactPredictionFile.java
index 3df9804..164d7cc 100644
--- a/src/jalview/io/PContactPredictionFile.java
+++ b/src/jalview/io/PContactPredictionFile.java
@@ -47,8 +47,8 @@ public class PContactPredictionFile extends AlignFile
 {
   protected static final String CONTACT_PREDICTION = "CONTACT_PREDICTION";
 
-  public PContactPredictionFile(String inFile, DataSourceType fileSourceType)
-          throws IOException
+  public PContactPredictionFile(String inFile,
+          DataSourceType fileSourceType) throws IOException
   {
     super(inFile, fileSourceType);
 
@@ -109,19 +109,23 @@ public class PContactPredictionFile extends AlignFile
 
         if (cm == null)
         {
-          cm = new ContactMatrix(true) {
+          cm = new ContactMatrix(true)
+          {
             @Override
             public String getType()
             {
               return CONTACT_PREDICTION;
             }
+
             @Override
             public int getHeight()
             {
               // TODO Auto-generated method stub
-              // return maximum contact height 
+              // return maximum contact height
               return 0;
-            }@Override
+            }
+
+            @Override
             public int getWidth()
             {
               // TODO Auto-generated method stub
@@ -140,15 +144,15 @@ public class PContactPredictionFile extends AlignFile
         } catch (Exception x)
         {
           error = true;
-          errormessage = "Couldn't process line: "
-                  + x.getLocalizedMessage() + "\n" + line;
+          errormessage = "Couldn't process line: " + x.getLocalizedMessage()
+                  + "\n" + line;
           return;
         }
         cm.addContact(left, right, (float) strength);
       }
     }
     // TODO COMPLETE
-    throw(new Error("Not Implemented yet."));
+    throw (new Error("Not Implemented yet."));
   }
 
   @Override
diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java
index eeadcbf..28f062f 100644
--- a/src/jalview/io/StockholmFile.java
+++ b/src/jalview/io/StockholmFile.java
@@ -218,8 +218,9 @@ public class StockholmFile extends AlignFile
     r = new Regex("# STOCKHOLM ([\\d\\.]+)");
     if (!r.search(nextLine()))
     {
-      throw new IOException(MessageManager
-			    .getString("exception.stockholm_invalid_format") +" ("+r+")");
+      throw new IOException(
+              MessageManager.getString("exception.stockholm_invalid_format")
+                      + " (" + r + ")");
     }
     else
     {
@@ -1052,11 +1053,11 @@ public class StockholmFile extends AlignFile
 
     while (i < slen && (seq = s[i]) != null)
     {
-      if (seq.getDescription()!=null)
+      if (seq.getDescription() != null)
       {
         // out.append("#=GR ");
-        out.append(new Format("%-" + maxid + "s").form(
-                "#=GS " + printId(seq, jvSuffix) + " DE " + seq.getDescription()));
+        out.append(new Format("%-" + maxid + "s").form("#=GS "
+                + printId(seq, jvSuffix) + " DE " + seq.getDescription()));
         out.append(newline);
       }
 
diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index c0d1774..1ac7bab 100644
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -394,8 +394,7 @@ public class Tree extends DatastoreItem
       {
         if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
         {
-          Object assocseq = ((BinaryNode) tnode)
-                  .element();
+          Object assocseq = ((BinaryNode) tnode).element();
           if (assocseq instanceof SequenceI)
           {
             Vobject vobj = this.getjv2vObj(assocseq);
diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index ddf2afd..913dffe 100644
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -1523,7 +1523,7 @@ public class Jalview2XML
                 ov.getCanvas().getResidueColour().getRGB());
         overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
         view.setOverview(overview);
-      } 
+      }
       if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
       {
         view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
@@ -2304,22 +2304,24 @@ public class Jalview2XML
           line.setColour(annotation.getThreshold().colour.getRGB());
           an.setThresholdLine(line);
         }
-        if (annotation.graph==AlignmentAnnotation.CONTACT_MAP)
+        if (annotation.graph == AlignmentAnnotation.CONTACT_MAP)
         {
-          if (annotation.sequenceRef.getContactMaps()!=null)
+          if (annotation.sequenceRef.getContactMaps() != null)
           {
-            ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation);
-            if (cm!=null)
+            ContactMatrixI cm = annotation.sequenceRef
+                    .getContactMatrixFor(annotation);
+            if (cm != null)
             {
               MatrixType xmlmat = new MatrixType();
               xmlmat.setType(cm.getType());
               xmlmat.setRows(BigInteger.valueOf(cm.getWidth()));
               xmlmat.setCols(BigInteger.valueOf(cm.getHeight()));
-              // consider using an opaque to/from -> allow instance to control its representation ?
+              // 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())
+                for (BitSet gp : cm.getGroups())
                 {
                   BigInteger val = new BigInteger(gp.toByteArray());
                   xmlmat.getGroups().add(val.toString());
@@ -2335,7 +2337,7 @@ public class Jalview2XML
               {
                 xmlmat.setCutHeight(cm.getCutHeight());
               }
-              
+
               // set/get properties
               an.getContactmatrix().add(xmlmat);
             }
@@ -3948,7 +3950,8 @@ public class Jalview2XML
         jaa.setCalcId(annotation.getCalcId());
         if (annotation.getProperty().size() > 0)
         {
-          for (jalview.xml.binding.jalview.Property prop : annotation.getProperty())
+          for (jalview.xml.binding.jalview.Property prop : annotation
+                  .getProperty())
           {
             jaa.setProperty(prop.getName(), prop.getValue());
           }
@@ -3975,29 +3978,37 @@ public class Jalview2XML
 
                   PAEContactMatrix newpae = new PAEContactMatrix(
                           jaa.sequenceRef, elements);
-                  List<BitSet> newgroups=new ArrayList<BitSet>();
-                  if (xmlmat.getGroups().size()>0)
+                  List<BitSet> newgroups = new ArrayList<BitSet>();
+                  if (xmlmat.getGroups().size() > 0)
                   {
-                    for (String sgroup:xmlmat.getGroups())
+                    for (String sgroup : xmlmat.getGroups())
                     {
-                      try {
+                      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);
+                        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)
+                  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;
+                  double thresh = xmlmat.getCutHeight() != null
+                          ? xmlmat.getCutHeight()
+                          : 0;
                   newpae.restoreGroups(newgroups, treeMethod, nwk, thresh);
                   jaa.sequenceRef.addContactListFor(jaa, newpae);
                 }
@@ -4246,8 +4257,8 @@ public class Jalview2XML
    */
   protected void loadOverview(Viewport view, String version, AlignFrame af)
   {
-    if (!isVersionStringLaterThan("2.11.3",
-            version) && view.getOverview()==null)
+    if (!isVersionStringLaterThan("2.11.3", version)
+            && view.getOverview() == null)
     {
       return;
     }
@@ -4394,8 +4405,8 @@ public class Jalview2XML
         {
           if (tree.isColumnWise())
           {
-            AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds.get(tree
-                    .getColumnReference());
+            AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds
+                    .get(tree.getColumnReference());
             if (aa == null)
             {
               Console.warn(
@@ -4953,10 +4964,11 @@ public class Jalview2XML
     viewport.setIncrement(safeInt(view.getConsThreshold()));
     viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
     viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
-    viewport.setFont(new Font(view.getFontName(),
-            safeInt(view.getFontStyle()), safeInt(view.getFontSize())),
-            (view.getCharWidth()!=null) ? false : true);
-    if (view.getCharWidth()!=null)
+    viewport.setFont(
+            new Font(view.getFontName(), safeInt(view.getFontStyle()),
+                    safeInt(view.getFontSize())),
+            (view.getCharWidth() != null) ? false : true);
+    if (view.getCharWidth() != null)
     {
       viewport.setCharWidth(view.getCharWidth());
       viewport.setCharHeight(view.getCharHeight());
@@ -5283,7 +5295,7 @@ public class Jalview2XML
               + annotationId);
       return null;
     }
-    // belt-and-braces create a threshold line if the 
+    // belt-and-braces create a threshold line if the
     // colourscheme needs one but the matchedAnnotation doesn't have one
     if (safeInt(viewAnnColour.getAboveThreshold()) != 0
             && matchedAnnotation.getThreshold() == null)
diff --git a/src/jalview/renderer/AnnotationRendererFactory.java b/src/jalview/renderer/AnnotationRendererFactory.java
index db2eb7a..85d22c9 100644
--- a/src/jalview/renderer/AnnotationRendererFactory.java
+++ b/src/jalview/renderer/AnnotationRendererFactory.java
@@ -7,8 +7,7 @@ import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 
 import java.util.IdentityHashMap;
 
-public class AnnotationRendererFactory implements
-        AnnotationRendererFactoryI
+public class AnnotationRendererFactory implements AnnotationRendererFactoryI
 {
 
   private static AnnotationRendererFactoryI factory = null;
@@ -40,8 +39,9 @@ public class AnnotationRendererFactory implements
       {
         return ContactMapRenderer.newPAERenderer();
       }
-      // TODO add potential for configuring renderer directly from the annotation row and/or viewmodel
-      
+      // TODO add potential for configuring renderer directly from the
+      // annotation row and/or viewmodel
+
     }
     return null;
   }
diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java
index e54f471..cbc4af9 100644
--- a/src/jalview/renderer/ContactMapRenderer.java
+++ b/src/jalview/renderer/ContactMapRenderer.java
@@ -25,6 +25,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 {
   /**
    * bean holding colours for shading
+   * 
    * @author jprocter
    *
    */
@@ -34,10 +35,12 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
      * shown when no data available from map
      */
     Color no_data;
+
     /**
      * shown for region not currently visible - should normally not see this
      */
     Color hidden;
+
     /**
      * linear shading scheme min/max
      */
@@ -66,6 +69,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
   /**
    * build an EBI-AlphaFold style renderer of PAE matrices
+   * 
    * @return
    */
   public static ContactMapRenderer newPAERenderer()
@@ -146,7 +150,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         x++;
         continue;
       }
-      Color gpcol = (cm==null) ? Color.white: cm.getColourForGroup(cm.getGroupsFor(column));
+      Color gpcol = (cm == null) ? Color.white
+              : cm.getColourForGroup(cm.getGroupsFor(column));
       // feature still in development - highlight or omit regions hidden in
       // the alignment - currently marks them as red rows
       boolean maskHiddenCols = false;
@@ -216,14 +221,17 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
         {
           col = shade.hidden;
         }
-        if (gpcol!=null && gpcol!=Color.white) {
+        if (gpcol != null && gpcol != Color.white)
+        {
           // todo - could overlay group as a transparent rectangle ?
-          col = new Color((int)(((float)(col.getRed()+gpcol.getRed()))/2f),
-                  (int)(((float)(col.getGreen()+gpcol.getGreen()))/2f),
-                  (int)(((float)(col.getBlue()+gpcol.getBlue()))/2f));
+          col = new Color(
+                  (int) (((float) (col.getRed() + gpcol.getRed())) / 2f),
+                  (int) (((float) (col.getGreen() + gpcol.getGreen()))
+                          / 2f),
+                  (int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f));
         }
         g.setColor(col);
-        
+
         if (cgeom.pixels_step > 1)
         {
           g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step);
@@ -240,8 +248,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI
 
   Color shadeFor(float min, float max, float value)
   {
-    return jalview.util.ColorUtils.getGraduatedColour(value, 0, shade.minColor,
-            max, shade.maxColor);
+    return jalview.util.ColorUtils.getGraduatedColour(value, 0,
+            shade.minColor, max, shade.maxColor);
   }
 
   public Color getColorForRange(float min, float max, ContactListI cl,
diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java
index ef4d04b..4cbb1ba 100644
--- a/src/jalview/renderer/OverviewResColourFinder.java
+++ b/src/jalview/renderer/OverviewResColourFinder.java
@@ -48,6 +48,7 @@ public class OverviewResColourFinder extends ResidueColourFinder
 
   /**
    * Constructor without colour settings (used by applet)
+   * 
    * @deprecated
    */
   @Deprecated
diff --git a/src/jalview/renderer/api/AnnotationRowRendererI.java b/src/jalview/renderer/api/AnnotationRowRendererI.java
index bedbad5..0907228 100644
--- a/src/jalview/renderer/api/AnnotationRowRendererI.java
+++ b/src/jalview/renderer/api/AnnotationRowRendererI.java
@@ -13,9 +13,8 @@ public interface AnnotationRowRendererI
 
   void renderRow(Graphics g, int charWidth, int charHeight,
           boolean hasHiddenColumns, AlignViewportI av,
-          HiddenColumns hiddenColumns,
-          ColumnSelection columnSelection, AlignmentAnnotation row,
-          Annotation[] row_annotations, int startRes, int endRes,
-          float graphMin, float graphMax, int y);
+          HiddenColumns hiddenColumns, ColumnSelection columnSelection,
+          AlignmentAnnotation row, Annotation[] row_annotations,
+          int startRes, int endRes, float graphMin, float graphMax, int y);
 
 }
diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
index e66b7d5..2d16fcd 100644
--- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java
+++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java
@@ -543,7 +543,7 @@ public class FeatureRenderer extends FeatureRendererModel
        */
       List<SequenceFeature> overlaps = seq.findFeatures(column, column,
               type);
-      for (int i = overlaps.size() - 1 ; i >= 0 ; i--)
+      for (int i = overlaps.size() - 1; i >= 0; i--)
       {
         SequenceFeature sequenceFeature = overlaps.get(i);
         if (!featureGroupNotShown(sequenceFeature))
diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java
index 36b0851..a8c93cf 100644
--- a/src/jalview/viewmodel/AlignmentViewport.java
+++ b/src/jalview/viewmodel/AlignmentViewport.java
@@ -2956,7 +2956,6 @@ public abstract class AlignmentViewport
     return alignment.getContactMatrixFor(alignmentAnnotation);
   }
 
-
   /**
    * get the consensus sequence as displayed under the PID consensus annotation
    * row.
diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java
index 0479a34..43689d3 100644
--- a/src/jalview/xml/binding/embl/EntrySetType.java
+++ b/src/jalview/xml/binding/embl/EntrySetType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:45 PM GMT 
 //
 
-
 package jalview.xml.binding.embl;
 
 import java.util.ArrayList;
@@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for EntrySetType complex type.
+ * <p>
+ * Java class for EntrySetType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="EntrySetType">
@@ -36,41 +37,42 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntrySetType", propOrder = {
-    "entry"
-})
-public class EntrySetType {
+@XmlType(name = "EntrySetType", propOrder = { "entry" })
+public class EntrySetType
+{
 
-    @XmlElement(required = true)
-    protected List<EntryType> entry;
+  @XmlElement(required = true)
+  protected List<EntryType> entry;
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the entry property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEntry().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EntryType }
-     * 
-     * 
-     */
-    public List<EntryType> getEntry() {
-        if (entry == null) {
-            entry = new ArrayList<EntryType>();
-        }
-        return this.entry;
+  /**
+   * Gets the value of the entry property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the entry property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEntry().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link EntryType }
+   * 
+   * 
+   */
+  public List<EntryType> getEntry()
+  {
+    if (entry == null)
+    {
+      entry = new ArrayList<EntryType>();
     }
+    return this.entry;
+  }
 
 }
diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java
index 6336ef1..bc3e556 100644
--- a/src/jalview/xml/binding/embl/EntryType.java
+++ b/src/jalview/xml/binding/embl/EntryType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:45 PM GMT 
 //
 
-
 package jalview.xml.binding.embl;
 
 import java.math.BigInteger;
@@ -20,11 +19,13 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.datatype.XMLGregorianCalendar;
 
-
 /**
- * <p>Java class for EntryType complex type.
+ * <p>
+ * Java class for EntryType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="EntryType">
@@ -225,669 +226,1666 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntryType", propOrder = {
-    "secondaryAccession",
-    "projectAccession",
-    "description",
-    "comment",
-    "keyword",
-    "reference",
-    "xref",
-    "feature",
-    "assembly",
-    "contig",
-    "sequence"
-})
-public class EntryType {
-
-    protected List<String> secondaryAccession;
-    protected List<String> projectAccession;
+@XmlType(
+  name = "EntryType",
+  propOrder =
+  { "secondaryAccession", "projectAccession", "description", "comment",
+      "keyword", "reference", "xref", "feature", "assembly", "contig",
+      "sequence" })
+public class EntryType
+{
+
+  protected List<String> secondaryAccession;
+
+  protected List<String> projectAccession;
+
+  @XmlElement(required = true)
+  protected String description;
+
+  protected String comment;
+
+  protected List<String> keyword;
+
+  protected List<EntryType.Reference> reference;
+
+  protected List<XrefType> xref;
+
+  protected List<EntryType.Feature> feature;
+
+  protected EntryType.Assembly assembly;
+
+  protected EntryType.Contig contig;
+
+  protected String sequence;
+
+  @XmlAttribute(name = "accession", required = true)
+  protected String accession;
+
+  @XmlAttribute(name = "version", required = true)
+  protected BigInteger version;
+
+  @XmlAttribute(name = "entryVersion")
+  protected BigInteger entryVersion;
+
+  @XmlAttribute(name = "dataClass", required = true)
+  protected String dataClass;
+
+  @XmlAttribute(name = "taxonomicDivision", required = true)
+  protected String taxonomicDivision;
+
+  @XmlAttribute(name = "moleculeType", required = true)
+  protected String moleculeType;
+
+  @XmlAttribute(name = "sequenceLength", required = true)
+  protected BigInteger sequenceLength;
+
+  @XmlAttribute(name = "topology", required = true)
+  protected String topology;
+
+  @XmlAttribute(name = "firstPublic")
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar firstPublic;
+
+  @XmlAttribute(name = "firstPublicRelease")
+  protected BigInteger firstPublicRelease;
+
+  @XmlAttribute(name = "lastUpdated")
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar lastUpdated;
+
+  @XmlAttribute(name = "lastUpdatedRelease")
+  protected BigInteger lastUpdatedRelease;
+
+  /**
+   * Gets the value of the secondaryAccession property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the secondaryAccession property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getSecondaryAccession().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getSecondaryAccession()
+  {
+    if (secondaryAccession == null)
+    {
+      secondaryAccession = new ArrayList<String>();
+    }
+    return this.secondaryAccession;
+  }
+
+  /**
+   * Gets the value of the projectAccession property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the projectAccession property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getProjectAccession().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getProjectAccession()
+  {
+    if (projectAccession == null)
+    {
+      projectAccession = new ArrayList<String>();
+    }
+    return this.projectAccession;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the comment property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getComment()
+  {
+    return comment;
+  }
+
+  /**
+   * Sets the value of the comment property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setComment(String value)
+  {
+    this.comment = value;
+  }
+
+  /**
+   * Gets the value of the keyword property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the keyword property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getKeyword().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getKeyword()
+  {
+    if (keyword == null)
+    {
+      keyword = new ArrayList<String>();
+    }
+    return this.keyword;
+  }
+
+  /**
+   * Gets the value of the reference property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the reference property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getReference().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EntryType.Reference }
+   * 
+   * 
+   */
+  public List<EntryType.Reference> getReference()
+  {
+    if (reference == null)
+    {
+      reference = new ArrayList<EntryType.Reference>();
+    }
+    return this.reference;
+  }
+
+  /**
+   * Gets the value of the xref property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the xref property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getXref().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link XrefType }
+   * 
+   * 
+   */
+  public List<XrefType> getXref()
+  {
+    if (xref == null)
+    {
+      xref = new ArrayList<XrefType>();
+    }
+    return this.xref;
+  }
+
+  /**
+   * Gets the value of the feature property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the feature property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getFeature().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EntryType.Feature }
+   * 
+   * 
+   */
+  public List<EntryType.Feature> getFeature()
+  {
+    if (feature == null)
+    {
+      feature = new ArrayList<EntryType.Feature>();
+    }
+    return this.feature;
+  }
+
+  /**
+   * Gets the value of the assembly property.
+   * 
+   * @return possible object is {@link EntryType.Assembly }
+   * 
+   */
+  public EntryType.Assembly getAssembly()
+  {
+    return assembly;
+  }
+
+  /**
+   * Sets the value of the assembly property.
+   * 
+   * @param value
+   *          allowed object is {@link EntryType.Assembly }
+   * 
+   */
+  public void setAssembly(EntryType.Assembly value)
+  {
+    this.assembly = value;
+  }
+
+  /**
+   * Gets the value of the contig property.
+   * 
+   * @return possible object is {@link EntryType.Contig }
+   * 
+   */
+  public EntryType.Contig getContig()
+  {
+    return contig;
+  }
+
+  /**
+   * Sets the value of the contig property.
+   * 
+   * @param value
+   *          allowed object is {@link EntryType.Contig }
+   * 
+   */
+  public void setContig(EntryType.Contig value)
+  {
+    this.contig = value;
+  }
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSequence(String value)
+  {
+    this.sequence = value;
+  }
+
+  /**
+   * Gets the value of the accession property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getAccession()
+  {
+    return accession;
+  }
+
+  /**
+   * Sets the value of the accession property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setAccession(String value)
+  {
+    this.accession = value;
+  }
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setVersion(BigInteger value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the entryVersion property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getEntryVersion()
+  {
+    return entryVersion;
+  }
+
+  /**
+   * Sets the value of the entryVersion property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setEntryVersion(BigInteger value)
+  {
+    this.entryVersion = value;
+  }
+
+  /**
+   * Gets the value of the dataClass property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDataClass()
+  {
+    return dataClass;
+  }
+
+  /**
+   * Sets the value of the dataClass property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDataClass(String value)
+  {
+    this.dataClass = value;
+  }
+
+  /**
+   * Gets the value of the taxonomicDivision property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getTaxonomicDivision()
+  {
+    return taxonomicDivision;
+  }
+
+  /**
+   * Sets the value of the taxonomicDivision property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setTaxonomicDivision(String value)
+  {
+    this.taxonomicDivision = value;
+  }
+
+  /**
+   * Gets the value of the moleculeType property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getMoleculeType()
+  {
+    return moleculeType;
+  }
+
+  /**
+   * Sets the value of the moleculeType property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setMoleculeType(String value)
+  {
+    this.moleculeType = value;
+  }
+
+  /**
+   * Gets the value of the sequenceLength property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getSequenceLength()
+  {
+    return sequenceLength;
+  }
+
+  /**
+   * Sets the value of the sequenceLength property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setSequenceLength(BigInteger value)
+  {
+    this.sequenceLength = value;
+  }
+
+  /**
+   * Gets the value of the topology property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getTopology()
+  {
+    return topology;
+  }
+
+  /**
+   * Sets the value of the topology property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setTopology(String value)
+  {
+    this.topology = value;
+  }
+
+  /**
+   * Gets the value of the firstPublic property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getFirstPublic()
+  {
+    return firstPublic;
+  }
+
+  /**
+   * Sets the value of the firstPublic property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setFirstPublic(XMLGregorianCalendar value)
+  {
+    this.firstPublic = value;
+  }
+
+  /**
+   * Gets the value of the firstPublicRelease property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getFirstPublicRelease()
+  {
+    return firstPublicRelease;
+  }
+
+  /**
+   * Sets the value of the firstPublicRelease property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setFirstPublicRelease(BigInteger value)
+  {
+    this.firstPublicRelease = value;
+  }
+
+  /**
+   * Gets the value of the lastUpdated property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getLastUpdated()
+  {
+    return lastUpdated;
+  }
+
+  /**
+   * Sets the value of the lastUpdated property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setLastUpdated(XMLGregorianCalendar value)
+  {
+    this.lastUpdated = value;
+  }
+
+  /**
+   * Gets the value of the lastUpdatedRelease property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getLastUpdatedRelease()
+  {
+    return lastUpdatedRelease;
+  }
+
+  /**
+   * Sets the value of the lastUpdatedRelease property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setLastUpdatedRelease(BigInteger value)
+  {
+    this.lastUpdatedRelease = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="range" maxOccurs="unbounded">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "range" })
+  public static class Assembly
+  {
+
     @XmlElement(required = true)
-    protected String description;
-    protected String comment;
-    protected List<String> keyword;
-    protected List<EntryType.Reference> reference;
-    protected List<XrefType> xref;
-    protected List<EntryType.Feature> feature;
-    protected EntryType.Assembly assembly;
-    protected EntryType.Contig contig;
-    protected String sequence;
-    @XmlAttribute(name = "accession", required = true)
-    protected String accession;
-    @XmlAttribute(name = "version", required = true)
-    protected BigInteger version;
-    @XmlAttribute(name = "entryVersion")
-    protected BigInteger entryVersion;
-    @XmlAttribute(name = "dataClass", required = true)
-    protected String dataClass;
-    @XmlAttribute(name = "taxonomicDivision", required = true)
-    protected String taxonomicDivision;
-    @XmlAttribute(name = "moleculeType", required = true)
-    protected String moleculeType;
-    @XmlAttribute(name = "sequenceLength", required = true)
-    protected BigInteger sequenceLength;
-    @XmlAttribute(name = "topology", required = true)
-    protected String topology;
-    @XmlAttribute(name = "firstPublic")
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar firstPublic;
-    @XmlAttribute(name = "firstPublicRelease")
-    protected BigInteger firstPublicRelease;
-    @XmlAttribute(name = "lastUpdated")
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar lastUpdated;
-    @XmlAttribute(name = "lastUpdatedRelease")
-    protected BigInteger lastUpdatedRelease;
+    protected List<EntryType.Assembly.Range> range;
 
     /**
-     * Gets the value of the secondaryAccession property.
+     * Gets the value of the range property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the secondaryAccession 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
+     * <CODE>set</CODE> method for the range property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getSecondaryAccession().add(newItem);
+     * getRange().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link String }
+     * {@link EntryType.Assembly.Range }
      * 
      * 
      */
-    public List<String> getSecondaryAccession() {
-        if (secondaryAccession == null) {
-            secondaryAccession = new ArrayList<String>();
-        }
-        return this.secondaryAccession;
+    public List<EntryType.Assembly.Range> getRange()
+    {
+      if (range == null)
+      {
+        range = new ArrayList<EntryType.Assembly.Range>();
+      }
+      return this.range;
     }
 
     /**
-     * Gets the value of the projectAccession property.
-     * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
+     * Java class for anonymous complex type.
      * 
      * <p>
-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * <pre>
-     *    getProjectAccession().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
      */
-    public List<String> getProjectAccession() {
-        if (projectAccession == null) {
-            projectAccession = new ArrayList<String>();
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Range
+    {
+
+      @XmlAttribute(name = "begin", required = true)
+      protected BigInteger begin;
+
+      @XmlAttribute(name = "end", required = true)
+      protected BigInteger end;
+
+      @XmlAttribute(name = "primaryBegin")
+      protected BigInteger primaryBegin;
+
+      @XmlAttribute(name = "primaryEnd")
+      protected BigInteger primaryEnd;
+
+      @XmlAttribute(name = "accession", required = true)
+      protected String accession;
+
+      @XmlAttribute(name = "version", required = true)
+      protected BigInteger version;
+
+      @XmlAttribute(name = "complement")
+      protected Boolean complement;
+
+      /**
+       * Gets the value of the begin property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getBegin()
+      {
+        return begin;
+      }
+
+      /**
+       * Sets the value of the begin property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setBegin(BigInteger value)
+      {
+        this.begin = value;
+      }
+
+      /**
+       * Gets the value of the end property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getEnd()
+      {
+        return end;
+      }
+
+      /**
+       * Sets the value of the end property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setEnd(BigInteger value)
+      {
+        this.end = value;
+      }
+
+      /**
+       * Gets the value of the primaryBegin property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getPrimaryBegin()
+      {
+        return primaryBegin;
+      }
+
+      /**
+       * Sets the value of the primaryBegin property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setPrimaryBegin(BigInteger value)
+      {
+        this.primaryBegin = value;
+      }
+
+      /**
+       * Gets the value of the primaryEnd property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getPrimaryEnd()
+      {
+        return primaryEnd;
+      }
+
+      /**
+       * Sets the value of the primaryEnd property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setPrimaryEnd(BigInteger value)
+      {
+        this.primaryEnd = value;
+      }
+
+      /**
+       * Gets the value of the accession property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getAccession()
+      {
+        return accession;
+      }
+
+      /**
+       * Sets the value of the accession property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setAccession(String value)
+      {
+        this.accession = value;
+      }
+
+      /**
+       * Gets the value of the version property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getVersion()
+      {
+        return version;
+      }
+
+      /**
+       * Sets the value of the version property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setVersion(BigInteger value)
+      {
+        this.version = value;
+      }
+
+      /**
+       * Gets the value of the complement property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public boolean isComplement()
+      {
+        if (complement == null)
+        {
+          return false;
         }
-        return this.projectAccession;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
+        else
+        {
+          return complement;
+        }
+      }
+
+      /**
+       * Sets the value of the complement property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setComplement(Boolean value)
+      {
+        this.complement = value;
+      }
 
-    /**
-     * Gets the value of the comment property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getComment() {
-        return comment;
     }
 
-    /**
-     * Sets the value of the comment property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setComment(String value) {
-        this.comment = value;
-    }
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;choice maxOccurs="unbounded" minOccurs="0">
+   *           &lt;element name="range">
+   *             &lt;complexType>
+   *               &lt;complexContent>
+   *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                   &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 &lt;/restriction>
+   *               &lt;/complexContent>
+   *             &lt;/complexType>
+   *           &lt;/element>
+   *           &lt;element name="gap">
+   *             &lt;complexType>
+   *               &lt;complexContent>
+   *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 &lt;/restriction>
+   *               &lt;/complexContent>
+   *             &lt;/complexType>
+   *           &lt;/element>
+   *         &lt;/choice>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "rangeOrGap" })
+  public static class Contig
+  {
+
+    @XmlElements({
+        @XmlElement(name = "range", type = EntryType.Contig.Range.class),
+        @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) })
+    protected List<Object> rangeOrGap;
 
     /**
-     * Gets the value of the keyword property.
+     * Gets the value of the rangeOrGap property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the keyword 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
+     * <CODE>set</CODE> method for the rangeOrGap property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
-     * <pre>
-     *    getKeyword().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getKeyword() {
-        if (keyword == null) {
-            keyword = new ArrayList<String>();
-        }
-        return this.keyword;
-    }
-
-    /**
-     * Gets the value of the reference property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the reference property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
      * <pre>
-     *    getReference().add(newItem);
+     * getRangeOrGap().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Reference }
+     * {@link EntryType.Contig.Range } {@link EntryType.Contig.Gap }
      * 
      * 
      */
-    public List<EntryType.Reference> getReference() {
-        if (reference == null) {
-            reference = new ArrayList<EntryType.Reference>();
-        }
-        return this.reference;
+    public List<Object> getRangeOrGap()
+    {
+      if (rangeOrGap == null)
+      {
+        rangeOrGap = new ArrayList<Object>();
+      }
+      return this.rangeOrGap;
     }
 
     /**
-     * Gets the value of the xref property.
-     * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the xref property.
+     * Java class for anonymous complex type.
      * 
      * <p>
-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * <pre>
-     *    getXref().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link XrefType }
-     * 
-     * 
      */
-    public List<XrefType> getXref() {
-        if (xref == null) {
-            xref = new ArrayList<XrefType>();
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Gap
+    {
+
+      @XmlAttribute(name = "begin", required = true)
+      protected BigInteger begin;
+
+      @XmlAttribute(name = "end", required = true)
+      protected BigInteger end;
+
+      @XmlAttribute(name = "length", required = true)
+      protected BigInteger length;
+
+      @XmlAttribute(name = "unknownLength")
+      protected Boolean unknownLength;
+
+      /**
+       * Gets the value of the begin property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getBegin()
+      {
+        return begin;
+      }
+
+      /**
+       * Sets the value of the begin property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setBegin(BigInteger value)
+      {
+        this.begin = value;
+      }
+
+      /**
+       * Gets the value of the end property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getEnd()
+      {
+        return end;
+      }
+
+      /**
+       * Sets the value of the end property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setEnd(BigInteger value)
+      {
+        this.end = value;
+      }
+
+      /**
+       * Gets the value of the length property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getLength()
+      {
+        return length;
+      }
+
+      /**
+       * Sets the value of the length property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setLength(BigInteger value)
+      {
+        this.length = value;
+      }
+
+      /**
+       * Gets the value of the unknownLength property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public boolean isUnknownLength()
+      {
+        if (unknownLength == null)
+        {
+          return false;
+        }
+        else
+        {
+          return unknownLength;
         }
-        return this.xref;
+      }
+
+      /**
+       * Sets the value of the unknownLength property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setUnknownLength(Boolean value)
+      {
+        this.unknownLength = value;
+      }
+
     }
 
     /**
-     * Gets the value of the feature property.
-     * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the feature property.
+     * Java class for anonymous complex type.
      * 
      * <p>
-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * <pre>
-     *    getFeature().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Feature }
-     * 
-     * 
      */
-    public List<EntryType.Feature> getFeature() {
-        if (feature == null) {
-            feature = new ArrayList<EntryType.Feature>();
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Range
+    {
+
+      @XmlAttribute(name = "begin", required = true)
+      protected BigInteger begin;
+
+      @XmlAttribute(name = "end", required = true)
+      protected BigInteger end;
+
+      @XmlAttribute(name = "primaryBegin")
+      protected BigInteger primaryBegin;
+
+      @XmlAttribute(name = "primaryEnd")
+      protected BigInteger primaryEnd;
+
+      @XmlAttribute(name = "accession", required = true)
+      protected String accession;
+
+      @XmlAttribute(name = "version", required = true)
+      protected BigInteger version;
+
+      @XmlAttribute(name = "complement")
+      protected Boolean complement;
+
+      /**
+       * Gets the value of the begin property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getBegin()
+      {
+        return begin;
+      }
+
+      /**
+       * Sets the value of the begin property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setBegin(BigInteger value)
+      {
+        this.begin = value;
+      }
+
+      /**
+       * Gets the value of the end property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getEnd()
+      {
+        return end;
+      }
+
+      /**
+       * Sets the value of the end property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setEnd(BigInteger value)
+      {
+        this.end = value;
+      }
+
+      /**
+       * Gets the value of the primaryBegin property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getPrimaryBegin()
+      {
+        return primaryBegin;
+      }
+
+      /**
+       * Sets the value of the primaryBegin property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setPrimaryBegin(BigInteger value)
+      {
+        this.primaryBegin = value;
+      }
+
+      /**
+       * Gets the value of the primaryEnd property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getPrimaryEnd()
+      {
+        return primaryEnd;
+      }
+
+      /**
+       * Sets the value of the primaryEnd property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setPrimaryEnd(BigInteger value)
+      {
+        this.primaryEnd = value;
+      }
+
+      /**
+       * Gets the value of the accession property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getAccession()
+      {
+        return accession;
+      }
+
+      /**
+       * Sets the value of the accession property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setAccession(String value)
+      {
+        this.accession = value;
+      }
+
+      /**
+       * Gets the value of the version property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getVersion()
+      {
+        return version;
+      }
+
+      /**
+       * Sets the value of the version property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setVersion(BigInteger value)
+      {
+        this.version = value;
+      }
+
+      /**
+       * Gets the value of the complement property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public boolean isComplement()
+      {
+        if (complement == null)
+        {
+          return false;
         }
-        return this.feature;
-    }
+        else
+        {
+          return complement;
+        }
+      }
+
+      /**
+       * Sets the value of the complement property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setComplement(Boolean value)
+      {
+        this.complement = value;
+      }
 
-    /**
-     * Gets the value of the assembly property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link EntryType.Assembly }
-     *     
-     */
-    public EntryType.Assembly getAssembly() {
-        return assembly;
     }
 
-    /**
-     * Sets the value of the assembly property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link EntryType.Assembly }
-     *     
-     */
-    public void setAssembly(EntryType.Assembly value) {
-        this.assembly = value;
-    }
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="taxon" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;sequence>
+   *                   &lt;element name="lineage" minOccurs="0">
+   *                     &lt;complexType>
+   *                       &lt;complexContent>
+   *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                           &lt;sequence>
+   *                             &lt;element name="taxon" maxOccurs="unbounded">
+   *                               &lt;complexType>
+   *                                 &lt;complexContent>
+   *                                   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                                     &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                                   &lt;/restriction>
+   *                                 &lt;/complexContent>
+   *                               &lt;/complexType>
+   *                             &lt;/element>
+   *                           &lt;/sequence>
+   *                         &lt;/restriction>
+   *                       &lt;/complexContent>
+   *                     &lt;/complexType>
+   *                   &lt;/element>
+   *                 &lt;/sequence>
+   *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;sequence>
+   *                   &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *                 &lt;/sequence>
+   *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *       &lt;/sequence>
+   *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "taxon", "xref", "qualifier" })
+  public static class Feature
+  {
+
+    protected EntryType.Feature.FeatureTaxon taxon;
 
-    /**
-     * Gets the value of the contig property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link EntryType.Contig }
-     *     
-     */
-    public EntryType.Contig getContig() {
-        return contig;
-    }
+    protected List<XrefType> xref;
 
-    /**
-     * Sets the value of the contig property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link EntryType.Contig }
-     *     
-     */
-    public void setContig(EntryType.Contig value) {
-        this.contig = value;
-    }
+    protected List<EntryType.Feature.Qualifier> qualifier;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSequence() {
-        return sequence;
-    }
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
 
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSequence(String value) {
-        this.sequence = value;
-    }
+    @XmlAttribute(name = "location", required = true)
+    protected String location;
 
     /**
-     * Gets the value of the accession property.
+     * Gets the value of the taxon property.
+     * 
+     * @return possible object is {@link EntryType.Feature.FeatureTaxon }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getAccession() {
-        return accession;
+    public EntryType.Feature.FeatureTaxon getTaxon()
+    {
+      return taxon;
     }
 
     /**
-     * Sets the value of the accession property.
+     * Sets the value of the taxon property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setAccession(String value) {
-        this.accession = value;
-    }
-
-    /**
-     * Gets the value of the version property.
+     *          allowed object is {@link EntryType.Feature.FeatureTaxon }
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
      */
-    public BigInteger getVersion() {
-        return version;
+    public void setTaxon(EntryType.Feature.FeatureTaxon value)
+    {
+      this.taxon = value;
     }
 
     /**
-     * Sets the value of the version property.
+     * Gets the value of the xref property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setVersion(BigInteger value) {
-        this.version = value;
-    }
-
-    /**
-     * Gets the value of the entryVersion property.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the xref property.
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getEntryVersion() {
-        return entryVersion;
-    }
-
-    /**
-     * Sets the value of the entryVersion property.
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setEntryVersion(BigInteger value) {
-        this.entryVersion = value;
-    }
-
-    /**
-     * Gets the value of the dataClass property.
+     * <pre>
+     * getXref().add(newItem);
+     * </pre>
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDataClass() {
-        return dataClass;
-    }
-
-    /**
-     * Sets the value of the dataClass property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDataClass(String value) {
-        this.dataClass = value;
-    }
-
-    /**
-     * Gets the value of the taxonomicDivision property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link XrefType
+     * }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getTaxonomicDivision() {
-        return taxonomicDivision;
-    }
-
-    /**
-     * Sets the value of the taxonomicDivision property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
      */
-    public void setTaxonomicDivision(String value) {
-        this.taxonomicDivision = value;
+    public List<XrefType> getXref()
+    {
+      if (xref == null)
+      {
+        xref = new ArrayList<XrefType>();
+      }
+      return this.xref;
     }
 
     /**
-     * Gets the value of the moleculeType property.
+     * Gets the value of the qualifier property.
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getMoleculeType() {
-        return moleculeType;
-    }
-
-    /**
-     * Sets the value of the moleculeType property.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the qualifier property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setMoleculeType(String value) {
-        this.moleculeType = value;
-    }
-
-    /**
-     * Gets the value of the sequenceLength property.
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getSequenceLength() {
-        return sequenceLength;
-    }
-
-    /**
-     * Sets the value of the sequenceLength property.
+     * <pre>
+     * getQualifier().add(newItem);
+     * </pre>
      * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setSequenceLength(BigInteger value) {
-        this.sequenceLength = value;
-    }
-
-    /**
-     * Gets the value of the topology property.
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getTopology() {
-        return topology;
-    }
-
-    /**
-     * Sets the value of the topology property.
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EntryType.Feature.Qualifier }
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setTopology(String value) {
-        this.topology = value;
-    }
-
-    /**
-     * Gets the value of the firstPublic property.
      * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
      */
-    public XMLGregorianCalendar getFirstPublic() {
-        return firstPublic;
+    public List<EntryType.Feature.Qualifier> getQualifier()
+    {
+      if (qualifier == null)
+      {
+        qualifier = new ArrayList<EntryType.Feature.Qualifier>();
+      }
+      return this.qualifier;
     }
 
     /**
-     * Sets the value of the firstPublic property.
+     * Gets the value of the name property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setFirstPublic(XMLGregorianCalendar value) {
-        this.firstPublic = value;
-    }
-
-    /**
-     * Gets the value of the firstPublicRelease property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
      */
-    public BigInteger getFirstPublicRelease() {
-        return firstPublicRelease;
+    public String getName()
+    {
+      return name;
     }
 
     /**
-     * Sets the value of the firstPublicRelease property.
+     * Sets the value of the name property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setFirstPublicRelease(BigInteger value) {
-        this.firstPublicRelease = value;
-    }
-
-    /**
-     * Gets the value of the lastUpdated property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
      */
-    public XMLGregorianCalendar getLastUpdated() {
-        return lastUpdated;
+    public void setName(String value)
+    {
+      this.name = value;
     }
 
     /**
-     * Sets the value of the lastUpdated property.
+     * Gets the value of the location property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setLastUpdated(XMLGregorianCalendar value) {
-        this.lastUpdated = value;
-    }
-
-    /**
-     * Gets the value of the lastUpdatedRelease property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
      */
-    public BigInteger getLastUpdatedRelease() {
-        return lastUpdatedRelease;
+    public String getLocation()
+    {
+      return location;
     }
 
     /**
-     * Sets the value of the lastUpdatedRelease property.
+     * Sets the value of the location property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setLastUpdatedRelease(BigInteger value) {
-        this.lastUpdatedRelease = value;
+    public void setLocation(String value)
+    {
+      this.location = value;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * <p>
+     * Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
      * 
      * <pre>
      * &lt;complexType>
      *   &lt;complexContent>
      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       &lt;sequence>
-     *         &lt;element name="range" maxOccurs="unbounded">
+     *         &lt;element name="lineage" minOccurs="0">
      *           &lt;complexType>
      *             &lt;complexContent>
      *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 &lt;sequence>
+     *                   &lt;element name="taxon" maxOccurs="unbounded">
+     *                     &lt;complexType>
+     *                       &lt;complexContent>
+     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         &lt;/restriction>
+     *                       &lt;/complexContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
      *               &lt;/restriction>
      *             &lt;/complexContent>
      *           &lt;/complexType>
      *         &lt;/element>
      *       &lt;/sequence>
+     *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
      *     &lt;/restriction>
      *   &lt;/complexContent>
      * &lt;/complexType>
@@ -896,366 +1894,198 @@ public class EntryType {
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "range"
-    })
-    public static class Assembly {
+    @XmlType(name = "", propOrder = { "lineage" })
+    public static class FeatureTaxon
+    {
+
+      protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+
+      @XmlAttribute(name = "scientificName", required = true)
+      protected String scientificName;
+
+      @XmlAttribute(name = "commonName")
+      protected String commonName;
+
+      @XmlAttribute(name = "taxId")
+      protected BigInteger taxId;
+
+      /**
+       * Gets the value of the lineage property.
+       * 
+       * @return possible object is
+       *         {@link EntryType.Feature.FeatureTaxon.Lineage }
+       * 
+       */
+      public EntryType.Feature.FeatureTaxon.Lineage getLineage()
+      {
+        return lineage;
+      }
+
+      /**
+       * Sets the value of the lineage property.
+       * 
+       * @param value
+       *          allowed object is
+       *          {@link EntryType.Feature.FeatureTaxon.Lineage }
+       * 
+       */
+      public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value)
+      {
+        this.lineage = value;
+      }
+
+      /**
+       * Gets the value of the scientificName property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getScientificName()
+      {
+        return scientificName;
+      }
+
+      /**
+       * Sets the value of the scientificName property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setScientificName(String value)
+      {
+        this.scientificName = value;
+      }
+
+      /**
+       * Gets the value of the commonName property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getCommonName()
+      {
+        return commonName;
+      }
+
+      /**
+       * Sets the value of the commonName property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setCommonName(String value)
+      {
+        this.commonName = value;
+      }
+
+      /**
+       * Gets the value of the taxId property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getTaxId()
+      {
+        return taxId;
+      }
+
+      /**
+       * Sets the value of the taxId property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setTaxId(BigInteger value)
+      {
+        this.taxId = value;
+      }
+
+      /**
+       * <p>
+       * Java class for anonymous complex type.
+       * 
+       * <p>
+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
+       * <pre>
+       * &lt;complexType>
+       *   &lt;complexContent>
+       *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       &lt;sequence>
+       *         &lt;element name="taxon" maxOccurs="unbounded">
+       *           &lt;complexType>
+       *             &lt;complexContent>
+       *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *               &lt;/restriction>
+       *             &lt;/complexContent>
+       *           &lt;/complexType>
+       *         &lt;/element>
+       *       &lt;/sequence>
+       *     &lt;/restriction>
+       *   &lt;/complexContent>
+       * &lt;/complexType>
+       * </pre>
+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "", propOrder = { "taxon" })
+      public static class Lineage
+      {
 
         @XmlElement(required = true)
-        protected List<EntryType.Assembly.Range> range;
+        protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
 
         /**
-         * Gets the value of the range property.
+         * Gets the value of the taxon property.
          * 
          * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the range 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
+         * <CODE>set</CODE> method for the taxon property.
          * 
          * <p>
          * For example, to add a new item, do as follows:
+         * 
          * <pre>
-         *    getRange().add(newItem);
+         * getTaxon().add(newItem);
          * </pre>
          * 
          * 
          * <p>
          * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Assembly.Range }
-         * 
-         * 
-         */
-        public List<EntryType.Assembly.Range> getRange() {
-            if (range == null) {
-                range = new ArrayList<EntryType.Assembly.Range>();
-            }
-            return this.range;
-        }
-
-
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
          * 
          * 
          */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Range {
-
-            @XmlAttribute(name = "begin", required = true)
-            protected BigInteger begin;
-            @XmlAttribute(name = "end", required = true)
-            protected BigInteger end;
-            @XmlAttribute(name = "primaryBegin")
-            protected BigInteger primaryBegin;
-            @XmlAttribute(name = "primaryEnd")
-            protected BigInteger primaryEnd;
-            @XmlAttribute(name = "accession", required = true)
-            protected String accession;
-            @XmlAttribute(name = "version", required = true)
-            protected BigInteger version;
-            @XmlAttribute(name = "complement")
-            protected Boolean complement;
-
-            /**
-             * Gets the value of the begin property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getBegin() {
-                return begin;
-            }
-
-            /**
-             * Sets the value of the begin property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setBegin(BigInteger value) {
-                this.begin = value;
-            }
-
-            /**
-             * Gets the value of the end property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getEnd() {
-                return end;
-            }
-
-            /**
-             * Sets the value of the end property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setEnd(BigInteger value) {
-                this.end = value;
-            }
-
-            /**
-             * Gets the value of the primaryBegin property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getPrimaryBegin() {
-                return primaryBegin;
-            }
-
-            /**
-             * Sets the value of the primaryBegin property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setPrimaryBegin(BigInteger value) {
-                this.primaryBegin = value;
-            }
-
-            /**
-             * Gets the value of the primaryEnd property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getPrimaryEnd() {
-                return primaryEnd;
-            }
-
-            /**
-             * Sets the value of the primaryEnd property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setPrimaryEnd(BigInteger value) {
-                this.primaryEnd = value;
-            }
-
-            /**
-             * Gets the value of the accession property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getAccession() {
-                return accession;
-            }
-
-            /**
-             * Sets the value of the accession property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setAccession(String value) {
-                this.accession = value;
-            }
-
-            /**
-             * Gets the value of the version property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getVersion() {
-                return version;
-            }
-
-            /**
-             * Sets the value of the version property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setVersion(BigInteger value) {
-                this.version = value;
-            }
-
-            /**
-             * Gets the value of the complement property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public boolean isComplement() {
-                if (complement == null) {
-                    return false;
-                } else {
-                    return complement;
-                }
-            }
-
-            /**
-             * Sets the value of the complement property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setComplement(Boolean value) {
-                this.complement = value;
-            }
-
+        public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon()
+        {
+          if (taxon == null)
+          {
+            taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
+          }
+          return this.taxon;
         }
 
-    }
-
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;choice maxOccurs="unbounded" minOccurs="0">
-     *           &lt;element name="range">
-     *             &lt;complexType>
-     *               &lt;complexContent>
-     *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                   &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 &lt;/restriction>
-     *               &lt;/complexContent>
-     *             &lt;/complexType>
-     *           &lt;/element>
-     *           &lt;element name="gap">
-     *             &lt;complexType>
-     *               &lt;complexContent>
-     *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                   &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 &lt;/restriction>
-     *               &lt;/complexContent>
-     *             &lt;/complexType>
-     *           &lt;/element>
-     *         &lt;/choice>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "rangeOrGap"
-    })
-    public static class Contig {
-
-        @XmlElements({
-            @XmlElement(name = "range", type = EntryType.Contig.Range.class),
-            @XmlElement(name = "gap", type = EntryType.Contig.Gap.class)
-        })
-        protected List<Object> rangeOrGap;
-
         /**
-         * Gets the value of the rangeOrGap property.
-         * 
          * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
+         * Java class for anonymous complex type.
          * 
          * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getRangeOrGap().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Contig.Range }
-         * {@link EntryType.Contig.Gap }
-         * 
-         * 
-         */
-        public List<Object> getRangeOrGap() {
-            if (rangeOrGap == null) {
-                rangeOrGap = new ArrayList<Object>();
-            }
-            return this.rangeOrGap;
-        }
-
-
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * The following schema fragment specifies the expected content
+         * contained within this class.
          * 
          * <pre>
          * &lt;complexType>
          *   &lt;complexContent>
          *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
          *     &lt;/restriction>
          *   &lt;/complexContent>
          * &lt;/complexType>
@@ -1265,397 +2095,57 @@ public class EntryType {
          */
         @XmlAccessorType(XmlAccessType.FIELD)
         @XmlType(name = "")
-        public static class Gap {
-
-            @XmlAttribute(name = "begin", required = true)
-            protected BigInteger begin;
-            @XmlAttribute(name = "end", required = true)
-            protected BigInteger end;
-            @XmlAttribute(name = "length", required = true)
-            protected BigInteger length;
-            @XmlAttribute(name = "unknownLength")
-            protected Boolean unknownLength;
-
-            /**
-             * Gets the value of the begin property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getBegin() {
-                return begin;
-            }
-
-            /**
-             * Sets the value of the begin property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setBegin(BigInteger value) {
-                this.begin = value;
-            }
-
-            /**
-             * Gets the value of the end property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getEnd() {
-                return end;
-            }
-
-            /**
-             * Sets the value of the end property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setEnd(BigInteger value) {
-                this.end = value;
-            }
-
-            /**
-             * Gets the value of the length property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getLength() {
-                return length;
-            }
-
-            /**
-             * Sets the value of the length property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setLength(BigInteger value) {
-                this.length = value;
-            }
-
-            /**
-             * Gets the value of the unknownLength property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public boolean isUnknownLength() {
-                if (unknownLength == null) {
-                    return false;
-                } else {
-                    return unknownLength;
-                }
-            }
-
-            /**
-             * Sets the value of the unknownLength property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setUnknownLength(Boolean value) {
-                this.unknownLength = value;
-            }
+        public static class Taxon
+        {
+
+          @XmlAttribute(name = "scientificName", required = true)
+          protected String scientificName;
+
+          /**
+           * Gets the value of the scientificName property.
+           * 
+           * @return possible object is {@link String }
+           * 
+           */
+          public String getScientificName()
+          {
+            return scientificName;
+          }
+
+          /**
+           * Sets the value of the scientificName property.
+           * 
+           * @param value
+           *          allowed object is {@link String }
+           * 
+           */
+          public void setScientificName(String value)
+          {
+            this.scientificName = value;
+          }
 
         }
 
-
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Range {
-
-            @XmlAttribute(name = "begin", required = true)
-            protected BigInteger begin;
-            @XmlAttribute(name = "end", required = true)
-            protected BigInteger end;
-            @XmlAttribute(name = "primaryBegin")
-            protected BigInteger primaryBegin;
-            @XmlAttribute(name = "primaryEnd")
-            protected BigInteger primaryEnd;
-            @XmlAttribute(name = "accession", required = true)
-            protected String accession;
-            @XmlAttribute(name = "version", required = true)
-            protected BigInteger version;
-            @XmlAttribute(name = "complement")
-            protected Boolean complement;
-
-            /**
-             * Gets the value of the begin property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getBegin() {
-                return begin;
-            }
-
-            /**
-             * Sets the value of the begin property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setBegin(BigInteger value) {
-                this.begin = value;
-            }
-
-            /**
-             * Gets the value of the end property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getEnd() {
-                return end;
-            }
-
-            /**
-             * Sets the value of the end property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setEnd(BigInteger value) {
-                this.end = value;
-            }
-
-            /**
-             * Gets the value of the primaryBegin property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getPrimaryBegin() {
-                return primaryBegin;
-            }
-
-            /**
-             * Sets the value of the primaryBegin property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setPrimaryBegin(BigInteger value) {
-                this.primaryBegin = value;
-            }
-
-            /**
-             * Gets the value of the primaryEnd property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getPrimaryEnd() {
-                return primaryEnd;
-            }
-
-            /**
-             * Sets the value of the primaryEnd property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setPrimaryEnd(BigInteger value) {
-                this.primaryEnd = value;
-            }
-
-            /**
-             * Gets the value of the accession property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getAccession() {
-                return accession;
-            }
-
-            /**
-             * Sets the value of the accession property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setAccession(String value) {
-                this.accession = value;
-            }
-
-            /**
-             * Gets the value of the version property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getVersion() {
-                return version;
-            }
-
-            /**
-             * Sets the value of the version property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setVersion(BigInteger value) {
-                this.version = value;
-            }
-
-            /**
-             * Gets the value of the complement property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public boolean isComplement() {
-                if (complement == null) {
-                    return false;
-                } else {
-                    return complement;
-                }
-            }
-
-            /**
-             * Sets the value of the complement property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setComplement(Boolean value) {
-                this.complement = value;
-            }
-
-        }
+      }
 
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * <p>
+     * Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
      * 
      * <pre>
      * &lt;complexType>
      *   &lt;complexContent>
      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       &lt;sequence>
-     *         &lt;element name="taxon" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="lineage" minOccurs="0">
-     *                     &lt;complexType>
-     *                       &lt;complexContent>
-     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           &lt;sequence>
-     *                             &lt;element name="taxon" maxOccurs="unbounded">
-     *                               &lt;complexType>
-     *                                 &lt;complexContent>
-     *                                   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                                     &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                                   &lt;/restriction>
-     *                                 &lt;/complexContent>
-     *                               &lt;/complexType>
-     *                             &lt;/element>
-     *                           &lt;/sequence>
-     *                         &lt;/restriction>
-     *                       &lt;/complexContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
-     *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *                 &lt;/sequence>
-     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
+     *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
      *       &lt;/sequence>
      *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
      *     &lt;/restriction>
      *   &lt;/complexContent>
      * &lt;/complexType>
@@ -1664,1017 +2154,578 @@ public class EntryType {
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "taxon",
-        "xref",
-        "qualifier"
-    })
-    public static class Feature {
-
-        protected EntryType.Feature.FeatureTaxon taxon;
-        protected List<XrefType> xref;
-        protected List<EntryType.Feature.Qualifier> qualifier;
-        @XmlAttribute(name = "name", required = true)
-        protected String name;
-        @XmlAttribute(name = "location", required = true)
-        protected String location;
+    @XmlType(name = "", propOrder = { "value" })
+    public static class Qualifier
+    {
+
+      protected String value;
+
+      @XmlAttribute(name = "name", required = true)
+      protected String name;
+
+      /**
+       * Gets the value of the value property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getValue()
+      {
+        return value;
+      }
+
+      /**
+       * Sets the value of the value property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setValue(String value)
+      {
+        this.value = value;
+      }
+
+      /**
+       * Gets the value of the 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 taxon property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EntryType.Feature.FeatureTaxon }
-         *     
-         */
-        public EntryType.Feature.FeatureTaxon getTaxon() {
-            return taxon;
-        }
+    }
 
-        /**
-         * Sets the value of the taxon property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EntryType.Feature.FeatureTaxon }
-         *     
-         */
-        public void setTaxon(EntryType.Feature.FeatureTaxon value) {
-            this.taxon = value;
-        }
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+   *         &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="type" use="required">
+   *         &lt;simpleType>
+   *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             &lt;enumeration value="submission"/>
+   *             &lt;enumeration value="book"/>
+   *             &lt;enumeration value="article"/>
+   *             &lt;enumeration value="patent"/>
+   *             &lt;enumeration value="thesis"/>
+   *             &lt;enumeration value="unpublished"/>
+   *           &lt;/restriction>
+   *         &lt;/simpleType>
+   *       &lt;/attribute>
+   *       &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "title", "author", "applicant", "consortium", "submissionDate",
+        "journal", "year", "volume", "issue", "firstPage", "lastPage",
+        "comment", "referenceLocation", "xref" })
+  public static class Reference
+  {
+
+    protected String title;
+
+    protected List<String> author;
+
+    protected List<String> applicant;
+
+    protected String consortium;
 
-        /**
-         * Gets the value of the xref property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the xref property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getXref().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link XrefType }
-         * 
-         * 
-         */
-        public List<XrefType> getXref() {
-            if (xref == null) {
-                xref = new ArrayList<XrefType>();
-            }
-            return this.xref;
-        }
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar submissionDate;
 
-        /**
-         * Gets the value of the qualifier property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the qualifier property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getQualifier().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Feature.Qualifier }
-         * 
-         * 
-         */
-        public List<EntryType.Feature.Qualifier> getQualifier() {
-            if (qualifier == null) {
-                qualifier = new ArrayList<EntryType.Feature.Qualifier>();
-            }
-            return this.qualifier;
-        }
+    protected String journal;
 
-        /**
-         * Gets the value of the name property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getName() {
-            return name;
-        }
+    protected String year;
 
-        /**
-         * Sets the value of the name property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setName(String value) {
-            this.name = value;
-        }
+    protected String volume;
 
-        /**
-         * Gets the value of the location property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getLocation() {
-            return location;
-        }
+    protected String issue;
 
-        /**
-         * Sets the value of the location property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setLocation(String value) {
-            this.location = value;
-        }
+    protected String firstPage;
 
+    protected String lastPage;
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="lineage" minOccurs="0">
-         *           &lt;complexType>
-         *             &lt;complexContent>
-         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 &lt;sequence>
-         *                   &lt;element name="taxon" maxOccurs="unbounded">
-         *                     &lt;complexType>
-         *                       &lt;complexContent>
-         *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                           &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                         &lt;/restriction>
-         *                       &lt;/complexContent>
-         *                     &lt;/complexType>
-         *                   &lt;/element>
-         *                 &lt;/sequence>
-         *               &lt;/restriction>
-         *             &lt;/complexContent>
-         *           &lt;/complexType>
-         *         &lt;/element>
-         *       &lt;/sequence>
-         *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "lineage"
-        })
-        public static class FeatureTaxon {
-
-            protected EntryType.Feature.FeatureTaxon.Lineage lineage;
-            @XmlAttribute(name = "scientificName", required = true)
-            protected String scientificName;
-            @XmlAttribute(name = "commonName")
-            protected String commonName;
-            @XmlAttribute(name = "taxId")
-            protected BigInteger taxId;
-
-            /**
-             * Gets the value of the lineage property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link EntryType.Feature.FeatureTaxon.Lineage }
-             *     
-             */
-            public EntryType.Feature.FeatureTaxon.Lineage getLineage() {
-                return lineage;
-            }
-
-            /**
-             * Sets the value of the lineage property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link EntryType.Feature.FeatureTaxon.Lineage }
-             *     
-             */
-            public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) {
-                this.lineage = value;
-            }
-
-            /**
-             * Gets the value of the scientificName property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getScientificName() {
-                return scientificName;
-            }
-
-            /**
-             * Sets the value of the scientificName property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setScientificName(String value) {
-                this.scientificName = value;
-            }
-
-            /**
-             * Gets the value of the commonName property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getCommonName() {
-                return commonName;
-            }
-
-            /**
-             * Sets the value of the commonName property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setCommonName(String value) {
-                this.commonName = value;
-            }
-
-            /**
-             * Gets the value of the taxId property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getTaxId() {
-                return taxId;
-            }
-
-            /**
-             * Sets the value of the taxId property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setTaxId(BigInteger value) {
-                this.taxId = value;
-            }
-
-
-            /**
-             * <p>Java class for anonymous complex type.
-             * 
-             * <p>The following schema fragment specifies the expected content contained within this class.
-             * 
-             * <pre>
-             * &lt;complexType>
-             *   &lt;complexContent>
-             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       &lt;sequence>
-             *         &lt;element name="taxon" maxOccurs="unbounded">
-             *           &lt;complexType>
-             *             &lt;complexContent>
-             *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *                 &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *               &lt;/restriction>
-             *             &lt;/complexContent>
-             *           &lt;/complexType>
-             *         &lt;/element>
-             *       &lt;/sequence>
-             *     &lt;/restriction>
-             *   &lt;/complexContent>
-             * &lt;/complexType>
-             * </pre>
-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "", propOrder = {
-                "taxon"
-            })
-            public static class Lineage {
-
-                @XmlElement(required = true)
-                protected List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> taxon;
-
-                /**
-                 * Gets the value of the taxon property.
-                 * 
-                 * <p>
-                 * This accessor method returns a reference to the live list,
-                 * not a snapshot. Therefore any modification you make to the
-                 * returned list will be present inside the JAXB object.
-                 * This is why there is not a <CODE>set</CODE> method for the taxon property.
-                 * 
-                 * <p>
-                 * For example, to add a new item, do as follows:
-                 * <pre>
-                 *    getTaxon().add(newItem);
-                 * </pre>
-                 * 
-                 * 
-                 * <p>
-                 * Objects of the following type(s) are allowed in the list
-                 * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
-                 * 
-                 * 
-                 */
-                public List<EntryType.Feature.FeatureTaxon.Lineage.Taxon> getTaxon() {
-                    if (taxon == null) {
-                        taxon = new ArrayList<EntryType.Feature.FeatureTaxon.Lineage.Taxon>();
-                    }
-                    return this.taxon;
-                }
-
-
-                /**
-                 * <p>Java class for anonymous complex type.
-                 * 
-                 * <p>The following schema fragment specifies the expected content contained within this class.
-                 * 
-                 * <pre>
-                 * &lt;complexType>
-                 *   &lt;complexContent>
-                 *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-                 *       &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-                 *     &lt;/restriction>
-                 *   &lt;/complexContent>
-                 * &lt;/complexType>
-                 * </pre>
-                 * 
-                 * 
-                 */
-                @XmlAccessorType(XmlAccessType.FIELD)
-                @XmlType(name = "")
-                public static class Taxon {
-
-                    @XmlAttribute(name = "scientificName", required = true)
-                    protected String scientificName;
-
-                    /**
-                     * Gets the value of the scientificName property.
-                     * 
-                     * @return
-                     *     possible object is
-                     *     {@link String }
-                     *     
-                     */
-                    public String getScientificName() {
-                        return scientificName;
-                    }
-
-                    /**
-                     * Sets the value of the scientificName property.
-                     * 
-                     * @param value
-                     *     allowed object is
-                     *     {@link String }
-                     *     
-                     */
-                    public void setScientificName(String value) {
-                        this.scientificName = value;
-                    }
-
-                }
-
-            }
+    protected String comment;
 
-        }
+    protected String referenceLocation;
 
+    protected List<XrefType> xref;
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-         *       &lt;/sequence>
-         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "value"
-        })
-        public static class Qualifier {
-
-            protected String value;
-            @XmlAttribute(name = "name", required = true)
-            protected String name;
-
-            /**
-             * Gets the value of the value property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getValue() {
-                return value;
-            }
-
-            /**
-             * Sets the value of the value property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setValue(String value) {
-                this.value = value;
-            }
-
-            /**
-             * Gets the value of the 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;
-            }
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
 
-        }
+    @XmlAttribute(name = "number", required = true)
+    protected BigInteger number;
+
+    @XmlAttribute(name = "location")
+    protected String location;
 
+    /**
+     * Gets the value of the title property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getTitle()
+    {
+      return title;
     }
 
+    /**
+     * Sets the value of the title property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setTitle(String value)
+    {
+      this.title = value;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the author property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the author property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
-     *         &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="type" use="required">
-     *         &lt;simpleType>
-     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             &lt;enumeration value="submission"/>
-     *             &lt;enumeration value="book"/>
-     *             &lt;enumeration value="article"/>
-     *             &lt;enumeration value="patent"/>
-     *             &lt;enumeration value="thesis"/>
-     *             &lt;enumeration value="unpublished"/>
-     *           &lt;/restriction>
-     *         &lt;/simpleType>
-     *       &lt;/attribute>
-     *       &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getAuthor().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link String }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "title",
-        "author",
-        "applicant",
-        "consortium",
-        "submissionDate",
-        "journal",
-        "year",
-        "volume",
-        "issue",
-        "firstPage",
-        "lastPage",
-        "comment",
-        "referenceLocation",
-        "xref"
-    })
-    public static class Reference {
-
-        protected String title;
-        protected List<String> author;
-        protected List<String> applicant;
-        protected String consortium;
-        @XmlSchemaType(name = "date")
-        protected XMLGregorianCalendar submissionDate;
-        protected String journal;
-        protected String year;
-        protected String volume;
-        protected String issue;
-        protected String firstPage;
-        protected String lastPage;
-        protected String comment;
-        protected String referenceLocation;
-        protected List<XrefType> xref;
-        @XmlAttribute(name = "type", required = true)
-        protected String type;
-        @XmlAttribute(name = "number", required = true)
-        protected BigInteger number;
-        @XmlAttribute(name = "location")
-        protected String location;
-
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getTitle() {
-            return title;
-        }
-
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setTitle(String value) {
-            this.title = value;
-        }
+    public List<String> getAuthor()
+    {
+      if (author == null)
+      {
+        author = new ArrayList<String>();
+      }
+      return this.author;
+    }
 
-        /**
-         * Gets the value of the author property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the author property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getAuthor().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List<String> getAuthor() {
-            if (author == null) {
-                author = new ArrayList<String>();
-            }
-            return this.author;
-        }
-
-        /**
-         * Gets the value of the applicant property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the applicant property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getApplicant().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List<String> getApplicant() {
-            if (applicant == null) {
-                applicant = new ArrayList<String>();
-            }
-            return this.applicant;
-        }
-
-        /**
-         * Gets the value of the consortium property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getConsortium() {
-            return consortium;
-        }
+    /**
+     * Gets the value of the applicant property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the applicant property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getApplicant().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link String }
+     * 
+     * 
+     */
+    public List<String> getApplicant()
+    {
+      if (applicant == null)
+      {
+        applicant = new ArrayList<String>();
+      }
+      return this.applicant;
+    }
 
-        /**
-         * Sets the value of the consortium property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setConsortium(String value) {
-            this.consortium = value;
-        }
+    /**
+     * Gets the value of the consortium property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getConsortium()
+    {
+      return consortium;
+    }
 
-        /**
-         * Gets the value of the submissionDate property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link XMLGregorianCalendar }
-         *     
-         */
-        public XMLGregorianCalendar getSubmissionDate() {
-            return submissionDate;
-        }
+    /**
+     * Sets the value of the consortium property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setConsortium(String value)
+    {
+      this.consortium = value;
+    }
 
-        /**
-         * Sets the value of the submissionDate property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link XMLGregorianCalendar }
-         *     
-         */
-        public void setSubmissionDate(XMLGregorianCalendar value) {
-            this.submissionDate = value;
-        }
+    /**
+     * Gets the value of the submissionDate property.
+     * 
+     * @return possible object is {@link XMLGregorianCalendar }
+     * 
+     */
+    public XMLGregorianCalendar getSubmissionDate()
+    {
+      return submissionDate;
+    }
 
-        /**
-         * Gets the value of the journal property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getJournal() {
-            return journal;
-        }
+    /**
+     * Sets the value of the submissionDate property.
+     * 
+     * @param value
+     *          allowed object is {@link XMLGregorianCalendar }
+     * 
+     */
+    public void setSubmissionDate(XMLGregorianCalendar value)
+    {
+      this.submissionDate = value;
+    }
 
-        /**
-         * Sets the value of the journal property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setJournal(String value) {
-            this.journal = value;
-        }
+    /**
+     * Gets the value of the journal property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getJournal()
+    {
+      return journal;
+    }
 
-        /**
-         * Gets the value of the year property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getYear() {
-            return year;
-        }
+    /**
+     * Sets the value of the journal property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setJournal(String value)
+    {
+      this.journal = value;
+    }
 
-        /**
-         * Sets the value of the year property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setYear(String value) {
-            this.year = value;
-        }
+    /**
+     * Gets the value of the year property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getYear()
+    {
+      return year;
+    }
 
-        /**
-         * Gets the value of the volume property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getVolume() {
-            return volume;
-        }
+    /**
+     * Sets the value of the year property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setYear(String value)
+    {
+      this.year = value;
+    }
 
-        /**
-         * Sets the value of the volume property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setVolume(String value) {
-            this.volume = value;
-        }
+    /**
+     * Gets the value of the volume property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getVolume()
+    {
+      return volume;
+    }
 
-        /**
-         * Gets the value of the issue property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getIssue() {
-            return issue;
-        }
+    /**
+     * Sets the value of the volume property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setVolume(String value)
+    {
+      this.volume = value;
+    }
 
-        /**
-         * Sets the value of the issue property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setIssue(String value) {
-            this.issue = value;
-        }
+    /**
+     * Gets the value of the issue property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getIssue()
+    {
+      return issue;
+    }
 
-        /**
-         * Gets the value of the firstPage property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getFirstPage() {
-            return firstPage;
-        }
+    /**
+     * Sets the value of the issue property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setIssue(String value)
+    {
+      this.issue = value;
+    }
 
-        /**
-         * Sets the value of the firstPage property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setFirstPage(String value) {
-            this.firstPage = value;
-        }
+    /**
+     * Gets the value of the firstPage property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getFirstPage()
+    {
+      return firstPage;
+    }
 
-        /**
-         * Gets the value of the lastPage property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getLastPage() {
-            return lastPage;
-        }
+    /**
+     * Sets the value of the firstPage property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setFirstPage(String value)
+    {
+      this.firstPage = value;
+    }
 
-        /**
-         * Sets the value of the lastPage property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setLastPage(String value) {
-            this.lastPage = value;
-        }
+    /**
+     * Gets the value of the lastPage property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getLastPage()
+    {
+      return lastPage;
+    }
 
-        /**
-         * Gets the value of the comment property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getComment() {
-            return comment;
-        }
+    /**
+     * Sets the value of the lastPage property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setLastPage(String value)
+    {
+      this.lastPage = value;
+    }
 
-        /**
-         * Sets the value of the comment property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setComment(String value) {
-            this.comment = value;
-        }
+    /**
+     * Gets the value of the comment property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getComment()
+    {
+      return comment;
+    }
 
-        /**
-         * Gets the value of the referenceLocation property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getReferenceLocation() {
-            return referenceLocation;
-        }
+    /**
+     * Sets the value of the comment property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setComment(String value)
+    {
+      this.comment = value;
+    }
 
-        /**
-         * Sets the value of the referenceLocation property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setReferenceLocation(String value) {
-            this.referenceLocation = value;
-        }
+    /**
+     * Gets the value of the referenceLocation property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getReferenceLocation()
+    {
+      return referenceLocation;
+    }
 
-        /**
-         * Gets the value of the xref property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the xref property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getXref().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link XrefType }
-         * 
-         * 
-         */
-        public List<XrefType> getXref() {
-            if (xref == null) {
-                xref = new ArrayList<XrefType>();
-            }
-            return this.xref;
-        }
+    /**
+     * Sets the value of the referenceLocation property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setReferenceLocation(String value)
+    {
+      this.referenceLocation = value;
+    }
 
-        /**
-         * Gets the value of the type property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getType() {
-            return type;
-        }
+    /**
+     * Gets the value of the xref property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the xref property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getXref().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link XrefType
+     * }
+     * 
+     * 
+     */
+    public List<XrefType> getXref()
+    {
+      if (xref == null)
+      {
+        xref = new ArrayList<XrefType>();
+      }
+      return this.xref;
+    }
 
-        /**
-         * Sets the value of the type property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setType(String value) {
-            this.type = value;
-        }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getType()
+    {
+      return type;
+    }
 
-        /**
-         * Gets the value of the number property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link BigInteger }
-         *     
-         */
-        public BigInteger getNumber() {
-            return number;
-        }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setType(String value)
+    {
+      this.type = value;
+    }
 
-        /**
-         * Sets the value of the number property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link BigInteger }
-         *     
-         */
-        public void setNumber(BigInteger value) {
-            this.number = value;
-        }
+    /**
+     * Gets the value of the number property.
+     * 
+     * @return possible object is {@link BigInteger }
+     * 
+     */
+    public BigInteger getNumber()
+    {
+      return number;
+    }
 
-        /**
-         * Gets the value of the location property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getLocation() {
-            return location;
-        }
+    /**
+     * Sets the value of the number property.
+     * 
+     * @param value
+     *          allowed object is {@link BigInteger }
+     * 
+     */
+    public void setNumber(BigInteger value)
+    {
+      this.number = value;
+    }
 
-        /**
-         * Sets the value of the location property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setLocation(String value) {
-            this.location = value;
-        }
+    /**
+     * Gets the value of the location property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getLocation()
+    {
+      return location;
+    }
 
+    /**
+     * Sets the value of the location property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setLocation(String value)
+    {
+      this.location = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/embl/ObjectFactory.java b/src/jalview/xml/binding/embl/ObjectFactory.java
index e1a917a..2fef24a 100644
--- a/src/jalview/xml/binding/embl/ObjectFactory.java
+++ b/src/jalview/xml/binding/embl/ObjectFactory.java
@@ -5,155 +5,167 @@
 // Generated on: 2023.03.17 at 05:31:45 PM GMT 
 //
 
-
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlRegistry;
 
-
 /**
- * This object contains factory methods for each 
- * Java content interface and Java element interface 
- * generated in the jalview.xml.binding.embl package. 
- * <p>An ObjectFactory allows you to programatically 
- * construct new instances of the Java representation 
- * for XML content. The Java representation of XML 
- * content can consist of schema derived interfaces 
- * and classes representing the binding of schema 
- * type definitions, element declarations and model 
- * groups.  Factory methods for each of these are 
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.embl package.
+ * <p>
+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory {
-
-
-    /**
-     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl
-     * 
-     */
-    public ObjectFactory() {
-    }
-
-    /**
-     * Create an instance of {@link EntryType }
-     * 
-     */
-    public EntryType createEntryType() {
-        return new EntryType();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Contig }
-     * 
-     */
-    public EntryType.Contig createEntryTypeContig() {
-        return new EntryType.Contig();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Assembly }
-     * 
-     */
-    public EntryType.Assembly createEntryTypeAssembly() {
-        return new EntryType.Assembly();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Feature }
-     * 
-     */
-    public EntryType.Feature createEntryTypeFeature() {
-        return new EntryType.Feature();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Feature.FeatureTaxon }
-     * 
-     */
-    public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() {
-        return new EntryType.Feature.FeatureTaxon();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
-     * 
-     */
-    public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() {
-        return new EntryType.Feature.FeatureTaxon.Lineage();
-    }
-
-    /**
-     * Create an instance of {@link ROOT }
-     * 
-     */
-    public ROOT createROOT() {
-        return new ROOT();
-    }
-
-    /**
-     * Create an instance of {@link EntrySetType }
-     * 
-     */
-    public EntrySetType createEntrySetType() {
-        return new EntrySetType();
-    }
-
-    /**
-     * Create an instance of {@link XrefType }
-     * 
-     */
-    public XrefType createXrefType() {
-        return new XrefType();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Reference }
-     * 
-     */
-    public EntryType.Reference createEntryTypeReference() {
-        return new EntryType.Reference();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Contig.Range }
-     * 
-     */
-    public EntryType.Contig.Range createEntryTypeContigRange() {
-        return new EntryType.Contig.Range();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Contig.Gap }
-     * 
-     */
-    public EntryType.Contig.Gap createEntryTypeContigGap() {
-        return new EntryType.Contig.Gap();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Assembly.Range }
-     * 
-     */
-    public EntryType.Assembly.Range createEntryTypeAssemblyRange() {
-        return new EntryType.Assembly.Range();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Feature.Qualifier }
-     * 
-     */
-    public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() {
-        return new EntryType.Feature.Qualifier();
-    }
-
-    /**
-     * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
-     * 
-     */
-    public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() {
-        return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
-    }
+public class ObjectFactory
+{
+
+  /**
+   * Create a new ObjectFactory that can be used to create new instances of
+   * schema derived classes for package: jalview.xml.binding.embl
+   * 
+   */
+  public ObjectFactory()
+  {
+  }
+
+  /**
+   * Create an instance of {@link EntryType }
+   * 
+   */
+  public EntryType createEntryType()
+  {
+    return new EntryType();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Contig }
+   * 
+   */
+  public EntryType.Contig createEntryTypeContig()
+  {
+    return new EntryType.Contig();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Assembly }
+   * 
+   */
+  public EntryType.Assembly createEntryTypeAssembly()
+  {
+    return new EntryType.Assembly();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Feature }
+   * 
+   */
+  public EntryType.Feature createEntryTypeFeature()
+  {
+    return new EntryType.Feature();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Feature.FeatureTaxon }
+   * 
+   */
+  public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon()
+  {
+    return new EntryType.Feature.FeatureTaxon();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage }
+   * 
+   */
+  public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage()
+  {
+    return new EntryType.Feature.FeatureTaxon.Lineage();
+  }
+
+  /**
+   * Create an instance of {@link ROOT }
+   * 
+   */
+  public ROOT createROOT()
+  {
+    return new ROOT();
+  }
+
+  /**
+   * Create an instance of {@link EntrySetType }
+   * 
+   */
+  public EntrySetType createEntrySetType()
+  {
+    return new EntrySetType();
+  }
+
+  /**
+   * Create an instance of {@link XrefType }
+   * 
+   */
+  public XrefType createXrefType()
+  {
+    return new XrefType();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Reference }
+   * 
+   */
+  public EntryType.Reference createEntryTypeReference()
+  {
+    return new EntryType.Reference();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Contig.Range }
+   * 
+   */
+  public EntryType.Contig.Range createEntryTypeContigRange()
+  {
+    return new EntryType.Contig.Range();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Contig.Gap }
+   * 
+   */
+  public EntryType.Contig.Gap createEntryTypeContigGap()
+  {
+    return new EntryType.Contig.Gap();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Assembly.Range }
+   * 
+   */
+  public EntryType.Assembly.Range createEntryTypeAssemblyRange()
+  {
+    return new EntryType.Assembly.Range();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Feature.Qualifier }
+   * 
+   */
+  public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier()
+  {
+    return new EntryType.Feature.Qualifier();
+  }
+
+  /**
+   * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
+   * 
+   */
+  public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon()
+  {
+    return new EntryType.Feature.FeatureTaxon.Lineage.Taxon();
+  }
 
 }
diff --git a/src/jalview/xml/binding/embl/ROOT.java b/src/jalview/xml/binding/embl/ROOT.java
index 958cdbc..f35812e 100644
--- a/src/jalview/xml/binding/embl/ROOT.java
+++ b/src/jalview/xml/binding/embl/ROOT.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:45 PM GMT 
 //
 
-
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -35,62 +36,59 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "entrySet",
-    "entry"
-})
+@XmlType(name = "", propOrder = { "entrySet", "entry" })
 @XmlRootElement(name = "ROOT")
-public class ROOT {
+public class ROOT
+{
+
+  protected EntrySetType entrySet;
 
-    protected EntrySetType entrySet;
-    protected EntryType entry;
+  protected EntryType entry;
 
-    /**
-     * Gets the value of the entrySet property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link EntrySetType }
-     *     
-     */
-    public EntrySetType getEntrySet() {
-        return entrySet;
-    }
+  /**
+   * Gets the value of the entrySet property.
+   * 
+   * @return possible object is {@link EntrySetType }
+   * 
+   */
+  public EntrySetType getEntrySet()
+  {
+    return entrySet;
+  }
 
-    /**
-     * Sets the value of the entrySet property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link EntrySetType }
-     *     
-     */
-    public void setEntrySet(EntrySetType value) {
-        this.entrySet = value;
-    }
+  /**
+   * Sets the value of the entrySet property.
+   * 
+   * @param value
+   *          allowed object is {@link EntrySetType }
+   * 
+   */
+  public void setEntrySet(EntrySetType value)
+  {
+    this.entrySet = value;
+  }
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link EntryType }
-     *     
-     */
-    public EntryType getEntry() {
-        return entry;
-    }
+  /**
+   * Gets the value of the entry property.
+   * 
+   * @return possible object is {@link EntryType }
+   * 
+   */
+  public EntryType getEntry()
+  {
+    return entry;
+  }
 
-    /**
-     * Sets the value of the entry property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link EntryType }
-     *     
-     */
-    public void setEntry(EntryType value) {
-        this.entry = value;
-    }
+  /**
+   * Sets the value of the entry property.
+   * 
+   * @param value
+   *          allowed object is {@link EntryType }
+   * 
+   */
+  public void setEntry(EntryType value)
+  {
+    this.entry = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/embl/XrefType.java b/src/jalview/xml/binding/embl/XrefType.java
index 244d0fe..d70f92c 100644
--- a/src/jalview/xml/binding/embl/XrefType.java
+++ b/src/jalview/xml/binding/embl/XrefType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:45 PM GMT 
 //
 
-
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +12,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Database cross-reference.
  * 
- * <p>Java class for XrefType complex type.
+ * <p>
+ * Java class for XrefType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="XrefType">
@@ -37,85 +38,85 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "XrefType")
-public class XrefType {
+public class XrefType
+{
+
+  @XmlAttribute(name = "db", required = true)
+  protected String db;
+
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
 
-    @XmlAttribute(name = "db", required = true)
-    protected String db;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "secondaryId")
-    protected String secondaryId;
+  @XmlAttribute(name = "secondaryId")
+  protected String secondaryId;
 
-    /**
-     * Gets the value of the db property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDb() {
-        return db;
-    }
+  /**
+   * Gets the value of the db property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDb()
+  {
+    return db;
+  }
 
-    /**
-     * Sets the value of the db property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDb(String value) {
-        this.db = value;
-    }
+  /**
+   * Sets the value of the db property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDb(String value)
+  {
+    this.db = value;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
-    /**
-     * Gets the value of the secondaryId property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSecondaryId() {
-        return secondaryId;
-    }
+  /**
+   * Gets the value of the secondaryId property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSecondaryId()
+  {
+    return secondaryId;
+  }
 
-    /**
-     * Sets the value of the secondaryId property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSecondaryId(String value) {
-        this.secondaryId = value;
-    }
+  /**
+   * Sets the value of the secondaryId property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSecondaryId(String value)
+  {
+    this.secondaryId = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index 2a40e11..5dcc0bd 100644
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -18,11 +17,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -61,266 +62,275 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "alcodon",
-    "alcodMap"
-})
+@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
 @XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame {
+public class AlcodonFrame
+{
+
+  protected List<AlcodonFrame.Alcodon> alcodon;
+
+  protected List<AlcodonFrame.AlcodMap> alcodMap;
 
-    protected List<AlcodonFrame.Alcodon> alcodon;
-    protected List<AlcodonFrame.AlcodMap> alcodMap;
+  /**
+   * Gets the value of the alcodon property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the alcodon property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAlcodon().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link AlcodonFrame.Alcodon }
+   * 
+   * 
+   */
+  public List<AlcodonFrame.Alcodon> getAlcodon()
+  {
+    if (alcodon == null)
+    {
+      alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+    }
+    return this.alcodon;
+  }
+
+  /**
+   * Gets the value of the alcodMap property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the alcodMap property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAlcodMap().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link AlcodonFrame.AlcodMap }
+   * 
+   * 
+   */
+  public List<AlcodonFrame.AlcodMap> getAlcodMap()
+  {
+    if (alcodMap == null)
+    {
+      alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+    }
+    return this.alcodMap;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "mapping" })
+  public static class AlcodMap
+  {
+
+    @XmlElement(name = "Mapping", required = true)
+    protected Mapping mapping;
+
+    @XmlAttribute(name = "dnasq", required = true)
+    protected String dnasq;
 
     /**
-     * Gets the value of the alcodon property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the alcodon property.
+     * a Mapping entry and an associated protein sequence
      * 
-     * <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 }
      * 
+     * @return possible object is {@link Mapping }
      * 
      */
-    public List<AlcodonFrame.Alcodon> getAlcodon() {
-        if (alcodon == null) {
-            alcodon = new ArrayList<AlcodonFrame.Alcodon>();
-        }
-        return this.alcodon;
+    public Mapping getMapping()
+    {
+      return mapping;
     }
 
     /**
-     * Gets the value of the alcodMap property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getAlcodMap().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link AlcodonFrame.AlcodMap }
+     * Sets the value of the mapping property.
      * 
+     * @param value
+     *          allowed object is {@link Mapping }
      * 
      */
-    public List<AlcodonFrame.AlcodMap> getAlcodMap() {
-        if (alcodMap == null) {
-            alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
-        }
-        return this.alcodMap;
+    public void setMapping(Mapping value)
+    {
+      this.mapping = value;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the dnasq property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public String getDnasq()
+    {
+      return dnasq;
+    }
+
+    /**
+     * Sets the value of the dnasq property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "mapping"
-    })
-    public static class AlcodMap {
+    public void setDnasq(String value)
+    {
+      this.dnasq = value;
+    }
 
-        @XmlElement(name = "Mapping", required = true)
-        protected Mapping mapping;
-        @XmlAttribute(name = "dnasq", required = true)
-        protected String dnasq;
+  }
 
-        /**
-         * 
-         * 										a Mapping entry and an associated protein sequence
-         * 									
-         * 
-         * @return
-         *     possible object is
-         *     {@link Mapping }
-         *     
-         */
-        public Mapping getMapping() {
-            return mapping;
-        }
+  /**
+   * 
+   * specifies a series of aligned codons from an associated DNA sequence
+   * alignment that when translated correspond to columns of a peptide
+   * alignment. Element may have either all pos1,2,3 attributes specified, or
+   * none at all (indicating a gapped column with no translated peptide).
+   * 
+   * 
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Alcodon
+  {
 
-        /**
-         * Sets the value of the mapping property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Mapping }
-         *     
-         */
-        public void setMapping(Mapping value) {
-            this.mapping = value;
-        }
+    @XmlAttribute(name = "pos1")
+    protected BigInteger pos1;
 
-        /**
-         * Gets the value of the dnasq property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getDnasq() {
-            return dnasq;
-        }
+    @XmlAttribute(name = "pos2")
+    protected BigInteger pos2;
 
-        /**
-         * Sets the value of the dnasq property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setDnasq(String value) {
-            this.dnasq = value;
-        }
+    @XmlAttribute(name = "pos3")
+    protected BigInteger pos3;
 
+    /**
+     * Gets the value of the pos1 property.
+     * 
+     * @return possible object is {@link BigInteger }
+     * 
+     */
+    public BigInteger getPos1()
+    {
+      return pos1;
     }
 
-
     /**
+     * Sets the value of the pos1 property.
      * 
-     * 								specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
-     * 								Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
-     * 							
+     * @param value
+     *          allowed object is {@link BigInteger }
      * 
-     * <p>Java class for anonymous complex type.
+     */
+    public void setPos1(BigInteger value)
+    {
+      this.pos1 = value;
+    }
+
+    /**
+     * Gets the value of the pos2 property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link BigInteger }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public BigInteger getPos2()
+    {
+      return pos2;
+    }
+
+    /**
+     * Sets the value of the pos2 property.
      * 
+     * @param value
+     *          allowed object is {@link BigInteger }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Alcodon {
-
-        @XmlAttribute(name = "pos1")
-        protected BigInteger pos1;
-        @XmlAttribute(name = "pos2")
-        protected BigInteger pos2;
-        @XmlAttribute(name = "pos3")
-        protected BigInteger pos3;
-
-        /**
-         * Gets the value of the pos1 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link BigInteger }
-         *     
-         */
-        public BigInteger getPos1() {
-            return pos1;
-        }
-
-        /**
-         * Sets the value of the pos1 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link BigInteger }
-         *     
-         */
-        public void setPos1(BigInteger value) {
-            this.pos1 = value;
-        }
-
-        /**
-         * Gets the value of the pos2 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link BigInteger }
-         *     
-         */
-        public BigInteger getPos2() {
-            return pos2;
-        }
-
-        /**
-         * Sets the value of the pos2 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link BigInteger }
-         *     
-         */
-        public void setPos2(BigInteger value) {
-            this.pos2 = value;
-        }
-
-        /**
-         * Gets the value of the pos3 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link BigInteger }
-         *     
-         */
-        public BigInteger getPos3() {
-            return pos3;
-        }
+    public void setPos2(BigInteger value)
+    {
+      this.pos2 = value;
+    }
 
-        /**
-         * Sets the value of the pos3 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link BigInteger }
-         *     
-         */
-        public void setPos3(BigInteger value) {
-            this.pos3 = value;
-        }
+    /**
+     * Gets the value of the pos3 property.
+     * 
+     * @return possible object is {@link BigInteger }
+     * 
+     */
+    public BigInteger getPos3()
+    {
+      return pos3;
+    }
 
+    /**
+     * Sets the value of the pos3 property.
+     * 
+     * @param value
+     *          allowed object is {@link BigInteger }
+     * 
+     */
+    public void setPos3(BigInteger value)
+    {
+      this.pos3 = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java
index 8d99141..985736e 100644
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -70,733 +71,755 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "annotationElement",
-    "label",
-    "description",
-    "thresholdLine",
-    "contactmatrix",
-    "property"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "annotationElement", "label", "description", "thresholdLine",
+      "contactmatrix", "property" })
 @XmlRootElement(name = "Annotation")
-public class Annotation {
-
-    protected List<AnnotationElement> annotationElement;
-    @XmlElement(required = true)
-    protected String label;
-    protected String description;
-    protected Annotation.ThresholdLine thresholdLine;
-    protected List<MatrixType> contactmatrix;
-    protected List<Property> property;
-    @XmlAttribute(name = "graph", required = true)
-    protected boolean graph;
-    @XmlAttribute(name = "graphType")
-    protected Integer graphType;
-    @XmlAttribute(name = "sequenceRef")
-    protected String sequenceRef;
-    @XmlAttribute(name = "groupRef")
-    protected String groupRef;
-    @XmlAttribute(name = "graphColour")
-    protected Integer graphColour;
-    @XmlAttribute(name = "graphGroup")
-    protected Integer graphGroup;
-    @XmlAttribute(name = "graphHeight")
-    protected Integer graphHeight;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "scoreOnly")
-    protected Boolean scoreOnly;
-    @XmlAttribute(name = "score")
-    protected Double score;
-    @XmlAttribute(name = "visible")
-    protected Boolean visible;
-    @XmlAttribute(name = "centreColLabels")
-    protected Boolean centreColLabels;
-    @XmlAttribute(name = "scaleColLabels")
-    protected Boolean scaleColLabels;
-    @XmlAttribute(name = "showAllColLabels")
-    protected Boolean showAllColLabels;
-    @XmlAttribute(name = "autoCalculated")
-    protected Boolean autoCalculated;
-    @XmlAttribute(name = "belowAlignment")
-    protected Boolean belowAlignment;
-    @XmlAttribute(name = "calcId")
-    protected String calcId;
-
-    /**
-     * Gets the value of the annotationElement property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getAnnotationElement().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link AnnotationElement }
-     * 
-     * 
-     */
-    public List<AnnotationElement> getAnnotationElement() {
-        if (annotationElement == null) {
-            annotationElement = new ArrayList<AnnotationElement>();
-        }
-        return this.annotationElement;
-    }
-
-    /**
-     * Gets the value of the label property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getLabel() {
-        return label;
-    }
-
-    /**
-     * Sets the value of the label property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setLabel(String value) {
-        this.label = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * Gets the value of the thresholdLine property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Annotation.ThresholdLine }
-     *     
-     */
-    public Annotation.ThresholdLine getThresholdLine() {
-        return thresholdLine;
-    }
-
-    /**
-     * Sets the value of the thresholdLine property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Annotation.ThresholdLine }
-     *     
-     */
-    public void setThresholdLine(Annotation.ThresholdLine value) {
-        this.thresholdLine = value;
-    }
-
-    /**
-     * Gets the value of the contactmatrix property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the contactmatrix property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getContactmatrix().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link MatrixType }
-     * 
-     * 
-     */
-    public List<MatrixType> getContactmatrix() {
-        if (contactmatrix == null) {
-            contactmatrix = new ArrayList<MatrixType>();
-        }
-        return this.contactmatrix;
-    }
-
-    /**
-     * Gets the value of the property property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the property property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getProperty().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Property }
-     * 
-     * 
-     */
-    public List<Property> getProperty() {
-        if (property == null) {
-            property = new ArrayList<Property>();
-        }
-        return this.property;
-    }
-
-    /**
-     * Gets the value of the graph property.
-     * 
-     */
-    public boolean isGraph() {
-        return graph;
-    }
-
-    /**
-     * Sets the value of the graph property.
-     * 
-     */
-    public void setGraph(boolean value) {
-        this.graph = value;
-    }
-
-    /**
-     * Gets the value of the graphType property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getGraphType() {
-        return graphType;
-    }
+public class Annotation
+{
 
-    /**
-     * Sets the value of the graphType property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setGraphType(Integer value) {
-        this.graphType = value;
-    }
-
-    /**
-     * Gets the value of the sequenceRef property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSequenceRef() {
-        return sequenceRef;
-    }
-
-    /**
-     * Sets the value of the sequenceRef property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSequenceRef(String value) {
-        this.sequenceRef = value;
-    }
-
-    /**
-     * Gets the value of the groupRef property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getGroupRef() {
-        return groupRef;
-    }
+  protected List<AnnotationElement> annotationElement;
 
-    /**
-     * Sets the value of the groupRef property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setGroupRef(String value) {
-        this.groupRef = value;
-    }
+  @XmlElement(required = true)
+  protected String label;
+
+  protected String description;
 
-    /**
-     * Gets the value of the graphColour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getGraphColour() {
-        return graphColour;
-    }
-
-    /**
-     * Sets the value of the graphColour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setGraphColour(Integer value) {
-        this.graphColour = value;
-    }
-
-    /**
-     * Gets the value of the graphGroup property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getGraphGroup() {
-        return graphGroup;
-    }
-
-    /**
-     * Sets the value of the graphGroup property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setGraphGroup(Integer value) {
-        this.graphGroup = value;
-    }
-
-    /**
-     * Gets the value of the graphHeight property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getGraphHeight() {
-        return graphHeight;
-    }
-
-    /**
-     * Sets the value of the graphHeight property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setGraphHeight(Integer value) {
-        this.graphHeight = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
-
-    /**
-     * Gets the value of the scoreOnly property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public boolean isScoreOnly() {
-        if (scoreOnly == null) {
-            return false;
-        } else {
-            return scoreOnly;
-        }
-    }
-
-    /**
-     * Sets the value of the scoreOnly property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setScoreOnly(Boolean value) {
-        this.scoreOnly = value;
-    }
-
-    /**
-     * Gets the value of the score property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Double }
-     *     
-     */
-    public Double getScore() {
-        return score;
-    }
+  protected Annotation.ThresholdLine thresholdLine;
+
+  protected List<MatrixType> contactmatrix;
+
+  protected List<Property> property;
+
+  @XmlAttribute(name = "graph", required = true)
+  protected boolean graph;
+
+  @XmlAttribute(name = "graphType")
+  protected Integer graphType;
+
+  @XmlAttribute(name = "sequenceRef")
+  protected String sequenceRef;
+
+  @XmlAttribute(name = "groupRef")
+  protected String groupRef;
+
+  @XmlAttribute(name = "graphColour")
+  protected Integer graphColour;
+
+  @XmlAttribute(name = "graphGroup")
+  protected Integer graphGroup;
+
+  @XmlAttribute(name = "graphHeight")
+  protected Integer graphHeight;
+
+  @XmlAttribute(name = "id")
+  protected String id;
+
+  @XmlAttribute(name = "scoreOnly")
+  protected Boolean scoreOnly;
+
+  @XmlAttribute(name = "score")
+  protected Double score;
+
+  @XmlAttribute(name = "visible")
+  protected Boolean visible;
+
+  @XmlAttribute(name = "centreColLabels")
+  protected Boolean centreColLabels;
+
+  @XmlAttribute(name = "scaleColLabels")
+  protected Boolean scaleColLabels;
+
+  @XmlAttribute(name = "showAllColLabels")
+  protected Boolean showAllColLabels;
+
+  @XmlAttribute(name = "autoCalculated")
+  protected Boolean autoCalculated;
+
+  @XmlAttribute(name = "belowAlignment")
+  protected Boolean belowAlignment;
+
+  @XmlAttribute(name = "calcId")
+  protected String calcId;
+
+  /**
+   * Gets the value of the annotationElement property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the annotationElement property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAnnotationElement().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link AnnotationElement }
+   * 
+   * 
+   */
+  public List<AnnotationElement> getAnnotationElement()
+  {
+    if (annotationElement == null)
+    {
+      annotationElement = new ArrayList<AnnotationElement>();
+    }
+    return this.annotationElement;
+  }
+
+  /**
+   * Gets the value of the label property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getLabel()
+  {
+    return label;
+  }
+
+  /**
+   * Sets the value of the label property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setLabel(String value)
+  {
+    this.label = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the thresholdLine property.
+   * 
+   * @return possible object is {@link Annotation.ThresholdLine }
+   * 
+   */
+  public Annotation.ThresholdLine getThresholdLine()
+  {
+    return thresholdLine;
+  }
+
+  /**
+   * Sets the value of the thresholdLine property.
+   * 
+   * @param value
+   *          allowed object is {@link Annotation.ThresholdLine }
+   * 
+   */
+  public void setThresholdLine(Annotation.ThresholdLine value)
+  {
+    this.thresholdLine = value;
+  }
+
+  /**
+   * Gets the value of the contactmatrix property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the contactmatrix property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getContactmatrix().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link MatrixType
+   * }
+   * 
+   * 
+   */
+  public List<MatrixType> getContactmatrix()
+  {
+    if (contactmatrix == null)
+    {
+      contactmatrix = new ArrayList<MatrixType>();
+    }
+    return this.contactmatrix;
+  }
+
+  /**
+   * Gets the value of the property property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the property property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getProperty().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Property }
+   * 
+   * 
+   */
+  public List<Property> getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList<Property>();
+    }
+    return this.property;
+  }
+
+  /**
+   * Gets the value of the graph property.
+   * 
+   */
+  public boolean isGraph()
+  {
+    return graph;
+  }
+
+  /**
+   * Sets the value of the graph property.
+   * 
+   */
+  public void setGraph(boolean value)
+  {
+    this.graph = value;
+  }
+
+  /**
+   * Gets the value of the graphType property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getGraphType()
+  {
+    return graphType;
+  }
+
+  /**
+   * Sets the value of the graphType property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setGraphType(Integer value)
+  {
+    this.graphType = value;
+  }
+
+  /**
+   * Gets the value of the sequenceRef property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSequenceRef()
+  {
+    return sequenceRef;
+  }
+
+  /**
+   * Sets the value of the sequenceRef property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSequenceRef(String value)
+  {
+    this.sequenceRef = value;
+  }
+
+  /**
+   * Gets the value of the groupRef property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getGroupRef()
+  {
+    return groupRef;
+  }
+
+  /**
+   * Sets the value of the groupRef property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setGroupRef(String value)
+  {
+    this.groupRef = value;
+  }
+
+  /**
+   * Gets the value of the graphColour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getGraphColour()
+  {
+    return graphColour;
+  }
+
+  /**
+   * Sets the value of the graphColour property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setGraphColour(Integer value)
+  {
+    this.graphColour = value;
+  }
+
+  /**
+   * Gets the value of the graphGroup property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getGraphGroup()
+  {
+    return graphGroup;
+  }
+
+  /**
+   * Sets the value of the graphGroup property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setGraphGroup(Integer value)
+  {
+    this.graphGroup = value;
+  }
+
+  /**
+   * Gets the value of the graphHeight property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getGraphHeight()
+  {
+    return graphHeight;
+  }
+
+  /**
+   * Sets the value of the graphHeight property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setGraphHeight(Integer value)
+  {
+    this.graphHeight = value;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
+
+  /**
+   * Gets the value of the scoreOnly property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public boolean isScoreOnly()
+  {
+    if (scoreOnly == null)
+    {
+      return false;
+    }
+    else
+    {
+      return scoreOnly;
+    }
+  }
+
+  /**
+   * Sets the value of the scoreOnly property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setScoreOnly(Boolean value)
+  {
+    this.scoreOnly = value;
+  }
+
+  /**
+   * Gets the value of the score property.
+   * 
+   * @return possible object is {@link Double }
+   * 
+   */
+  public Double getScore()
+  {
+    return score;
+  }
+
+  /**
+   * Sets the value of the score property.
+   * 
+   * @param value
+   *          allowed object is {@link Double }
+   * 
+   */
+  public void setScore(Double value)
+  {
+    this.score = value;
+  }
+
+  /**
+   * Gets the value of the visible property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isVisible()
+  {
+    return visible;
+  }
+
+  /**
+   * Sets the value of the visible property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setVisible(Boolean value)
+  {
+    this.visible = value;
+  }
+
+  /**
+   * Gets the value of the centreColLabels property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isCentreColLabels()
+  {
+    return centreColLabels;
+  }
+
+  /**
+   * Sets the value of the centreColLabels property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setCentreColLabels(Boolean value)
+  {
+    this.centreColLabels = value;
+  }
+
+  /**
+   * Gets the value of the scaleColLabels property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isScaleColLabels()
+  {
+    return scaleColLabels;
+  }
+
+  /**
+   * Sets the value of the scaleColLabels property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setScaleColLabels(Boolean value)
+  {
+    this.scaleColLabels = value;
+  }
+
+  /**
+   * Gets the value of the showAllColLabels property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isShowAllColLabels()
+  {
+    return showAllColLabels;
+  }
+
+  /**
+   * Sets the value of the showAllColLabels property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setShowAllColLabels(Boolean value)
+  {
+    this.showAllColLabels = value;
+  }
+
+  /**
+   * Gets the value of the autoCalculated property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public boolean isAutoCalculated()
+  {
+    if (autoCalculated == null)
+    {
+      return false;
+    }
+    else
+    {
+      return autoCalculated;
+    }
+  }
+
+  /**
+   * Sets the value of the autoCalculated property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setAutoCalculated(Boolean value)
+  {
+    this.autoCalculated = value;
+  }
+
+  /**
+   * Gets the value of the belowAlignment property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public boolean isBelowAlignment()
+  {
+    if (belowAlignment == null)
+    {
+      return true;
+    }
+    else
+    {
+      return belowAlignment;
+    }
+  }
+
+  /**
+   * Sets the value of the belowAlignment property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setBelowAlignment(Boolean value)
+  {
+    this.belowAlignment = value;
+  }
+
+  /**
+   * Gets the value of the calcId property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getCalcId()
+  {
+    return calcId;
+  }
+
+  /**
+   * Sets the value of the calcId property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setCalcId(String value)
+  {
+    this.calcId = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class ThresholdLine
+  {
+
+    @XmlAttribute(name = "label")
+    protected String label;
 
-    /**
-     * Sets the value of the score property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Double }
-     *     
-     */
-    public void setScore(Double value) {
-        this.score = value;
-    }
+    @XmlAttribute(name = "value")
+    protected Float value;
 
-    /**
-     * Gets the value of the visible property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isVisible() {
-        return visible;
-    }
+    @XmlAttribute(name = "colour")
+    protected Integer colour;
 
     /**
-     * Sets the value of the visible property.
+     * Gets the value of the label property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setVisible(Boolean value) {
-        this.visible = value;
-    }
-
-    /**
-     * Gets the value of the centreColLabels property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
      */
-    public Boolean isCentreColLabels() {
-        return centreColLabels;
+    public String getLabel()
+    {
+      return label;
     }
 
     /**
-     * Sets the value of the centreColLabels property.
+     * Sets the value of the label property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setCentreColLabels(Boolean value) {
-        this.centreColLabels = value;
-    }
-
-    /**
-     * Gets the value of the scaleColLabels property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
      */
-    public Boolean isScaleColLabels() {
-        return scaleColLabels;
+    public void setLabel(String value)
+    {
+      this.label = value;
     }
 
     /**
-     * Sets the value of the scaleColLabels property.
+     * Gets the value of the value property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setScaleColLabels(Boolean value) {
-        this.scaleColLabels = value;
-    }
-
-    /**
-     * Gets the value of the showAllColLabels property.
+     * @return possible object is {@link Float }
      * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
      */
-    public Boolean isShowAllColLabels() {
-        return showAllColLabels;
+    public Float getValue()
+    {
+      return value;
     }
 
     /**
-     * Sets the value of the showAllColLabels property.
+     * Sets the value of the value property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setShowAllColLabels(Boolean value) {
-        this.showAllColLabels = value;
-    }
-
-    /**
-     * Gets the value of the autoCalculated property.
+     *          allowed object is {@link Float }
      * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
      */
-    public boolean isAutoCalculated() {
-        if (autoCalculated == null) {
-            return false;
-        } else {
-            return autoCalculated;
-        }
+    public void setValue(Float value)
+    {
+      this.value = value;
     }
 
     /**
-     * Sets the value of the autoCalculated property.
+     * Gets the value of the colour property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setAutoCalculated(Boolean value) {
-        this.autoCalculated = value;
-    }
-
-    /**
-     * Gets the value of the belowAlignment property.
+     * @return possible object is {@link Integer }
      * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
      */
-    public boolean isBelowAlignment() {
-        if (belowAlignment == null) {
-            return true;
-        } else {
-            return belowAlignment;
-        }
+    public Integer getColour()
+    {
+      return colour;
     }
 
     /**
-     * Sets the value of the belowAlignment property.
+     * Sets the value of the colour property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setBelowAlignment(Boolean value) {
-        this.belowAlignment = value;
-    }
-
-    /**
-     * Gets the value of the calcId property.
+     *          allowed object is {@link Integer }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getCalcId() {
-        return calcId;
+    public void setColour(Integer value)
+    {
+      this.colour = value;
     }
 
-    /**
-     * Sets the value of the calcId property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setCalcId(String value) {
-        this.calcId = value;
-    }
-
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class ThresholdLine {
-
-        @XmlAttribute(name = "label")
-        protected String label;
-        @XmlAttribute(name = "value")
-        protected Float value;
-        @XmlAttribute(name = "colour")
-        protected Integer colour;
-
-        /**
-         * Gets the value of the label property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getLabel() {
-            return label;
-        }
-
-        /**
-         * Sets the value of the label property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setLabel(String value) {
-            this.label = value;
-        }
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setValue(Float value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the colour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getColour() {
-            return colour;
-        }
-
-        /**
-         * Sets the value of the colour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setColour(Integer value) {
-            this.colour = value;
-        }
-
-    }
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index 27e0cc6..c7bc579 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for AnnotationColourScheme complex type.
+ * <p>
+ * Java class for AnnotationColourScheme complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="AnnotationColourScheme">
@@ -40,215 +41,215 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme {
-
-    @XmlAttribute(name = "aboveThreshold")
-    protected Integer aboveThreshold;
-    @XmlAttribute(name = "annotation")
-    protected String annotation;
-    @XmlAttribute(name = "minColour")
-    protected Integer minColour;
-    @XmlAttribute(name = "maxColour")
-    protected Integer maxColour;
-    @XmlAttribute(name = "colourScheme")
-    protected String colourScheme;
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-    @XmlAttribute(name = "perSequence")
-    protected Boolean perSequence;
-    @XmlAttribute(name = "predefinedColours")
-    protected Boolean predefinedColours;
-
-    /**
-     * Gets the value of the aboveThreshold property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getAboveThreshold() {
-        return aboveThreshold;
-    }
-
-    /**
-     * Sets the value of the aboveThreshold property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setAboveThreshold(Integer value) {
-        this.aboveThreshold = value;
-    }
-
-    /**
-     * Gets the value of the annotation property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getAnnotation() {
-        return annotation;
-    }
-
-    /**
-     * Sets the value of the annotation property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setAnnotation(String value) {
-        this.annotation = value;
-    }
-
-    /**
-     * Gets the value of the minColour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getMinColour() {
-        return minColour;
-    }
-
-    /**
-     * Sets the value of the minColour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setMinColour(Integer value) {
-        this.minColour = value;
-    }
-
-    /**
-     * Gets the value of the maxColour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getMaxColour() {
-        return maxColour;
-    }
-
-    /**
-     * Sets the value of the maxColour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setMaxColour(Integer value) {
-        this.maxColour = value;
-    }
-
-    /**
-     * Gets the value of the colourScheme property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getColourScheme() {
-        return colourScheme;
-    }
-
-    /**
-     * Sets the value of the colourScheme property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setColourScheme(String value) {
-        this.colourScheme = value;
-    }
-
-    /**
-     * Gets the value of the threshold property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Float }
-     *     
-     */
-    public Float getThreshold() {
-        return threshold;
-    }
-
-    /**
-     * Sets the value of the threshold property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Float }
-     *     
-     */
-    public void setThreshold(Float value) {
-        this.threshold = value;
-    }
-
-    /**
-     * Gets the value of the perSequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isPerSequence() {
-        return perSequence;
-    }
-
-    /**
-     * Sets the value of the perSequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setPerSequence(Boolean value) {
-        this.perSequence = value;
-    }
-
-    /**
-     * Gets the value of the predefinedColours property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isPredefinedColours() {
-        return predefinedColours;
-    }
-
-    /**
-     * Sets the value of the predefinedColours property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setPredefinedColours(Boolean value) {
-        this.predefinedColours = value;
-    }
+public class AnnotationColourScheme
+{
+
+  @XmlAttribute(name = "aboveThreshold")
+  protected Integer aboveThreshold;
+
+  @XmlAttribute(name = "annotation")
+  protected String annotation;
+
+  @XmlAttribute(name = "minColour")
+  protected Integer minColour;
+
+  @XmlAttribute(name = "maxColour")
+  protected Integer maxColour;
+
+  @XmlAttribute(name = "colourScheme")
+  protected String colourScheme;
+
+  @XmlAttribute(name = "threshold")
+  protected Float threshold;
+
+  @XmlAttribute(name = "perSequence")
+  protected Boolean perSequence;
+
+  @XmlAttribute(name = "predefinedColours")
+  protected Boolean predefinedColours;
+
+  /**
+   * Gets the value of the aboveThreshold property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getAboveThreshold()
+  {
+    return aboveThreshold;
+  }
+
+  /**
+   * Sets the value of the aboveThreshold property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setAboveThreshold(Integer value)
+  {
+    this.aboveThreshold = value;
+  }
+
+  /**
+   * Gets the value of the annotation property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getAnnotation()
+  {
+    return annotation;
+  }
+
+  /**
+   * Sets the value of the annotation property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setAnnotation(String value)
+  {
+    this.annotation = value;
+  }
+
+  /**
+   * Gets the value of the minColour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getMinColour()
+  {
+    return minColour;
+  }
+
+  /**
+   * Sets the value of the minColour property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setMinColour(Integer value)
+  {
+    this.minColour = value;
+  }
+
+  /**
+   * Gets the value of the maxColour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getMaxColour()
+  {
+    return maxColour;
+  }
+
+  /**
+   * Sets the value of the maxColour property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setMaxColour(Integer value)
+  {
+    this.maxColour = value;
+  }
+
+  /**
+   * Gets the value of the colourScheme property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getColourScheme()
+  {
+    return colourScheme;
+  }
+
+  /**
+   * Sets the value of the colourScheme property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setColourScheme(String value)
+  {
+    this.colourScheme = value;
+  }
+
+  /**
+   * Gets the value of the threshold property.
+   * 
+   * @return possible object is {@link Float }
+   * 
+   */
+  public Float getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * Sets the value of the threshold property.
+   * 
+   * @param value
+   *          allowed object is {@link Float }
+   * 
+   */
+  public void setThreshold(Float value)
+  {
+    this.threshold = value;
+  }
+
+  /**
+   * Gets the value of the perSequence property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isPerSequence()
+  {
+    return perSequence;
+  }
+
+  /**
+   * Sets the value of the perSequence property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setPerSequence(Boolean value)
+  {
+    this.perSequence = value;
+  }
+
+  /**
+   * Gets the value of the predefinedColours property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isPredefinedColours()
+  {
+    return predefinedColours;
+  }
+
+  /**
+   * Sets the value of the predefinedColours property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setPredefinedColours(Boolean value)
+  {
+    this.predefinedColours = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index c5f75e0..e461296 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,11 +13,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -46,158 +47,159 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "displayCharacter",
-    "description",
-    "secondaryStructure",
-    "value"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "displayCharacter", "description", "secondaryStructure", "value" })
 @XmlRootElement(name = "annotationElement")
-public class AnnotationElement {
-
-    protected String displayCharacter;
-    protected String description;
-    protected String secondaryStructure;
-    protected Float value;
-    @XmlAttribute(name = "position", required = true)
-    protected int position;
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
-
-    /**
-     * Gets the value of the displayCharacter property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDisplayCharacter() {
-        return displayCharacter;
-    }
-
-    /**
-     * Sets the value of the displayCharacter property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDisplayCharacter(String value) {
-        this.displayCharacter = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * Gets the value of the secondaryStructure property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSecondaryStructure() {
-        return secondaryStructure;
-    }
-
-    /**
-     * Sets the value of the secondaryStructure property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSecondaryStructure(String value) {
-        this.secondaryStructure = value;
-    }
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Float }
-     *     
-     */
-    public Float getValue() {
-        return value;
-    }
-
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Float }
-     *     
-     */
-    public void setValue(Float value) {
-        this.value = value;
-    }
-
-    /**
-     * Gets the value of the position property.
-     * 
-     */
-    public int getPosition() {
-        return position;
-    }
-
-    /**
-     * Sets the value of the position property.
-     * 
-     */
-    public void setPosition(int value) {
-        this.position = value;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getColour() {
-        return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setColour(Integer value) {
-        this.colour = value;
-    }
+public class AnnotationElement
+{
+
+  protected String displayCharacter;
+
+  protected String description;
+
+  protected String secondaryStructure;
+
+  protected Float value;
+
+  @XmlAttribute(name = "position", required = true)
+  protected int position;
+
+  @XmlAttribute(name = "colour")
+  protected Integer colour;
+
+  /**
+   * Gets the value of the displayCharacter property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDisplayCharacter()
+  {
+    return displayCharacter;
+  }
+
+  /**
+   * Sets the value of the displayCharacter property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDisplayCharacter(String value)
+  {
+    this.displayCharacter = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the secondaryStructure property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSecondaryStructure()
+  {
+    return secondaryStructure;
+  }
+
+  /**
+   * Sets the value of the secondaryStructure property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSecondaryStructure(String value)
+  {
+    this.secondaryStructure = value;
+  }
+
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link Float }
+   * 
+   */
+  public Float getValue()
+  {
+    return value;
+  }
+
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link Float }
+   * 
+   */
+  public void setValue(Float value)
+  {
+    this.value = value;
+  }
+
+  /**
+   * Gets the value of the position property.
+   * 
+   */
+  public int getPosition()
+  {
+    return position;
+  }
+
+  /**
+   * Sets the value of the position property.
+   * 
+   */
+  public void setPosition(int value)
+  {
+    this.position = value;
+  }
+
+  /**
+   * Gets the value of the colour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getColour()
+  {
+    return colour;
+  }
+
+  /**
+   * Sets the value of the colour property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setColour(Integer value)
+  {
+    this.colour = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index 9be9876..b1a738b 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for DoubleMatrix complex type.
+ * <p>
+ * Java class for DoubleMatrix complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="DoubleMatrix">
@@ -41,146 +42,150 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
-    "row",
-    "d",
-    "e"
-})
-public class DoubleMatrix {
-
-    protected List<DoubleVector> row;
-    @XmlElement(name = "D")
-    protected DoubleVector d;
-    @XmlElement(name = "E")
-    protected DoubleVector e;
-    @XmlAttribute(name = "rows")
-    protected Integer rows;
-    @XmlAttribute(name = "columns")
-    protected Integer columns;
-
-    /**
-     * Gets the value of the row property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the row property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getRow().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link DoubleVector }
-     * 
-     * 
-     */
-    public List<DoubleVector> getRow() {
-        if (row == null) {
-            row = new ArrayList<DoubleVector>();
-        }
-        return this.row;
-    }
-
-    /**
-     * Gets the value of the d property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public DoubleVector getD() {
-        return d;
-    }
-
-    /**
-     * Sets the value of the d property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public void setD(DoubleVector value) {
-        this.d = value;
-    }
-
-    /**
-     * Gets the value of the e property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public DoubleVector getE() {
-        return e;
-    }
-
-    /**
-     * Sets the value of the e property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public void setE(DoubleVector value) {
-        this.e = value;
-    }
-
-    /**
-     * Gets the value of the rows property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getRows() {
-        return rows;
-    }
-
-    /**
-     * Sets the value of the rows property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setRows(Integer value) {
-        this.rows = value;
-    }
-
-    /**
-     * Gets the value of the columns property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getColumns() {
-        return columns;
-    }
-
-    /**
-     * Sets the value of the columns property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setColumns(Integer value) {
-        this.columns = value;
+@XmlType(
+  name = "DoubleMatrix",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "row", "d", "e" })
+public class DoubleMatrix
+{
+
+  protected List<DoubleVector> row;
+
+  @XmlElement(name = "D")
+  protected DoubleVector d;
+
+  @XmlElement(name = "E")
+  protected DoubleVector e;
+
+  @XmlAttribute(name = "rows")
+  protected Integer rows;
+
+  @XmlAttribute(name = "columns")
+  protected Integer columns;
+
+  /**
+   * Gets the value of the row property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the row property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getRow().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link DoubleVector }
+   * 
+   * 
+   */
+  public List<DoubleVector> getRow()
+  {
+    if (row == null)
+    {
+      row = new ArrayList<DoubleVector>();
     }
+    return this.row;
+  }
+
+  /**
+   * Gets the value of the d property.
+   * 
+   * @return possible object is {@link DoubleVector }
+   * 
+   */
+  public DoubleVector getD()
+  {
+    return d;
+  }
+
+  /**
+   * Sets the value of the d property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleVector }
+   * 
+   */
+  public void setD(DoubleVector value)
+  {
+    this.d = value;
+  }
+
+  /**
+   * Gets the value of the e property.
+   * 
+   * @return possible object is {@link DoubleVector }
+   * 
+   */
+  public DoubleVector getE()
+  {
+    return e;
+  }
+
+  /**
+   * Sets the value of the e property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleVector }
+   * 
+   */
+  public void setE(DoubleVector value)
+  {
+    this.e = value;
+  }
+
+  /**
+   * Gets the value of the rows property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getRows()
+  {
+    return rows;
+  }
+
+  /**
+   * Sets the value of the rows property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setRows(Integer value)
+  {
+    this.rows = value;
+  }
+
+  /**
+   * Gets the value of the columns property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getColumns()
+  {
+    return columns;
+  }
+
+  /**
+   * Sets the value of the columns property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setColumns(Integer value)
+  {
+    this.columns = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index 6546be9..12f39c0 100644
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for DoubleVector complex type.
+ * <p>
+ * Java class for DoubleVector complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="DoubleVector">
@@ -36,41 +37,46 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
-    "v"
-})
-public class DoubleVector {
+@XmlType(
+  name = "DoubleVector",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "v" })
+public class DoubleVector
+{
 
-    @XmlElement(type = Double.class)
-    protected List<Double> v;
+  @XmlElement(type = Double.class)
+  protected List<Double> v;
 
-    /**
-     * Gets the value of the v property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the v property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getV().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Double }
-     * 
-     * 
-     */
-    public List<Double> getV() {
-        if (v == null) {
-            v = new ArrayList<Double>();
-        }
-        return this.v;
+  /**
+   * Gets the value of the v property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the v property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getV().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Double }
+   * 
+   * 
+   */
+  public List<Double> getV()
+  {
+    if (v == null)
+    {
+      v = new ArrayList<Double>();
     }
+    return this.v;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index a124e62..9ac7b58 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for feature complex type.
+ * <p>
+ * Java class for feature complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="feature">
@@ -53,311 +54,325 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
-    "otherData"
-})
-public class Feature {
-
-    protected List<Feature.OtherData> otherData;
-    @XmlAttribute(name = "begin", required = true)
-    protected int begin;
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "description")
-    protected String description;
-    @XmlAttribute(name = "status")
-    protected String status;
-    @XmlAttribute(name = "featureGroup")
-    protected String featureGroup;
-    @XmlAttribute(name = "score")
-    protected Float score;
-
-    /**
-     * Gets the value of the otherData property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the otherData property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getOtherData().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Feature.OtherData }
-     * 
-     * 
-     */
-    public List<Feature.OtherData> getOtherData() {
-        if (otherData == null) {
-            otherData = new ArrayList<Feature.OtherData>();
-        }
-        return this.otherData;
+@XmlType(
+  name = "feature",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "otherData" })
+public class Feature
+{
+
+  protected List<Feature.OtherData> otherData;
+
+  @XmlAttribute(name = "begin", required = true)
+  protected int begin;
+
+  @XmlAttribute(name = "end", required = true)
+  protected int end;
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
+
+  @XmlAttribute(name = "description")
+  protected String description;
+
+  @XmlAttribute(name = "status")
+  protected String status;
+
+  @XmlAttribute(name = "featureGroup")
+  protected String featureGroup;
+
+  @XmlAttribute(name = "score")
+  protected Float score;
+
+  /**
+   * Gets the value of the otherData property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the otherData property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getOtherData().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link Feature.OtherData }
+   * 
+   * 
+   */
+  public List<Feature.OtherData> getOtherData()
+  {
+    if (otherData == null)
+    {
+      otherData = new ArrayList<Feature.OtherData>();
     }
+    return this.otherData;
+  }
+
+  /**
+   * Gets the value of the begin property.
+   * 
+   */
+  public int getBegin()
+  {
+    return begin;
+  }
+
+  /**
+   * Sets the value of the begin property.
+   * 
+   */
+  public void setBegin(int value)
+  {
+    this.begin = value;
+  }
+
+  /**
+   * Gets the value of the end property.
+   * 
+   */
+  public int getEnd()
+  {
+    return end;
+  }
+
+  /**
+   * Sets the value of the end property.
+   * 
+   */
+  public void setEnd(int value)
+  {
+    this.end = value;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the status property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getStatus()
+  {
+    return status;
+  }
+
+  /**
+   * Sets the value of the status property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setStatus(String value)
+  {
+    this.status = value;
+  }
+
+  /**
+   * Gets the value of the featureGroup property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getFeatureGroup()
+  {
+    return featureGroup;
+  }
+
+  /**
+   * Sets the value of the featureGroup property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setFeatureGroup(String value)
+  {
+    this.featureGroup = value;
+  }
+
+  /**
+   * Gets the value of the score property.
+   * 
+   * @return possible object is {@link Float }
+   * 
+   */
+  public Float getScore()
+  {
+    return score;
+  }
+
+  /**
+   * Sets the value of the score property.
+   * 
+   * @param value
+   *          allowed object is {@link Float }
+   * 
+   */
+  public void setScore(Float value)
+  {
+    this.score = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class OtherData
+  {
+
+    @XmlAttribute(name = "key", required = true)
+    protected String key;
+
+    @XmlAttribute(name = "key2")
+    protected String key2;
+
+    @XmlAttribute(name = "value", required = true)
+    protected String value;
 
     /**
-     * Gets the value of the begin property.
+     * Gets the value of the key property.
      * 
-     */
-    public int getBegin() {
-        return begin;
-    }
-
-    /**
-     * Sets the value of the begin property.
-     * 
-     */
-    public void setBegin(int value) {
-        this.begin = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     */
-    public int getEnd() {
-        return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     */
-    public void setEnd(int value) {
-        this.end = value;
-    }
-
-    /**
-     * Gets the value of the type property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getType() {
-        return type;
+    public String getKey()
+    {
+      return key;
     }
 
     /**
-     * Sets the value of the type property.
+     * Sets the value of the key property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
-
-    /**
-     * Gets the value of the description property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getDescription() {
-        return description;
+    public void setKey(String value)
+    {
+      this.key = value;
     }
 
     /**
-     * Sets the value of the description property.
+     * Gets the value of the key2 property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * Gets the value of the status property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getStatus() {
-        return status;
+    public String getKey2()
+    {
+      return key2;
     }
 
     /**
-     * Sets the value of the status property.
+     * Sets the value of the key2 property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setStatus(String value) {
-        this.status = value;
-    }
-
-    /**
-     * Gets the value of the featureGroup property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getFeatureGroup() {
-        return featureGroup;
+    public void setKey2(String value)
+    {
+      this.key2 = value;
     }
 
     /**
-     * Sets the value of the featureGroup property.
+     * Gets the value of the value property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setFeatureGroup(String value) {
-        this.featureGroup = value;
-    }
-
-    /**
-     * Gets the value of the score property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link Float }
-     *     
      */
-    public Float getScore() {
-        return score;
+    public String getValue()
+    {
+      return value;
     }
 
     /**
-     * Sets the value of the score property.
+     * Sets the value of the value property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link Float }
-     *     
-     */
-    public void setScore(Float value) {
-        this.score = value;
-    }
-
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class OtherData {
-
-        @XmlAttribute(name = "key", required = true)
-        protected String key;
-        @XmlAttribute(name = "key2")
-        protected String key2;
-        @XmlAttribute(name = "value", required = true)
-        protected String value;
-
-        /**
-         * Gets the value of the key property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getKey() {
-            return key;
-        }
-
-        /**
-         * Sets the value of the key property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setKey(String value) {
-            this.key = value;
-        }
-
-        /**
-         * Gets the value of the key2 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getKey2() {
-            return key2;
-        }
-
-        /**
-         * Sets the value of the key2 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setKey2(String value) {
-            this.key2 = value;
-        }
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
+    public void setValue(String value)
+    {
+      this.value = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index 61e66ce..1b1abff 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for FeatureMatcher complex type.
+ * <p>
+ * Java class for FeatureMatcher complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="FeatureMatcher">
@@ -40,121 +41,124 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
-    "attributeName",
-    "condition",
-    "value"
-})
-public class FeatureMatcher {
+@XmlType(
+  name = "FeatureMatcher",
+  namespace = "www.jalview.org/colours",
+  propOrder =
+  { "attributeName", "condition", "value" })
+public class FeatureMatcher
+{
 
-    @XmlElement(namespace = "")
-    protected List<String> attributeName;
-    @XmlElement(namespace = "", required = true)
-    protected String condition;
-    @XmlElement(namespace = "", required = true)
-    protected String value;
-    @XmlAttribute(name = "by")
-    protected FilterBy by;
+  @XmlElement(namespace = "")
+  protected List<String> attributeName;
 
-    /**
-     * Gets the value of the attributeName property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the attributeName property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getAttributeName().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getAttributeName() {
-        if (attributeName == null) {
-            attributeName = new ArrayList<String>();
-        }
-        return this.attributeName;
-    }
+  @XmlElement(namespace = "", required = true)
+  protected String condition;
 
-    /**
-     * Gets the value of the condition property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getCondition() {
-        return condition;
-    }
+  @XmlElement(namespace = "", required = true)
+  protected String value;
 
-    /**
-     * Sets the value of the condition property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setCondition(String value) {
-        this.condition = value;
-    }
+  @XmlAttribute(name = "by")
+  protected FilterBy by;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
+  /**
+   * Gets the value of the attributeName property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the attributeName property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAttributeName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getAttributeName()
+  {
+    if (attributeName == null)
+    {
+      attributeName = new ArrayList<String>();
     }
+    return this.attributeName;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Gets the value of the condition property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getCondition()
+  {
+    return condition;
+  }
 
-    /**
-     * Gets the value of the by property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link FilterBy }
-     *     
-     */
-    public FilterBy getBy() {
-        return by;
-    }
+  /**
+   * Sets the value of the condition property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setCondition(String value)
+  {
+    this.condition = value;
+  }
 
-    /**
-     * Sets the value of the by property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link FilterBy }
-     *     
-     */
-    public void setBy(FilterBy value) {
-        this.by = value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
+
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
+
+  /**
+   * Gets the value of the by property.
+   * 
+   * @return possible object is {@link FilterBy }
+   * 
+   */
+  public FilterBy getBy()
+  {
+    return by;
+  }
+
+  /**
+   * Sets the value of the by property.
+   * 
+   * @param value
+   *          allowed object is {@link FilterBy }
+   * 
+   */
+  public void setBy(FilterBy value)
+  {
+    this.by = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index 24190b8..a071af8 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * A feature match condition, which may be simple or compound
  * 
- * <p>Java class for FeatureMatcherSet complex type.
+ * <p>
+ * Java class for FeatureMatcherSet complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="FeatureMatcherSet">
@@ -51,142 +52,150 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
-    "matchCondition",
-    "compoundMatcher"
-})
-public class FeatureMatcherSet {
-
-    @XmlElement(namespace = "")
-    protected FeatureMatcher matchCondition;
-    @XmlElement(namespace = "")
-    protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+@XmlType(
+  name = "FeatureMatcherSet",
+  namespace = "www.jalview.org/colours",
+  propOrder =
+  { "matchCondition", "compoundMatcher" })
+public class FeatureMatcherSet
+{
+
+  @XmlElement(namespace = "")
+  protected FeatureMatcher matchCondition;
+
+  @XmlElement(namespace = "")
+  protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+
+  /**
+   * Gets the value of the matchCondition property.
+   * 
+   * @return possible object is {@link FeatureMatcher }
+   * 
+   */
+  public FeatureMatcher getMatchCondition()
+  {
+    return matchCondition;
+  }
+
+  /**
+   * Sets the value of the matchCondition property.
+   * 
+   * @param value
+   *          allowed object is {@link FeatureMatcher }
+   * 
+   */
+  public void setMatchCondition(FeatureMatcher value)
+  {
+    this.matchCondition = value;
+  }
+
+  /**
+   * Gets the value of the compoundMatcher property.
+   * 
+   * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
+   * 
+   */
+  public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
+  {
+    return compoundMatcher;
+  }
+
+  /**
+   * Sets the value of the compoundMatcher property.
+   * 
+   * @param value
+   *          allowed object is {@link FeatureMatcherSet.CompoundMatcher }
+   * 
+   */
+  public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
+  {
+    this.compoundMatcher = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "matcherSet" })
+  public static class CompoundMatcher
+  {
+
+    @XmlElement(namespace = "", required = true)
+    protected List<FeatureMatcherSet> matcherSet;
+
+    @XmlAttribute(name = "and", required = true)
+    protected boolean and;
 
     /**
-     * Gets the value of the matchCondition property.
+     * Gets the value of the matcherSet property.
      * 
-     * @return
-     *     possible object is
-     *     {@link FeatureMatcher }
-     *     
-     */
-    public FeatureMatcher getMatchCondition() {
-        return matchCondition;
-    }
-
-    /**
-     * Sets the value of the matchCondition property.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the matcherSet property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getMatcherSet().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link FeatureMatcherSet }
      * 
-     * @param value
-     *     allowed object is
-     *     {@link FeatureMatcher }
-     *     
-     */
-    public void setMatchCondition(FeatureMatcher value) {
-        this.matchCondition = value;
-    }
-
-    /**
-     * Gets the value of the compoundMatcher property.
      * 
-     * @return
-     *     possible object is
-     *     {@link FeatureMatcherSet.CompoundMatcher }
-     *     
      */
-    public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
-        return compoundMatcher;
+    public List<FeatureMatcherSet> getMatcherSet()
+    {
+      if (matcherSet == null)
+      {
+        matcherSet = new ArrayList<FeatureMatcherSet>();
+      }
+      return this.matcherSet;
     }
 
     /**
-     * Sets the value of the compoundMatcher property.
+     * Gets the value of the and property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link FeatureMatcherSet.CompoundMatcher }
-     *     
      */
-    public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
-        this.compoundMatcher = value;
+    public boolean isAnd()
+    {
+      return and;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
+     * Sets the value of the and property.
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "matcherSet"
-    })
-    public static class CompoundMatcher {
-
-        @XmlElement(namespace = "", required = true)
-        protected List<FeatureMatcherSet> matcherSet;
-        @XmlAttribute(name = "and", required = true)
-        protected boolean and;
-
-        /**
-         * Gets the value of the matcherSet property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getMatcherSet().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link FeatureMatcherSet }
-         * 
-         * 
-         */
-        public List<FeatureMatcherSet> getMatcherSet() {
-            if (matcherSet == null) {
-                matcherSet = new ArrayList<FeatureMatcherSet>();
-            }
-            return this.matcherSet;
-        }
-
-        /**
-         * Gets the value of the and property.
-         * 
-         */
-        public boolean isAnd() {
-            return and;
-        }
-
-        /**
-         * Sets the value of the and property.
-         * 
-         */
-        public void setAnd(boolean value) {
-            this.and = value;
-        }
-
+    public void setAnd(boolean value)
+    {
+      this.and = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java
index 3a9428c..d71051e 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -5,19 +5,21 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for FilterBy.
+ * <p>
+ * Java class for FilterBy.
  * 
- * <p>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.
+ * <p>
+ * 
  * <pre>
  * &lt;simpleType name="FilterBy">
  *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -31,31 +33,36 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum FilterBy {
-
-    @XmlEnumValue("byLabel")
-    BY_LABEL("byLabel"),
-    @XmlEnumValue("byScore")
-    BY_SCORE("byScore"),
-    @XmlEnumValue("byAttribute")
-    BY_ATTRIBUTE("byAttribute");
-    private final String value;
-
-    FilterBy(String v) {
-        value = v;
-    }
+public enum FilterBy
+{
 
-    public String value() {
-        return value;
-    }
+  @XmlEnumValue("byLabel")
+  BY_LABEL("byLabel"), @XmlEnumValue("byScore")
+  BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
+  BY_ATTRIBUTE("byAttribute");
+
+  private final String value;
+
+  FilterBy(String v)
+  {
+    value = v;
+  }
+
+  public String value()
+  {
+    return value;
+  }
 
-    public static FilterBy fromValue(String v) {
-        for (FilterBy c: FilterBy.values()) {
-            if (c.value.equals(v)) {
-                return c;
-            }
-        }
-        throw new IllegalArgumentException(v);
+  public static FilterBy fromValue(String v)
+  {
+    for (FilterBy c : FilterBy.values())
+    {
+      if (c.value.equals(v))
+      {
+        return c;
+      }
     }
+    throw new IllegalArgumentException(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 22b2533..b77d98d 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -22,11 +21,13 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 import javax.xml.datatype.XMLGregorianCalendar;
 
-
 /**
- * <p>Java class for JalviewModel complex type.
+ * <p>
+ * Java class for JalviewModel complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="JalviewModel">
@@ -381,2762 +382,3475 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
-    "creationDate",
-    "version",
-    "vamsasModel",
-    "jSeq",
-    "jGroup",
-    "viewport",
-    "userColours",
-    "tree",
-    "pcaViewer",
-    "featureSettings"
-})
-public class JalviewModel {
-
-    @XmlElement(required = true)
-    @XmlSchemaType(name = "dateTime")
-    protected XMLGregorianCalendar creationDate;
-    @XmlElement(required = true)
-    protected String version;
-    @XmlElement(required = true)
-    protected VAMSAS vamsasModel;
-    @XmlElement(name = "JSeq")
-    protected List<JalviewModel.JSeq> jSeq;
-    @XmlElement(name = "JGroup")
-    protected List<JalviewModel.JGroup> jGroup;
-    @XmlElement(name = "Viewport")
-    protected List<JalviewModel.Viewport> viewport;
-    @XmlElement(name = "UserColours")
-    protected List<JalviewModel.UserColours> userColours;
-    protected List<JalviewModel.Tree> tree;
-    @XmlElement(name = "PcaViewer")
-    protected List<JalviewModel.PcaViewer> pcaViewer;
-    @XmlElement(name = "FeatureSettings")
-    protected JalviewModel.FeatureSettings featureSettings;
-
-    /**
-     * Gets the value of the creationDate property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public XMLGregorianCalendar getCreationDate() {
-        return creationDate;
-    }
-
-    /**
-     * Sets the value of the creationDate property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setCreationDate(XMLGregorianCalendar value) {
-        this.creationDate = value;
+@XmlType(
+  name = "JalviewModel",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+      "userColours", "tree", "pcaViewer", "featureSettings" })
+public class JalviewModel
+{
+
+  @XmlElement(required = true)
+  @XmlSchemaType(name = "dateTime")
+  protected XMLGregorianCalendar creationDate;
+
+  @XmlElement(required = true)
+  protected String version;
+
+  @XmlElement(required = true)
+  protected VAMSAS vamsasModel;
+
+  @XmlElement(name = "JSeq")
+  protected List<JalviewModel.JSeq> jSeq;
+
+  @XmlElement(name = "JGroup")
+  protected List<JalviewModel.JGroup> jGroup;
+
+  @XmlElement(name = "Viewport")
+  protected List<JalviewModel.Viewport> viewport;
+
+  @XmlElement(name = "UserColours")
+  protected List<JalviewModel.UserColours> userColours;
+
+  protected List<JalviewModel.Tree> tree;
+
+  @XmlElement(name = "PcaViewer")
+  protected List<JalviewModel.PcaViewer> pcaViewer;
+
+  @XmlElement(name = "FeatureSettings")
+  protected JalviewModel.FeatureSettings featureSettings;
+
+  /**
+   * Gets the value of the creationDate property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getCreationDate()
+  {
+    return creationDate;
+  }
+
+  /**
+   * Sets the value of the creationDate property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setCreationDate(XMLGregorianCalendar value)
+  {
+    this.creationDate = value;
+  }
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the vamsasModel property.
+   * 
+   * @return possible object is {@link VAMSAS }
+   * 
+   */
+  public VAMSAS getVamsasModel()
+  {
+    return vamsasModel;
+  }
+
+  /**
+   * Sets the value of the vamsasModel property.
+   * 
+   * @param value
+   *          allowed object is {@link VAMSAS }
+   * 
+   */
+  public void setVamsasModel(VAMSAS value)
+  {
+    this.vamsasModel = value;
+  }
+
+  /**
+   * Gets the value of the jSeq property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the jSeq property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getJSeq().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewModel.JSeq }
+   * 
+   * 
+   */
+  public List<JalviewModel.JSeq> getJSeq()
+  {
+    if (jSeq == null)
+    {
+      jSeq = new ArrayList<JalviewModel.JSeq>();
     }
-
-    /**
-     * Gets the value of the version property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getVersion() {
-        return version;
+    return this.jSeq;
+  }
+
+  /**
+   * Gets the value of the jGroup property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the jGroup property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getJGroup().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewModel.JGroup }
+   * 
+   * 
+   */
+  public List<JalviewModel.JGroup> getJGroup()
+  {
+    if (jGroup == null)
+    {
+      jGroup = new ArrayList<JalviewModel.JGroup>();
     }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setVersion(String value) {
-        this.version = value;
+    return this.jGroup;
+  }
+
+  /**
+   * Gets the value of the viewport property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the viewport property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getViewport().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewModel.Viewport }
+   * 
+   * 
+   */
+  public List<JalviewModel.Viewport> getViewport()
+  {
+    if (viewport == null)
+    {
+      viewport = new ArrayList<JalviewModel.Viewport>();
     }
-
-    /**
-     * Gets the value of the vamsasModel property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link VAMSAS }
-     *     
-     */
-    public VAMSAS getVamsasModel() {
-        return vamsasModel;
+    return this.viewport;
+  }
+
+  /**
+   * Gets the value of the userColours property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the userColours property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getUserColours().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewModel.UserColours }
+   * 
+   * 
+   */
+  public List<JalviewModel.UserColours> getUserColours()
+  {
+    if (userColours == null)
+    {
+      userColours = new ArrayList<JalviewModel.UserColours>();
     }
-
-    /**
-     * Sets the value of the vamsasModel property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link VAMSAS }
-     *     
-     */
-    public void setVamsasModel(VAMSAS value) {
-        this.vamsasModel = value;
+    return this.userColours;
+  }
+
+  /**
+   * Gets the value of the tree property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the tree property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getTree().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewModel.Tree }
+   * 
+   * 
+   */
+  public List<JalviewModel.Tree> getTree()
+  {
+    if (tree == null)
+    {
+      tree = new ArrayList<JalviewModel.Tree>();
+    }
+    return this.tree;
+  }
+
+  /**
+   * Gets the value of the pcaViewer property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the pcaViewer property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getPcaViewer().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewModel.PcaViewer }
+   * 
+   * 
+   */
+  public List<JalviewModel.PcaViewer> getPcaViewer()
+  {
+    if (pcaViewer == null)
+    {
+      pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
     }
+    return this.pcaViewer;
+  }
+
+  /**
+   * Gets the value of the featureSettings property.
+   * 
+   * @return possible object is {@link JalviewModel.FeatureSettings }
+   * 
+   */
+  public JalviewModel.FeatureSettings getFeatureSettings()
+  {
+    return featureSettings;
+  }
+
+  /**
+   * Sets the value of the featureSettings property.
+   * 
+   * @param value
+   *          allowed object is {@link JalviewModel.FeatureSettings }
+   * 
+   */
+  public void setFeatureSettings(JalviewModel.FeatureSettings value)
+  {
+    this.featureSettings = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;sequence>
+   *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+   *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+   *                 &lt;/sequence>
+   *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+   *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "setting", "group" })
+  public static class FeatureSettings
+  {
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List<JalviewModel.FeatureSettings.Setting> setting;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List<JalviewModel.FeatureSettings.Group> group;
 
     /**
-     * Gets the value of the jSeq property.
+     * Gets the value of the setting property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the setting property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getJSeq().add(newItem);
+     * getSetting().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JSeq }
+     * {@link JalviewModel.FeatureSettings.Setting }
      * 
      * 
      */
-    public List<JalviewModel.JSeq> getJSeq() {
-        if (jSeq == null) {
-            jSeq = new ArrayList<JalviewModel.JSeq>();
-        }
-        return this.jSeq;
+    public List<JalviewModel.FeatureSettings.Setting> getSetting()
+    {
+      if (setting == null)
+      {
+        setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+      }
+      return this.setting;
     }
 
     /**
-     * Gets the value of the jGroup property.
+     * Gets the value of the group property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the group property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getJGroup().add(newItem);
+     * getGroup().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JGroup }
+     * {@link JalviewModel.FeatureSettings.Group }
      * 
      * 
      */
-    public List<JalviewModel.JGroup> getJGroup() {
-        if (jGroup == null) {
-            jGroup = new ArrayList<JalviewModel.JGroup>();
-        }
-        return this.jGroup;
+    public List<JalviewModel.FeatureSettings.Group> getGroup()
+    {
+      if (group == null)
+      {
+        group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+      }
+      return this.group;
     }
 
     /**
-     * Gets the value of the viewport property.
-     * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the viewport property.
+     * Java class for anonymous complex type.
      * 
      * <p>
-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * <pre>
-     *    getViewport().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Group
+    {
+
+      @XmlAttribute(name = "name", required = true)
+      protected String name;
+
+      @XmlAttribute(name = "display", required = true)
+      protected boolean display;
+
+      /**
+       * Gets the value of the name property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getName()
+      {
+        return name;
+      }
+
+      /**
+       * Sets the value of the name property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setName(String value)
+      {
+        this.name = value;
+      }
+
+      /**
+       * Gets the value of the display property.
+       * 
+       */
+      public boolean isDisplay()
+      {
+        return display;
+      }
+
+      /**
+       * Sets the value of the display property.
+       * 
+       */
+      public void setDisplay(boolean value)
+      {
+        this.display = value;
+      }
+
+    }
+
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
      * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Viewport }
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
      * 
      * 
      */
-    public List<JalviewModel.Viewport> getViewport() {
-        if (viewport == null) {
-            viewport = new ArrayList<JalviewModel.Viewport>();
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+    public static class Setting
+    {
+
+      @XmlElement(namespace = "www.jalview.org")
+      protected List<String> attributeName;
+
+      @XmlElement(namespace = "www.jalview.org")
+      protected FeatureMatcherSet matcherSet;
+
+      @XmlAttribute(name = "type", required = true)
+      protected String type;
+
+      @XmlAttribute(name = "colour", required = true)
+      protected int colour;
+
+      @XmlAttribute(name = "display", required = true)
+      protected boolean display;
+
+      @XmlAttribute(name = "order")
+      protected Float order;
+
+      @XmlAttribute(name = "mincolour")
+      protected Integer mincolour;
+
+      @XmlAttribute(name = "noValueColour")
+      protected NoValueColour noValueColour;
+
+      @XmlAttribute(name = "threshold")
+      protected Float threshold;
+
+      @XmlAttribute(name = "threshstate")
+      protected Integer threshstate;
+
+      @XmlAttribute(name = "max")
+      protected Float max;
+
+      @XmlAttribute(name = "min")
+      protected Float min;
+
+      @XmlAttribute(name = "colourByLabel")
+      protected Boolean colourByLabel;
+
+      @XmlAttribute(name = "autoScale")
+      protected Boolean autoScale;
+
+      /**
+       * Gets the value of the attributeName property.
+       * 
+       * <p>
+       * This accessor method returns a reference to the live list, not a
+       * snapshot. Therefore any modification you make to the returned list will
+       * be present inside the JAXB object. This is why there is not a
+       * <CODE>set</CODE> method for the attributeName property.
+       * 
+       * <p>
+       * For example, to add a new item, do as follows:
+       * 
+       * <pre>
+       * getAttributeName().add(newItem);
+       * </pre>
+       * 
+       * 
+       * <p>
+       * Objects of the following type(s) are allowed in the list {@link String
+       * }
+       * 
+       * 
+       */
+      public List<String> getAttributeName()
+      {
+        if (attributeName == null)
+        {
+          attributeName = new ArrayList<String>();
+        }
+        return this.attributeName;
+      }
+
+      /**
+       * Gets the value of the matcherSet property.
+       * 
+       * @return possible object is {@link FeatureMatcherSet }
+       * 
+       */
+      public FeatureMatcherSet getMatcherSet()
+      {
+        return matcherSet;
+      }
+
+      /**
+       * Sets the value of the matcherSet property.
+       * 
+       * @param value
+       *          allowed object is {@link FeatureMatcherSet }
+       * 
+       */
+      public void setMatcherSet(FeatureMatcherSet value)
+      {
+        this.matcherSet = value;
+      }
+
+      /**
+       * Gets the value of the type property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getType()
+      {
+        return type;
+      }
+
+      /**
+       * Sets the value of the type property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setType(String value)
+      {
+        this.type = value;
+      }
+
+      /**
+       * Gets the value of the colour property.
+       * 
+       */
+      public int getColour()
+      {
+        return colour;
+      }
+
+      /**
+       * Sets the value of the colour property.
+       * 
+       */
+      public void setColour(int value)
+      {
+        this.colour = value;
+      }
+
+      /**
+       * Gets the value of the display property.
+       * 
+       */
+      public boolean isDisplay()
+      {
+        return display;
+      }
+
+      /**
+       * Sets the value of the display property.
+       * 
+       */
+      public void setDisplay(boolean value)
+      {
+        this.display = value;
+      }
+
+      /**
+       * Gets the value of the order property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getOrder()
+      {
+        return order;
+      }
+
+      /**
+       * Sets the value of the order property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setOrder(Float value)
+      {
+        this.order = value;
+      }
+
+      /**
+       * Gets the value of the mincolour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getMincolour()
+      {
+        return mincolour;
+      }
+
+      /**
+       * Sets the value of the mincolour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setMincolour(Integer value)
+      {
+        this.mincolour = value;
+      }
+
+      /**
+       * Gets the value of the noValueColour property.
+       * 
+       * @return possible object is {@link NoValueColour }
+       * 
+       */
+      public NoValueColour getNoValueColour()
+      {
+        if (noValueColour == null)
+        {
+          return NoValueColour.MIN;
         }
-        return this.viewport;
+        else
+        {
+          return noValueColour;
+        }
+      }
+
+      /**
+       * Sets the value of the noValueColour property.
+       * 
+       * @param value
+       *          allowed object is {@link NoValueColour }
+       * 
+       */
+      public void setNoValueColour(NoValueColour value)
+      {
+        this.noValueColour = value;
+      }
+
+      /**
+       * Gets the value of the threshold property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getThreshold()
+      {
+        return threshold;
+      }
+
+      /**
+       * Sets the value of the threshold property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setThreshold(Float value)
+      {
+        this.threshold = value;
+      }
+
+      /**
+       * Gets the value of the threshstate property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getThreshstate()
+      {
+        return threshstate;
+      }
+
+      /**
+       * Sets the value of the threshstate property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setThreshstate(Integer value)
+      {
+        this.threshstate = value;
+      }
+
+      /**
+       * Gets the value of the max property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getMax()
+      {
+        return max;
+      }
+
+      /**
+       * Sets the value of the max property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setMax(Float value)
+      {
+        this.max = value;
+      }
+
+      /**
+       * Gets the value of the min property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getMin()
+      {
+        return min;
+      }
+
+      /**
+       * Sets the value of the min property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setMin(Float value)
+      {
+        this.min = value;
+      }
+
+      /**
+       * Gets the value of the colourByLabel property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public Boolean isColourByLabel()
+      {
+        return colourByLabel;
+      }
+
+      /**
+       * Sets the value of the colourByLabel property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setColourByLabel(Boolean value)
+      {
+        this.colourByLabel = value;
+      }
+
+      /**
+       * Gets the value of the autoScale property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public Boolean isAutoScale()
+      {
+        return autoScale;
+      }
+
+      /**
+       * Sets the value of the autoScale property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setAutoScale(Boolean value)
+      {
+        this.autoScale = value;
+      }
+
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+   *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+  public static class JGroup
+  {
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List<String> seq;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected AnnotationColourScheme annotationColours;
+
+    @XmlAttribute(name = "start")
+    protected Integer start;
+
+    @XmlAttribute(name = "end")
+    protected Integer end;
+
+    @XmlAttribute(name = "name")
+    protected String name;
+
+    @XmlAttribute(name = "colour")
+    protected String colour;
+
+    @XmlAttribute(name = "consThreshold")
+    protected Integer consThreshold;
+
+    @XmlAttribute(name = "pidThreshold")
+    protected Integer pidThreshold;
+
+    @XmlAttribute(name = "outlineColour")
+    protected Integer outlineColour;
+
+    @XmlAttribute(name = "displayBoxes")
+    protected Boolean displayBoxes;
+
+    @XmlAttribute(name = "displayText")
+    protected Boolean displayText;
+
+    @XmlAttribute(name = "colourText")
+    protected Boolean colourText;
+
+    @XmlAttribute(name = "textCol1")
+    protected Integer textCol1;
+
+    @XmlAttribute(name = "textCol2")
+    protected Integer textCol2;
+
+    @XmlAttribute(name = "textColThreshold")
+    protected Integer textColThreshold;
+
+    @XmlAttribute(name = "showUnconserved")
+    protected Boolean showUnconserved;
+
+    @XmlAttribute(name = "ignoreGapsinConsensus")
+    protected Boolean ignoreGapsinConsensus;
+
+    @XmlAttribute(name = "showConsensusHistogram")
+    protected Boolean showConsensusHistogram;
+
+    @XmlAttribute(name = "showSequenceLogo")
+    protected Boolean showSequenceLogo;
+
+    @XmlAttribute(name = "normaliseSequenceLogo")
+    protected Boolean normaliseSequenceLogo;
+
+    @XmlAttribute(name = "id")
+    protected String id;
+
     /**
-     * Gets the value of the userColours property.
+     * Gets the value of the seq property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the userColours property.
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the seq property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getUserColours().add(newItem);
+     * getSeq().add(newItem);
      * </pre>
      * 
      * 
      * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.UserColours }
+     * Objects of the following type(s) are allowed in the list {@link String }
      * 
      * 
      */
-    public List<JalviewModel.UserColours> getUserColours() {
-        if (userColours == null) {
-            userColours = new ArrayList<JalviewModel.UserColours>();
-        }
-        return this.userColours;
+    public List<String> getSeq()
+    {
+      if (seq == null)
+      {
+        seq = new ArrayList<String>();
+      }
+      return this.seq;
     }
 
     /**
-     * Gets the value of the tree property.
+     * Gets the value of the annotationColours property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the tree property.
+     * @return possible object is {@link AnnotationColourScheme }
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getTree().add(newItem);
-     * </pre>
+     */
+    public AnnotationColourScheme getAnnotationColours()
+    {
+      return annotationColours;
+    }
+
+    /**
+     * Sets the value of the annotationColours property.
      * 
+     * @param value
+     *          allowed object is {@link AnnotationColourScheme }
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Tree }
+     */
+    public void setAnnotationColours(AnnotationColourScheme value)
+    {
+      this.annotationColours = value;
+    }
+
+    /**
+     * Gets the value of the start property.
      * 
+     * @return possible object is {@link Integer }
      * 
      */
-    public List<JalviewModel.Tree> getTree() {
-        if (tree == null) {
-            tree = new ArrayList<JalviewModel.Tree>();
-        }
-        return this.tree;
+    public Integer getStart()
+    {
+      return start;
     }
 
     /**
-     * Gets the value of the pcaViewer property.
+     * Sets the value of the start property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+     * @param value
+     *          allowed object is {@link Integer }
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getPcaViewer().add(newItem);
-     * </pre>
+     */
+    public void setStart(Integer value)
+    {
+      this.start = value;
+    }
+
+    /**
+     * Gets the value of the end property.
      * 
+     * @return possible object is {@link Integer }
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer }
+     */
+    public Integer getEnd()
+    {
+      return end;
+    }
+
+    /**
+     * Sets the value of the end property.
      * 
+     * @param value
+     *          allowed object is {@link Integer }
      * 
      */
-    public List<JalviewModel.PcaViewer> getPcaViewer() {
-        if (pcaViewer == null) {
-            pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
-        }
-        return this.pcaViewer;
+    public void setEnd(Integer value)
+    {
+      this.end = value;
     }
 
     /**
-     * Gets the value of the featureSettings property.
+     * Gets the value of the name property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link JalviewModel.FeatureSettings }
-     *     
      */
-    public JalviewModel.FeatureSettings getFeatureSettings() {
-        return featureSettings;
+    public String getName()
+    {
+      return name;
     }
 
     /**
-     * Sets the value of the featureSettings property.
+     * Sets the value of the name property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link JalviewModel.FeatureSettings }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setFeatureSettings(JalviewModel.FeatureSettings value) {
-        this.featureSettings = value;
+    public void setName(String value)
+    {
+      this.name = value;
     }
 
+    /**
+     * Gets the value of the colour property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getColour()
+    {
+      return colour;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Sets the value of the colour property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *                 &lt;/sequence>
-     *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public void setColour(String value)
+    {
+      this.colour = value;
+    }
+
+    /**
+     * Gets the value of the consThreshold property.
      * 
+     * @return possible object is {@link Integer }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "setting",
-        "group"
-    })
-    public static class FeatureSettings {
+    public Integer getConsThreshold()
+    {
+      return consThreshold;
+    }
 
-        @XmlElement(namespace = "www.jalview.org")
-        protected List<JalviewModel.FeatureSettings.Setting> setting;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List<JalviewModel.FeatureSettings.Group> group;
+    /**
+     * Sets the value of the consThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setConsThreshold(Integer value)
+    {
+      this.consThreshold = value;
+    }
 
-        /**
-         * Gets the value of the setting property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the setting property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getSetting().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.FeatureSettings.Setting }
-         * 
-         * 
-         */
-        public List<JalviewModel.FeatureSettings.Setting> getSetting() {
-            if (setting == null) {
-                setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
-            }
-            return this.setting;
-        }
+    /**
+     * Gets the value of the pidThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getPidThreshold()
+    {
+      return pidThreshold;
+    }
 
-        /**
-         * Gets the value of the group property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the group property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getGroup().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.FeatureSettings.Group }
-         * 
-         * 
-         */
-        public List<JalviewModel.FeatureSettings.Group> getGroup() {
-            if (group == null) {
-                group = new ArrayList<JalviewModel.FeatureSettings.Group>();
-            }
-            return this.group;
-        }
+    /**
+     * Sets the value of the pidThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setPidThreshold(Integer value)
+    {
+      this.pidThreshold = value;
+    }
 
+    /**
+     * Gets the value of the outlineColour property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getOutlineColour()
+    {
+      return outlineColour;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Group {
-
-            @XmlAttribute(name = "name", required = true)
-            protected String name;
-            @XmlAttribute(name = "display", required = true)
-            protected boolean display;
-
-            /**
-             * Gets the value of the name property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getName() {
-                return name;
-            }
-
-            /**
-             * Sets the value of the name property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setName(String value) {
-                this.name = value;
-            }
-
-            /**
-             * Gets the value of the display property.
-             * 
-             */
-            public boolean isDisplay() {
-                return display;
-            }
-
-            /**
-             * Sets the value of the display property.
-             * 
-             */
-            public void setDisplay(boolean value) {
-                this.display = value;
-            }
+    /**
+     * Sets the value of the outlineColour property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setOutlineColour(Integer value)
+    {
+      this.outlineColour = value;
+    }
 
-        }
+    /**
+     * Gets the value of the displayBoxes property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isDisplayBoxes()
+    {
+      return displayBoxes;
+    }
 
+    /**
+     * Sets the value of the displayBoxes property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setDisplayBoxes(Boolean value)
+    {
+      this.displayBoxes = value;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-         *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-         *       &lt;/sequence>
-         *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-         *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "attributeName",
-            "matcherSet"
-        })
-        public static class Setting {
-
-            @XmlElement(namespace = "www.jalview.org")
-            protected List<String> attributeName;
-            @XmlElement(namespace = "www.jalview.org")
-            protected FeatureMatcherSet matcherSet;
-            @XmlAttribute(name = "type", required = true)
-            protected String type;
-            @XmlAttribute(name = "colour", required = true)
-            protected int colour;
-            @XmlAttribute(name = "display", required = true)
-            protected boolean display;
-            @XmlAttribute(name = "order")
-            protected Float order;
-            @XmlAttribute(name = "mincolour")
-            protected Integer mincolour;
-            @XmlAttribute(name = "noValueColour")
-            protected NoValueColour noValueColour;
-            @XmlAttribute(name = "threshold")
-            protected Float threshold;
-            @XmlAttribute(name = "threshstate")
-            protected Integer threshstate;
-            @XmlAttribute(name = "max")
-            protected Float max;
-            @XmlAttribute(name = "min")
-            protected Float min;
-            @XmlAttribute(name = "colourByLabel")
-            protected Boolean colourByLabel;
-            @XmlAttribute(name = "autoScale")
-            protected Boolean autoScale;
-
-            /**
-             * Gets the value of the attributeName property.
-             * 
-             * <p>
-             * This accessor method returns a reference to the live list,
-             * not a snapshot. Therefore any modification you make to the
-             * returned list will be present inside the JAXB object.
-             * This is why there is not a <CODE>set</CODE> method for the attributeName property.
-             * 
-             * <p>
-             * For example, to add a new item, do as follows:
-             * <pre>
-             *    getAttributeName().add(newItem);
-             * </pre>
-             * 
-             * 
-             * <p>
-             * Objects of the following type(s) are allowed in the list
-             * {@link String }
-             * 
-             * 
-             */
-            public List<String> getAttributeName() {
-                if (attributeName == null) {
-                    attributeName = new ArrayList<String>();
-                }
-                return this.attributeName;
-            }
-
-            /**
-             * Gets the value of the matcherSet property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link FeatureMatcherSet }
-             *     
-             */
-            public FeatureMatcherSet getMatcherSet() {
-                return matcherSet;
-            }
-
-            /**
-             * Sets the value of the matcherSet property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link FeatureMatcherSet }
-             *     
-             */
-            public void setMatcherSet(FeatureMatcherSet value) {
-                this.matcherSet = value;
-            }
-
-            /**
-             * Gets the value of the type property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getType() {
-                return type;
-            }
-
-            /**
-             * Sets the value of the type property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setType(String value) {
-                this.type = value;
-            }
-
-            /**
-             * Gets the value of the colour property.
-             * 
-             */
-            public int getColour() {
-                return colour;
-            }
-
-            /**
-             * Sets the value of the colour property.
-             * 
-             */
-            public void setColour(int value) {
-                this.colour = value;
-            }
-
-            /**
-             * Gets the value of the display property.
-             * 
-             */
-            public boolean isDisplay() {
-                return display;
-            }
-
-            /**
-             * Sets the value of the display property.
-             * 
-             */
-            public void setDisplay(boolean value) {
-                this.display = value;
-            }
-
-            /**
-             * Gets the value of the order property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getOrder() {
-                return order;
-            }
-
-            /**
-             * Sets the value of the order property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setOrder(Float value) {
-                this.order = value;
-            }
-
-            /**
-             * Gets the value of the mincolour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getMincolour() {
-                return mincolour;
-            }
-
-            /**
-             * Sets the value of the mincolour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setMincolour(Integer value) {
-                this.mincolour = value;
-            }
-
-            /**
-             * Gets the value of the noValueColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link NoValueColour }
-             *     
-             */
-            public NoValueColour getNoValueColour() {
-                if (noValueColour == null) {
-                    return NoValueColour.MIN;
-                } else {
-                    return noValueColour;
-                }
-            }
-
-            /**
-             * Sets the value of the noValueColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link NoValueColour }
-             *     
-             */
-            public void setNoValueColour(NoValueColour value) {
-                this.noValueColour = value;
-            }
-
-            /**
-             * Gets the value of the threshold property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getThreshold() {
-                return threshold;
-            }
-
-            /**
-             * Sets the value of the threshold property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setThreshold(Float value) {
-                this.threshold = value;
-            }
-
-            /**
-             * Gets the value of the threshstate property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getThreshstate() {
-                return threshstate;
-            }
-
-            /**
-             * Sets the value of the threshstate property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setThreshstate(Integer value) {
-                this.threshstate = value;
-            }
-
-            /**
-             * Gets the value of the max property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getMax() {
-                return max;
-            }
-
-            /**
-             * Sets the value of the max property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setMax(Float value) {
-                this.max = value;
-            }
-
-            /**
-             * Gets the value of the min property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getMin() {
-                return min;
-            }
-
-            /**
-             * Sets the value of the min property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setMin(Float value) {
-                this.min = value;
-            }
-
-            /**
-             * Gets the value of the colourByLabel property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isColourByLabel() {
-                return colourByLabel;
-            }
-
-            /**
-             * Sets the value of the colourByLabel property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setColourByLabel(Boolean value) {
-                this.colourByLabel = value;
-            }
-
-            /**
-             * Gets the value of the autoScale property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isAutoScale() {
-                return autoScale;
-            }
-
-            /**
-             * Sets the value of the autoScale property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setAutoScale(Boolean value) {
-                this.autoScale = value;
-            }
+    /**
+     * Gets the value of the displayText property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isDisplayText()
+    {
+      return displayText;
+    }
 
-        }
+    /**
+     * Sets the value of the displayText property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setDisplayText(Boolean value)
+    {
+      this.displayText = value;
+    }
 
+    /**
+     * Gets the value of the colourText property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isColourText()
+    {
+      return colourText;
     }
 
+    /**
+     * Sets the value of the colourText property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setColourText(Boolean value)
+    {
+      this.colourText = value;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the textCol1 property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link Integer }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public Integer getTextCol1()
+    {
+      return textCol1;
+    }
+
+    /**
+     * Sets the value of the textCol1 property.
      * 
+     * @param value
+     *          allowed object is {@link Integer }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "seq",
-        "annotationColours"
-    })
-    public static class JGroup {
-
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List<String> seq;
-        @XmlElement(namespace = "www.jalview.org")
-        protected AnnotationColourScheme annotationColours;
-        @XmlAttribute(name = "start")
-        protected Integer start;
-        @XmlAttribute(name = "end")
-        protected Integer end;
-        @XmlAttribute(name = "name")
-        protected String name;
-        @XmlAttribute(name = "colour")
-        protected String colour;
-        @XmlAttribute(name = "consThreshold")
-        protected Integer consThreshold;
-        @XmlAttribute(name = "pidThreshold")
-        protected Integer pidThreshold;
-        @XmlAttribute(name = "outlineColour")
-        protected Integer outlineColour;
-        @XmlAttribute(name = "displayBoxes")
-        protected Boolean displayBoxes;
-        @XmlAttribute(name = "displayText")
-        protected Boolean displayText;
-        @XmlAttribute(name = "colourText")
-        protected Boolean colourText;
-        @XmlAttribute(name = "textCol1")
-        protected Integer textCol1;
-        @XmlAttribute(name = "textCol2")
-        protected Integer textCol2;
-        @XmlAttribute(name = "textColThreshold")
-        protected Integer textColThreshold;
-        @XmlAttribute(name = "showUnconserved")
-        protected Boolean showUnconserved;
-        @XmlAttribute(name = "ignoreGapsinConsensus")
-        protected Boolean ignoreGapsinConsensus;
-        @XmlAttribute(name = "showConsensusHistogram")
-        protected Boolean showConsensusHistogram;
-        @XmlAttribute(name = "showSequenceLogo")
-        protected Boolean showSequenceLogo;
-        @XmlAttribute(name = "normaliseSequenceLogo")
-        protected Boolean normaliseSequenceLogo;
-        @XmlAttribute(name = "id")
-        protected String id;
+    public void setTextCol1(Integer value)
+    {
+      this.textCol1 = value;
+    }
 
-        /**
-         * Gets the value of the seq property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the seq property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getSeq().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List<String> getSeq() {
-            if (seq == null) {
-                seq = new ArrayList<String>();
-            }
-            return this.seq;
-        }
+    /**
+     * Gets the value of the textCol2 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol2()
+    {
+      return textCol2;
+    }
+
+    /**
+     * Sets the value of the textCol2 property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextCol2(Integer value)
+    {
+      this.textCol2 = value;
+    }
+
+    /**
+     * Gets the value of the textColThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextColThreshold()
+    {
+      return textColThreshold;
+    }
+
+    /**
+     * Sets the value of the textColThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextColThreshold(Integer value)
+    {
+      this.textColThreshold = value;
+    }
+
+    /**
+     * Gets the value of the showUnconserved property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowUnconserved()
+    {
+      return showUnconserved;
+    }
+
+    /**
+     * Sets the value of the showUnconserved property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowUnconserved(Boolean value)
+    {
+      this.showUnconserved = value;
+    }
+
+    /**
+     * Gets the value of the ignoreGapsinConsensus property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isIgnoreGapsinConsensus()
+    {
+      if (ignoreGapsinConsensus == null)
+      {
+        return true;
+      }
+      else
+      {
+        return ignoreGapsinConsensus;
+      }
+    }
+
+    /**
+     * Sets the value of the ignoreGapsinConsensus property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIgnoreGapsinConsensus(Boolean value)
+    {
+      this.ignoreGapsinConsensus = value;
+    }
+
+    /**
+     * Gets the value of the showConsensusHistogram property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowConsensusHistogram()
+    {
+      if (showConsensusHistogram == null)
+      {
+        return true;
+      }
+      else
+      {
+        return showConsensusHistogram;
+      }
+    }
+
+    /**
+     * Sets the value of the showConsensusHistogram property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowConsensusHistogram(Boolean value)
+    {
+      this.showConsensusHistogram = value;
+    }
+
+    /**
+     * Gets the value of the showSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowSequenceLogo()
+    {
+      if (showSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showSequenceLogo;
+      }
+    }
+
+    /**
+     * Sets the value of the showSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowSequenceLogo(Boolean value)
+    {
+      this.showSequenceLogo = value;
+    }
+
+    /**
+     * Gets the value of the normaliseSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isNormaliseSequenceLogo()
+    {
+      if (normaliseSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return normaliseSequenceLogo;
+      }
+    }
+
+    /**
+     * Sets the value of the normaliseSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setNormaliseSequenceLogo(Boolean value)
+    {
+      this.normaliseSequenceLogo = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setId(String value)
+    {
+      this.id = value;
+    }
+
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;extension base="{www.jalview.org}pdbentry">
+   *                 &lt;sequence>
+   *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+   *                     &lt;complexType>
+   *                       &lt;simpleContent>
+   *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+   *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+   *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         &lt;/extension>
+   *                       &lt;/simpleContent>
+   *                     &lt;/complexType>
+   *                   &lt;/element>
+   *                 &lt;/sequence>
+   *               &lt;/extension>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;sequence>
+   *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
+   *                     &lt;complexType>
+   *                       &lt;complexContent>
+   *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         &lt;/restriction>
+   *                       &lt;/complexContent>
+   *                     &lt;/complexType>
+   *                   &lt;/element>
+   *                 &lt;/sequence>
+   *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *       &lt;/sequence>
+   *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
+  public static class JSeq
+  {
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List<Feature> features;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List<JalviewModel.JSeq.Pdbids> pdbids;
+
+    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+    protected List<Integer> hiddenSequences;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
+
+    @XmlAttribute(name = "colour")
+    protected Integer colour;
+
+    @XmlAttribute(name = "start", required = true)
+    protected int start;
+
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
+
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+
+    @XmlAttribute(name = "hidden")
+    protected Boolean hidden;
+
+    @XmlAttribute(name = "viewreference")
+    protected Boolean viewreference;
+
+    /**
+     * Gets the value of the features property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the features property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getFeatures().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link Feature }
+     * 
+     * 
+     */
+    public List<Feature> getFeatures()
+    {
+      if (features == null)
+      {
+        features = new ArrayList<Feature>();
+      }
+      return this.features;
+    }
+
+    /**
+     * Gets the value of the pdbids property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the pdbids property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getPdbids().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JSeq.Pdbids }
+     * 
+     * 
+     */
+    public List<JalviewModel.JSeq.Pdbids> getPdbids()
+    {
+      if (pdbids == null)
+      {
+        pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+      }
+      return this.pdbids;
+    }
+
+    /**
+     * Gets the value of the hiddenSequences property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the hiddenSequences property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getHiddenSequences().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * 
+     * 
+     */
+    public List<Integer> getHiddenSequences()
+    {
+      if (hiddenSequences == null)
+      {
+        hiddenSequences = new ArrayList<Integer>();
+      }
+      return this.hiddenSequences;
+    }
+
+    /**
+     * Gets the value of the rnaViewer property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the rnaViewer property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getRnaViewer().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JSeq.RnaViewer }
+     * 
+     * 
+     */
+    public List<JalviewModel.JSeq.RnaViewer> getRnaViewer()
+    {
+      if (rnaViewer == null)
+      {
+        rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+      }
+      return this.rnaViewer;
+    }
+
+    /**
+     * Gets the value of the colour property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getColour()
+    {
+      return colour;
+    }
+
+    /**
+     * Sets the value of the colour property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setColour(Integer value)
+    {
+      this.colour = value;
+    }
+
+    /**
+     * Gets the value of the start property.
+     * 
+     */
+    public int getStart()
+    {
+      return start;
+    }
+
+    /**
+     * Sets the value of the start property.
+     * 
+     */
+    public void setStart(int value)
+    {
+      this.start = value;
+    }
+
+    /**
+     * Gets the value of the end property.
+     * 
+     */
+    public int getEnd()
+    {
+      return end;
+    }
+
+    /**
+     * Sets the value of the end property.
+     * 
+     */
+    public void setEnd(int value)
+    {
+      this.end = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setId(String value)
+    {
+      this.id = value;
+    }
+
+    /**
+     * Gets the value of the hidden property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isHidden()
+    {
+      return hidden;
+    }
+
+    /**
+     * Sets the value of the hidden property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setHidden(Boolean value)
+    {
+      this.hidden = value;
+    }
+
+    /**
+     * Gets the value of the viewreference property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isViewreference()
+    {
+      return viewreference;
+    }
+
+    /**
+     * Sets the value of the viewreference property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setViewreference(Boolean value)
+    {
+      this.viewreference = value;
+    }
+
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;extension base="{www.jalview.org}pdbentry">
+     *       &lt;sequence>
+     *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;simpleContent>
+     *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               &lt;/extension>
+     *             &lt;/simpleContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *     &lt;/extension>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = { "structureState" })
+    public static class Pdbids extends Pdbentry
+    {
+
+      @XmlElement(namespace = "www.jalview.org")
+      protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+      /**
+       * Gets the value of the structureState property.
+       * 
+       * <p>
+       * This accessor method returns a reference to the live list, not a
+       * snapshot. Therefore any modification you make to the returned list will
+       * be present inside the JAXB object. This is why there is not a
+       * <CODE>set</CODE> method for the structureState property.
+       * 
+       * <p>
+       * For example, to add a new item, do as follows:
+       * 
+       * <pre>
+       * getStructureState().add(newItem);
+       * </pre>
+       * 
+       * 
+       * <p>
+       * Objects of the following type(s) are allowed in the list
+       * {@link JalviewModel.JSeq.Pdbids.StructureState }
+       * 
+       * 
+       */
+      public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState()
+      {
+        if (structureState == null)
+        {
+          structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+        }
+        return this.structureState;
+      }
+
+      /**
+       * <p>
+       * Java class for anonymous complex type.
+       * 
+       * <p>
+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
+       * <pre>
+       * &lt;complexType>
+       *   &lt;simpleContent>
+       *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+       *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+       *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+       *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     &lt;/extension>
+       *   &lt;/simpleContent>
+       * &lt;/complexType>
+       * </pre>
+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "", propOrder = { "value" })
+      public static class StructureState
+      {
+
+        @XmlValue
+        protected String value;
+
+        @XmlAttribute(name = "visible")
+        protected Boolean visible;
+
+        @XmlAttribute(name = "viewId")
+        protected String viewId;
+
+        @XmlAttribute(name = "alignwithAlignPanel")
+        protected Boolean alignwithAlignPanel;
+
+        @XmlAttribute(name = "colourwithAlignPanel")
+        protected Boolean colourwithAlignPanel;
+
+        @XmlAttribute(name = "colourByJmol")
+        protected Boolean colourByJmol;
+
+        @XmlAttribute(name = "type")
+        protected String type;
+
+        @XmlAttribute(name = "width")
+        protected Integer width;
+
+        @XmlAttribute(name = "height")
+        protected Integer height;
+
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
 
-        /**
-         * Gets the value of the annotationColours property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link AnnotationColourScheme }
-         *     
-         */
-        public AnnotationColourScheme getAnnotationColours() {
-            return annotationColours;
-        }
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
         /**
-         * Sets the value of the annotationColours property.
+         * Gets the value of the value property.
          * 
-         * @param value
-         *     allowed object is
-         *     {@link AnnotationColourScheme }
-         *     
-         */
-        public void setAnnotationColours(AnnotationColourScheme value) {
-            this.annotationColours = value;
-        }
-
-        /**
-         * Gets the value of the start property.
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getStart() {
-            return start;
+        public String getValue()
+        {
+          return value;
         }
 
         /**
-         * Sets the value of the start property.
+         * Sets the value of the value property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setStart(Integer value) {
-            this.start = value;
-        }
-
-        /**
-         * Gets the value of the end property.
+         *          allowed object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getEnd() {
-            return end;
+        public void setValue(String value)
+        {
+          this.value = value;
         }
 
         /**
-         * Sets the value of the end property.
+         * Gets the value of the visible property.
          * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setEnd(Integer value) {
-            this.end = value;
-        }
-
-        /**
-         * Gets the value of the name property.
+         * @return possible object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
          */
-        public String getName() {
-            return name;
+        public Boolean isVisible()
+        {
+          return visible;
         }
 
         /**
-         * Sets the value of the name property.
+         * Sets the value of the visible property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setName(String value) {
-            this.name = value;
-        }
-
-        /**
-         * Gets the value of the colour property.
+         *          allowed object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
          */
-        public String getColour() {
-            return colour;
+        public void setVisible(Boolean value)
+        {
+          this.visible = value;
         }
 
         /**
-         * Sets the value of the colour property.
+         * Gets the value of the viewId property.
          * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setColour(String value) {
-            this.colour = value;
-        }
-
-        /**
-         * Gets the value of the consThreshold property.
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getConsThreshold() {
-            return consThreshold;
+        public String getViewId()
+        {
+          return viewId;
         }
 
         /**
-         * Sets the value of the consThreshold property.
+         * Sets the value of the viewId property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setConsThreshold(Integer value) {
-            this.consThreshold = value;
-        }
-
-        /**
-         * Gets the value of the pidThreshold property.
+         *          allowed object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getPidThreshold() {
-            return pidThreshold;
+        public void setViewId(String value)
+        {
+          this.viewId = value;
         }
 
         /**
-         * Sets the value of the pidThreshold property.
+         * Gets the value of the alignwithAlignPanel property.
          * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setPidThreshold(Integer value) {
-            this.pidThreshold = value;
-        }
-
-        /**
-         * Gets the value of the outlineColour property.
+         * @return possible object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getOutlineColour() {
-            return outlineColour;
+        public boolean isAlignwithAlignPanel()
+        {
+          if (alignwithAlignPanel == null)
+          {
+            return true;
+          }
+          else
+          {
+            return alignwithAlignPanel;
+          }
         }
 
         /**
-         * Sets the value of the outlineColour property.
+         * Sets the value of the alignwithAlignPanel property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setOutlineColour(Integer value) {
-            this.outlineColour = value;
-        }
-
-        /**
-         * Gets the value of the displayBoxes property.
+         *          allowed object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public Boolean isDisplayBoxes() {
-            return displayBoxes;
+        public void setAlignwithAlignPanel(Boolean value)
+        {
+          this.alignwithAlignPanel = value;
         }
 
         /**
-         * Sets the value of the displayBoxes property.
+         * Gets the value of the colourwithAlignPanel property.
          * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setDisplayBoxes(Boolean value) {
-            this.displayBoxes = value;
-        }
-
-        /**
-         * Gets the value of the displayText property.
+         * @return possible object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public Boolean isDisplayText() {
-            return displayText;
+        public boolean isColourwithAlignPanel()
+        {
+          if (colourwithAlignPanel == null)
+          {
+            return false;
+          }
+          else
+          {
+            return colourwithAlignPanel;
+          }
         }
 
         /**
-         * Sets the value of the displayText property.
+         * Sets the value of the colourwithAlignPanel property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link Boolean }
+         * 
          */
-        public void setDisplayText(Boolean value) {
-            this.displayText = value;
+        public void setColourwithAlignPanel(Boolean value)
+        {
+          this.colourwithAlignPanel = value;
         }
 
         /**
-         * Gets the value of the colourText property.
+         * Gets the value of the colourByJmol property.
+         * 
+         * @return possible object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public Boolean isColourText() {
-            return colourText;
+        public boolean isColourByJmol()
+        {
+          if (colourByJmol == null)
+          {
+            return true;
+          }
+          else
+          {
+            return colourByJmol;
+          }
         }
 
         /**
-         * Sets the value of the colourText property.
+         * Sets the value of the colourByJmol property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link Boolean }
+         * 
          */
-        public void setColourText(Boolean value) {
-            this.colourText = value;
+        public void setColourByJmol(Boolean value)
+        {
+          this.colourByJmol = value;
         }
 
         /**
-         * Gets the value of the textCol1 property.
+         * Gets the value of the type property.
+         * 
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getTextCol1() {
-            return textCol1;
+        public String getType()
+        {
+          return type;
         }
 
         /**
-         * Sets the value of the textCol1 property.
+         * Sets the value of the type property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
+         *          allowed object is {@link String }
+         * 
          */
-        public void setTextCol1(Integer value) {
-            this.textCol1 = value;
+        public void setType(String value)
+        {
+          this.type = value;
         }
 
         /**
-         * Gets the value of the textCol2 property.
+         * Gets the value of the width property.
+         * 
+         * @return possible object is {@link Integer }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getTextCol2() {
-            return textCol2;
+        public Integer getWidth()
+        {
+          return width;
         }
 
         /**
-         * Sets the value of the textCol2 property.
+         * Sets the value of the width property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
+         *          allowed object is {@link Integer }
+         * 
          */
-        public void setTextCol2(Integer value) {
-            this.textCol2 = value;
+        public void setWidth(Integer value)
+        {
+          this.width = value;
         }
 
         /**
-         * Gets the value of the textColThreshold property.
+         * Gets the value of the height property.
+         * 
+         * @return possible object is {@link Integer }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getTextColThreshold() {
-            return textColThreshold;
+        public Integer getHeight()
+        {
+          return height;
         }
 
         /**
-         * Sets the value of the textColThreshold property.
+         * Sets the value of the height property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
+         *          allowed object is {@link Integer }
+         * 
          */
-        public void setTextColThreshold(Integer value) {
-            this.textColThreshold = value;
+        public void setHeight(Integer value)
+        {
+          this.height = value;
         }
 
         /**
-         * Gets the value of the showUnconserved property.
+         * Gets the value of the xpos property.
+         * 
+         * @return possible object is {@link Integer }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public Boolean isShowUnconserved() {
-            return showUnconserved;
+        public Integer getXpos()
+        {
+          return xpos;
         }
 
         /**
-         * Sets the value of the showUnconserved property.
+         * Sets the value of the xpos property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link Integer }
+         * 
          */
-        public void setShowUnconserved(Boolean value) {
-            this.showUnconserved = value;
+        public void setXpos(Integer value)
+        {
+          this.xpos = value;
         }
 
         /**
-         * Gets the value of the ignoreGapsinConsensus property.
+         * Gets the value of the ypos property.
+         * 
+         * @return possible object is {@link Integer }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public boolean isIgnoreGapsinConsensus() {
-            if (ignoreGapsinConsensus == null) {
-                return true;
-            } else {
-                return ignoreGapsinConsensus;
-            }
+        public Integer getYpos()
+        {
+          return ypos;
         }
 
         /**
-         * Sets the value of the ignoreGapsinConsensus property.
+         * Sets the value of the ypos property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link Integer }
+         * 
          */
-        public void setIgnoreGapsinConsensus(Boolean value) {
-            this.ignoreGapsinConsensus = value;
+        public void setYpos(Integer value)
+        {
+          this.ypos = value;
         }
 
+      }
+
+    }
+
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = { "secondaryStructure" })
+    public static class RnaViewer
+    {
+
+      @XmlElement(namespace = "www.jalview.org", required = true)
+      protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
+
+      @XmlAttribute(name = "title")
+      protected String title;
+
+      @XmlAttribute(name = "viewId")
+      protected String viewId;
+
+      @XmlAttribute(name = "dividerLocation")
+      protected Integer dividerLocation;
+
+      @XmlAttribute(name = "selectedRna")
+      protected Integer selectedRna;
+
+      @XmlAttribute(name = "width")
+      protected Integer width;
+
+      @XmlAttribute(name = "height")
+      protected Integer height;
+
+      @XmlAttribute(name = "xpos")
+      protected Integer xpos;
+
+      @XmlAttribute(name = "ypos")
+      protected Integer ypos;
+
+      /**
+       * Gets the value of the secondaryStructure property.
+       * 
+       * <p>
+       * This accessor method returns a reference to the live list, not a
+       * snapshot. Therefore any modification you make to the returned list will
+       * be present inside the JAXB object. This is why there is not a
+       * <CODE>set</CODE> method for the secondaryStructure property.
+       * 
+       * <p>
+       * For example, to add a new item, do as follows:
+       * 
+       * <pre>
+       * getSecondaryStructure().add(newItem);
+       * </pre>
+       * 
+       * 
+       * <p>
+       * Objects of the following type(s) are allowed in the list
+       * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+       * 
+       * 
+       */
+      public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure()
+      {
+        if (secondaryStructure == null)
+        {
+          secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+        }
+        return this.secondaryStructure;
+      }
+
+      /**
+       * Gets the value of the title property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getTitle()
+      {
+        return title;
+      }
+
+      /**
+       * Sets the value of the title property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setTitle(String value)
+      {
+        this.title = value;
+      }
+
+      /**
+       * Gets the value of the viewId property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getViewId()
+      {
+        return viewId;
+      }
+
+      /**
+       * Sets the value of the viewId property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setViewId(String value)
+      {
+        this.viewId = value;
+      }
+
+      /**
+       * Gets the value of the dividerLocation property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getDividerLocation()
+      {
+        return dividerLocation;
+      }
+
+      /**
+       * Sets the value of the dividerLocation property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setDividerLocation(Integer value)
+      {
+        this.dividerLocation = value;
+      }
+
+      /**
+       * Gets the value of the selectedRna property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getSelectedRna()
+      {
+        return selectedRna;
+      }
+
+      /**
+       * Sets the value of the selectedRna property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setSelectedRna(Integer value)
+      {
+        this.selectedRna = value;
+      }
+
+      /**
+       * Gets the value of the width property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getWidth()
+      {
+        return width;
+      }
+
+      /**
+       * Sets the value of the width property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setWidth(Integer value)
+      {
+        this.width = value;
+      }
+
+      /**
+       * Gets the value of the height property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getHeight()
+      {
+        return height;
+      }
+
+      /**
+       * Sets the value of the height property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setHeight(Integer value)
+      {
+        this.height = value;
+      }
+
+      /**
+       * Gets the value of the xpos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getXpos()
+      {
+        return xpos;
+      }
+
+      /**
+       * Sets the value of the xpos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setXpos(Integer value)
+      {
+        this.xpos = value;
+      }
+
+      /**
+       * Gets the value of the ypos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getYpos()
+      {
+        return ypos;
+      }
+
+      /**
+       * Sets the value of the ypos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setYpos(Integer value)
+      {
+        this.ypos = value;
+      }
+
+      /**
+       * <p>
+       * Java class for anonymous complex type.
+       * 
+       * <p>
+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
+       * <pre>
+       * &lt;complexType>
+       *   &lt;complexContent>
+       *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     &lt;/restriction>
+       *   &lt;/complexContent>
+       * &lt;/complexType>
+       * </pre>
+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "")
+      public static class SecondaryStructure
+      {
+
+        @XmlAttribute(name = "title")
+        protected String title;
+
+        @XmlAttribute(name = "annotationId", required = true)
+        protected String annotationId;
+
+        @XmlAttribute(name = "gapped")
+        protected Boolean gapped;
+
+        @XmlAttribute(name = "viewerState")
+        protected String viewerState;
+
         /**
-         * Gets the value of the showConsensusHistogram property.
+         * Gets the value of the title property.
+         * 
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public boolean isShowConsensusHistogram() {
-            if (showConsensusHistogram == null) {
-                return true;
-            } else {
-                return showConsensusHistogram;
-            }
+        public String getTitle()
+        {
+          return title;
         }
 
         /**
-         * Sets the value of the showConsensusHistogram property.
+         * Sets the value of the title property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link String }
+         * 
          */
-        public void setShowConsensusHistogram(Boolean value) {
-            this.showConsensusHistogram = value;
+        public void setTitle(String value)
+        {
+          this.title = value;
         }
 
         /**
-         * Gets the value of the showSequenceLogo property.
+         * Gets the value of the annotationId property.
+         * 
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public boolean isShowSequenceLogo() {
-            if (showSequenceLogo == null) {
-                return false;
-            } else {
-                return showSequenceLogo;
-            }
+        public String getAnnotationId()
+        {
+          return annotationId;
         }
 
         /**
-         * Sets the value of the showSequenceLogo property.
+         * Sets the value of the annotationId property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link String }
+         * 
          */
-        public void setShowSequenceLogo(Boolean value) {
-            this.showSequenceLogo = value;
+        public void setAnnotationId(String value)
+        {
+          this.annotationId = value;
         }
 
         /**
-         * Gets the value of the normaliseSequenceLogo property.
+         * Gets the value of the gapped property.
+         * 
+         * @return possible object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public boolean isNormaliseSequenceLogo() {
-            if (normaliseSequenceLogo == null) {
-                return false;
-            } else {
-                return normaliseSequenceLogo;
-            }
+        public Boolean isGapped()
+        {
+          return gapped;
         }
 
         /**
-         * Sets the value of the normaliseSequenceLogo property.
+         * Sets the value of the gapped property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link Boolean }
+         * 
          */
-        public void setNormaliseSequenceLogo(Boolean value) {
-            this.normaliseSequenceLogo = value;
+        public void setGapped(Boolean value)
+        {
+          this.gapped = value;
         }
 
         /**
-         * Gets the value of the id property.
+         * Gets the value of the viewerState property.
+         * 
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
          */
-        public String getId() {
-            return id;
+        public String getViewerState()
+        {
+          return viewerState;
         }
 
         /**
-         * Sets the value of the id property.
+         * Sets the value of the viewerState property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
+         *          allowed object is {@link String }
+         * 
          */
-        public void setId(String value) {
-            this.id = value;
+        public void setViewerState(String value)
+        {
+          this.viewerState = value;
         }
 
+      }
+
+    }
+
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="sequencePoint" maxOccurs="unbounded">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attGroup ref="{www.jalview.org}position"/>
+   *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attGroup ref="{www.jalview.org}position"/>
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="seqPointMin">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attGroup ref="{www.jalview.org}position"/>
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="seqPointMax">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attGroup ref="{www.jalview.org}position"/>
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+   *       &lt;/sequence>
+   *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
+   *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+   *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
+  public static class PcaViewer
+  {
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List<JalviewModel.PcaViewer.Axis> axis;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected PcaDataType pcaData;
+
+    @XmlAttribute(name = "title")
+    protected String title;
+
+    @XmlAttribute(name = "scoreModelName")
+    protected String scoreModelName;
+
+    @XmlAttribute(name = "xDim")
+    protected Integer xDim;
+
+    @XmlAttribute(name = "yDim")
+    protected Integer yDim;
+
+    @XmlAttribute(name = "zDim")
+    protected Integer zDim;
+
+    @XmlAttribute(name = "bgColour")
+    protected Integer bgColour;
+
+    @XmlAttribute(name = "scaleFactor")
+    protected Float scaleFactor;
+
+    @XmlAttribute(name = "showLabels")
+    protected Boolean showLabels;
+
+    @XmlAttribute(name = "linkToAllViews")
+    protected Boolean linkToAllViews;
+
+    @XmlAttribute(name = "includeGaps")
+    protected Boolean includeGaps;
+
+    @XmlAttribute(name = "matchGaps")
+    protected Boolean matchGaps;
+
+    @XmlAttribute(name = "includeGappedColumns")
+    protected Boolean includeGappedColumns;
+
+    @XmlAttribute(name = "denominateByShortestLength")
+    protected Boolean denominateByShortestLength;
+
+    @XmlAttribute(name = "width")
+    protected Integer width;
+
+    @XmlAttribute(name = "height")
+    protected Integer height;
+
+    @XmlAttribute(name = "xpos")
+    protected Integer xpos;
+
+    @XmlAttribute(name = "ypos")
+    protected Integer ypos;
+
+    /**
+     * Gets the value of the sequencePoint property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the sequencePoint property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getSequencePoint().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer.SequencePoint }
+     * 
+     * 
+     */
+    public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint()
+    {
+      if (sequencePoint == null)
+      {
+        sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+      }
+      return this.sequencePoint;
+    }
+
+    /**
+     * Gets the value of the axis property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the axis property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getAxis().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer.Axis }
+     * 
+     * 
+     */
+    public List<JalviewModel.PcaViewer.Axis> getAxis()
+    {
+      if (axis == null)
+      {
+        axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+      }
+      return this.axis;
+    }
+
+    /**
+     * Gets the value of the seqPointMin property.
+     * 
+     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
+    {
+      return seqPointMin;
+    }
+
+    /**
+     * Sets the value of the seqPointMin property.
+     * 
+     * @param value
+     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
+     * 
+     */
+    public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
+    {
+      this.seqPointMin = value;
+    }
+
+    /**
+     * Gets the value of the seqPointMax property.
+     * 
+     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
+    {
+      return seqPointMax;
+    }
+
+    /**
+     * Sets the value of the seqPointMax property.
+     * 
+     * @param value
+     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
+     * 
+     */
+    public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
+    {
+      this.seqPointMax = value;
+    }
+
+    /**
+     * Gets the value of the pcaData property.
+     * 
+     * @return possible object is {@link PcaDataType }
+     * 
+     */
+    public PcaDataType getPcaData()
+    {
+      return pcaData;
+    }
+
+    /**
+     * Sets the value of the pcaData property.
+     * 
+     * @param value
+     *          allowed object is {@link PcaDataType }
+     * 
+     */
+    public void setPcaData(PcaDataType value)
+    {
+      this.pcaData = value;
+    }
+
+    /**
+     * Gets the value of the title property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getTitle()
+    {
+      return title;
+    }
+
+    /**
+     * Sets the value of the title property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setTitle(String value)
+    {
+      this.title = value;
+    }
+
+    /**
+     * Gets the value of the scoreModelName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getScoreModelName()
+    {
+      return scoreModelName;
+    }
+
+    /**
+     * Sets the value of the scoreModelName property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setScoreModelName(String value)
+    {
+      this.scoreModelName = value;
+    }
+
+    /**
+     * Gets the value of the xDim property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXDim()
+    {
+      return xDim;
+    }
+
+    /**
+     * Sets the value of the xDim property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setXDim(Integer value)
+    {
+      this.xDim = value;
     }
 
+    /**
+     * Gets the value of the yDim property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getYDim()
+    {
+      return yDim;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Sets the value of the yDim property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Integer }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;extension base="{www.jalview.org}pdbentry">
-     *                 &lt;sequence>
-     *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *                     &lt;complexType>
-     *                       &lt;simpleContent>
-     *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         &lt;/extension>
-     *                       &lt;/simpleContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
-     *               &lt;/extension>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
-     *                     &lt;complexType>
-     *                       &lt;complexContent>
-     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         &lt;/restriction>
-     *                       &lt;/complexContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
-     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public void setYDim(Integer value)
+    {
+      this.yDim = value;
+    }
+
+    /**
+     * Gets the value of the zDim property.
      * 
+     * @return possible object is {@link Integer }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "features",
-        "pdbids",
-        "hiddenSequences",
-        "rnaViewer"
-    })
-    public static class JSeq {
-
-        @XmlElement(namespace = "www.jalview.org")
-        protected List<Feature> features;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List<JalviewModel.JSeq.Pdbids> pdbids;
-        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-        protected List<Integer> hiddenSequences;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
-        @XmlAttribute(name = "colour")
-        protected Integer colour;
-        @XmlAttribute(name = "start", required = true)
-        protected int start;
-        @XmlAttribute(name = "end", required = true)
-        protected int end;
-        @XmlAttribute(name = "id", required = true)
-        protected String id;
-        @XmlAttribute(name = "hidden")
-        protected Boolean hidden;
-        @XmlAttribute(name = "viewreference")
-        protected Boolean viewreference;
+    public Integer getZDim()
+    {
+      return zDim;
+    }
 
-        /**
-         * Gets the value of the features property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the features property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getFeatures().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link Feature }
-         * 
-         * 
-         */
-        public List<Feature> getFeatures() {
-            if (features == null) {
-                features = new ArrayList<Feature>();
-            }
-            return this.features;
-        }
+    /**
+     * Sets the value of the zDim property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setZDim(Integer value)
+    {
+      this.zDim = value;
+    }
 
-        /**
-         * Gets the value of the pdbids property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the pdbids property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getPdbids().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.JSeq.Pdbids }
-         * 
-         * 
-         */
-        public List<JalviewModel.JSeq.Pdbids> getPdbids() {
-            if (pdbids == null) {
-                pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
-            }
-            return this.pdbids;
-        }
+    /**
+     * Gets the value of the bgColour property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getBgColour()
+    {
+      return bgColour;
+    }
 
-        /**
-         * Gets the value of the hiddenSequences property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getHiddenSequences().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List<Integer> getHiddenSequences() {
-            if (hiddenSequences == null) {
-                hiddenSequences = new ArrayList<Integer>();
-            }
-            return this.hiddenSequences;
-        }
+    /**
+     * Sets the value of the bgColour property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setBgColour(Integer value)
+    {
+      this.bgColour = value;
+    }
 
-        /**
-         * Gets the value of the rnaViewer property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getRnaViewer().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.JSeq.RnaViewer }
-         * 
-         * 
-         */
-        public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
-            if (rnaViewer == null) {
-                rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
-            }
-            return this.rnaViewer;
-        }
+    /**
+     * Gets the value of the scaleFactor property.
+     * 
+     * @return possible object is {@link Float }
+     * 
+     */
+    public Float getScaleFactor()
+    {
+      return scaleFactor;
+    }
 
-        /**
-         * Gets the value of the colour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getColour() {
-            return colour;
-        }
+    /**
+     * Sets the value of the scaleFactor property.
+     * 
+     * @param value
+     *          allowed object is {@link Float }
+     * 
+     */
+    public void setScaleFactor(Float value)
+    {
+      this.scaleFactor = value;
+    }
 
-        /**
-         * Sets the value of the colour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setColour(Integer value) {
-            this.colour = value;
-        }
+    /**
+     * Gets the value of the showLabels property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowLabels()
+    {
+      return showLabels;
+    }
 
-        /**
-         * Gets the value of the start property.
-         * 
-         */
-        public int getStart() {
-            return start;
-        }
+    /**
+     * Sets the value of the showLabels property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowLabels(Boolean value)
+    {
+      this.showLabels = value;
+    }
 
-        /**
-         * Sets the value of the start property.
-         * 
-         */
-        public void setStart(int value) {
-            this.start = value;
-        }
+    /**
+     * Gets the value of the linkToAllViews property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isLinkToAllViews()
+    {
+      return linkToAllViews;
+    }
 
-        /**
-         * Gets the value of the end property.
-         * 
-         */
-        public int getEnd() {
-            return end;
-        }
+    /**
+     * Sets the value of the linkToAllViews property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setLinkToAllViews(Boolean value)
+    {
+      this.linkToAllViews = value;
+    }
 
-        /**
-         * Sets the value of the end property.
-         * 
-         */
-        public void setEnd(int value) {
-            this.end = value;
-        }
+    /**
+     * Gets the value of the includeGaps property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isIncludeGaps()
+    {
+      return includeGaps;
+    }
 
-        /**
-         * Gets the value of the id property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getId() {
-            return id;
-        }
+    /**
+     * Sets the value of the includeGaps property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIncludeGaps(Boolean value)
+    {
+      this.includeGaps = value;
+    }
 
-        /**
-         * Sets the value of the id property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
+    /**
+     * Gets the value of the matchGaps property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isMatchGaps()
+    {
+      return matchGaps;
+    }
 
-        /**
-         * Gets the value of the hidden property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isHidden() {
-            return hidden;
-        }
+    /**
+     * Sets the value of the matchGaps property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setMatchGaps(Boolean value)
+    {
+      this.matchGaps = value;
+    }
 
-        /**
-         * Sets the value of the hidden property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setHidden(Boolean value) {
-            this.hidden = value;
-        }
+    /**
+     * Gets the value of the includeGappedColumns property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isIncludeGappedColumns()
+    {
+      return includeGappedColumns;
+    }
 
-        /**
-         * Gets the value of the viewreference property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isViewreference() {
-            return viewreference;
-        }
+    /**
+     * Sets the value of the includeGappedColumns property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIncludeGappedColumns(Boolean value)
+    {
+      this.includeGappedColumns = value;
+    }
 
-        /**
-         * Sets the value of the viewreference property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setViewreference(Boolean value) {
-            this.viewreference = value;
-        }
+    /**
+     * Gets the value of the denominateByShortestLength property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isDenominateByShortestLength()
+    {
+      return denominateByShortestLength;
+    }
 
+    /**
+     * Sets the value of the denominateByShortestLength property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setDenominateByShortestLength(Boolean value)
+    {
+      this.denominateByShortestLength = value;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;extension base="{www.jalview.org}pdbentry">
-         *       &lt;sequence>
-         *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-         *           &lt;complexType>
-         *             &lt;simpleContent>
-         *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-         *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-         *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               &lt;/extension>
-         *             &lt;/simpleContent>
-         *           &lt;/complexType>
-         *         &lt;/element>
-         *       &lt;/sequence>
-         *     &lt;/extension>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "structureState"
-        })
-        public static class Pdbids
-            extends Pdbentry
-        {
+    /**
+     * Gets the value of the width property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getWidth()
+    {
+      return width;
+    }
 
-            @XmlElement(namespace = "www.jalview.org")
-            protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
-
-            /**
-             * Gets the value of the structureState property.
-             * 
-             * <p>
-             * This accessor method returns a reference to the live list,
-             * not a snapshot. Therefore any modification you make to the
-             * returned list will be present inside the JAXB object.
-             * This is why there is not a <CODE>set</CODE> method for the structureState property.
-             * 
-             * <p>
-             * For example, to add a new item, do as follows:
-             * <pre>
-             *    getStructureState().add(newItem);
-             * </pre>
-             * 
-             * 
-             * <p>
-             * Objects of the following type(s) are allowed in the list
-             * {@link JalviewModel.JSeq.Pdbids.StructureState }
-             * 
-             * 
-             */
-            public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
-                if (structureState == null) {
-                    structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
-                }
-                return this.structureState;
-            }
-
-
-            /**
-             * <p>Java class for anonymous complex type.
-             * 
-             * <p>The following schema fragment specifies the expected content contained within this class.
-             * 
-             * <pre>
-             * &lt;complexType>
-             *   &lt;simpleContent>
-             *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-             *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-             *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-             *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     &lt;/extension>
-             *   &lt;/simpleContent>
-             * &lt;/complexType>
-             * </pre>
-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "", propOrder = {
-                "value"
-            })
-            public static class StructureState {
-
-                @XmlValue
-                protected String value;
-                @XmlAttribute(name = "visible")
-                protected Boolean visible;
-                @XmlAttribute(name = "viewId")
-                protected String viewId;
-                @XmlAttribute(name = "alignwithAlignPanel")
-                protected Boolean alignwithAlignPanel;
-                @XmlAttribute(name = "colourwithAlignPanel")
-                protected Boolean colourwithAlignPanel;
-                @XmlAttribute(name = "colourByJmol")
-                protected Boolean colourByJmol;
-                @XmlAttribute(name = "type")
-                protected String type;
-                @XmlAttribute(name = "width")
-                protected Integer width;
-                @XmlAttribute(name = "height")
-                protected Integer height;
-                @XmlAttribute(name = "xpos")
-                protected Integer xpos;
-                @XmlAttribute(name = "ypos")
-                protected Integer ypos;
-
-                /**
-                 * Gets the value of the value property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getValue() {
-                    return value;
-                }
-
-                /**
-                 * Sets the value of the value property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setValue(String value) {
-                    this.value = value;
-                }
-
-                /**
-                 * Gets the value of the visible property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public Boolean isVisible() {
-                    return visible;
-                }
-
-                /**
-                 * Sets the value of the visible property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setVisible(Boolean value) {
-                    this.visible = value;
-                }
-
-                /**
-                 * Gets the value of the viewId property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getViewId() {
-                    return viewId;
-                }
-
-                /**
-                 * Sets the value of the viewId property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setViewId(String value) {
-                    this.viewId = value;
-                }
-
-                /**
-                 * Gets the value of the alignwithAlignPanel property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isAlignwithAlignPanel() {
-                    if (alignwithAlignPanel == null) {
-                        return true;
-                    } else {
-                        return alignwithAlignPanel;
-                    }
-                }
-
-                /**
-                 * Sets the value of the alignwithAlignPanel property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setAlignwithAlignPanel(Boolean value) {
-                    this.alignwithAlignPanel = value;
-                }
-
-                /**
-                 * Gets the value of the colourwithAlignPanel property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isColourwithAlignPanel() {
-                    if (colourwithAlignPanel == null) {
-                        return false;
-                    } else {
-                        return colourwithAlignPanel;
-                    }
-                }
-
-                /**
-                 * Sets the value of the colourwithAlignPanel property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setColourwithAlignPanel(Boolean value) {
-                    this.colourwithAlignPanel = value;
-                }
-
-                /**
-                 * Gets the value of the colourByJmol property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isColourByJmol() {
-                    if (colourByJmol == null) {
-                        return true;
-                    } else {
-                        return colourByJmol;
-                    }
-                }
-
-                /**
-                 * Sets the value of the colourByJmol property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setColourByJmol(Boolean value) {
-                    this.colourByJmol = value;
-                }
-
-                /**
-                 * Gets the value of the type property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getType() {
-                    return type;
-                }
-
-                /**
-                 * Sets the value of the type property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setType(String value) {
-                    this.type = value;
-                }
-
-                /**
-                 * Gets the value of the width property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getWidth() {
-                    return width;
-                }
-
-                /**
-                 * Sets the value of the width property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setWidth(Integer value) {
-                    this.width = value;
-                }
-
-                /**
-                 * Gets the value of the height property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getHeight() {
-                    return height;
-                }
-
-                /**
-                 * Sets the value of the height property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setHeight(Integer value) {
-                    this.height = value;
-                }
-
-                /**
-                 * Gets the value of the xpos property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getXpos() {
-                    return xpos;
-                }
-
-                /**
-                 * Sets the value of the xpos property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setXpos(Integer value) {
-                    this.xpos = value;
-                }
-
-                /**
-                 * Gets the value of the ypos property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getYpos() {
-                    return ypos;
-                }
-
-                /**
-                 * Sets the value of the ypos property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setYpos(Integer value) {
-                    this.ypos = value;
-                }
-
-            }
+    /**
+     * Sets the value of the width property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setWidth(Integer value)
+    {
+      this.width = value;
+    }
 
-        }
+    /**
+     * Gets the value of the height property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getHeight()
+    {
+      return height;
+    }
 
+    /**
+     * Sets the value of the height property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setHeight(Integer value)
+    {
+      this.height = value;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
-         *           &lt;complexType>
-         *             &lt;complexContent>
-         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               &lt;/restriction>
-         *             &lt;/complexContent>
-         *           &lt;/complexType>
-         *         &lt;/element>
-         *       &lt;/sequence>
-         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "secondaryStructure"
-        })
-        public static class RnaViewer {
-
-            @XmlElement(namespace = "www.jalview.org", required = true)
-            protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
-            @XmlAttribute(name = "title")
-            protected String title;
-            @XmlAttribute(name = "viewId")
-            protected String viewId;
-            @XmlAttribute(name = "dividerLocation")
-            protected Integer dividerLocation;
-            @XmlAttribute(name = "selectedRna")
-            protected Integer selectedRna;
-            @XmlAttribute(name = "width")
-            protected Integer width;
-            @XmlAttribute(name = "height")
-            protected Integer height;
-            @XmlAttribute(name = "xpos")
-            protected Integer xpos;
-            @XmlAttribute(name = "ypos")
-            protected Integer ypos;
-
-            /**
-             * Gets the value of the secondaryStructure property.
-             * 
-             * <p>
-             * This accessor method returns a reference to the live list,
-             * not a snapshot. Therefore any modification you make to the
-             * returned list will be present inside the JAXB object.
-             * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
-             * 
-             * <p>
-             * For example, to add a new item, do as follows:
-             * <pre>
-             *    getSecondaryStructure().add(newItem);
-             * </pre>
-             * 
-             * 
-             * <p>
-             * Objects of the following type(s) are allowed in the list
-             * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-             * 
-             * 
-             */
-            public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
-                if (secondaryStructure == null) {
-                    secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
-                }
-                return this.secondaryStructure;
-            }
-
-            /**
-             * Gets the value of the title property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getTitle() {
-                return title;
-            }
-
-            /**
-             * Sets the value of the title property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setTitle(String value) {
-                this.title = value;
-            }
-
-            /**
-             * Gets the value of the viewId property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getViewId() {
-                return viewId;
-            }
-
-            /**
-             * Sets the value of the viewId property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setViewId(String value) {
-                this.viewId = value;
-            }
-
-            /**
-             * Gets the value of the dividerLocation property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getDividerLocation() {
-                return dividerLocation;
-            }
-
-            /**
-             * Sets the value of the dividerLocation property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setDividerLocation(Integer value) {
-                this.dividerLocation = value;
-            }
-
-            /**
-             * Gets the value of the selectedRna property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getSelectedRna() {
-                return selectedRna;
-            }
-
-            /**
-             * Sets the value of the selectedRna property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setSelectedRna(Integer value) {
-                this.selectedRna = value;
-            }
-
-            /**
-             * Gets the value of the width property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getWidth() {
-                return width;
-            }
-
-            /**
-             * Sets the value of the width property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setWidth(Integer value) {
-                this.width = value;
-            }
-
-            /**
-             * Gets the value of the height property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getHeight() {
-                return height;
-            }
-
-            /**
-             * Sets the value of the height property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setHeight(Integer value) {
-                this.height = value;
-            }
-
-            /**
-             * Gets the value of the xpos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getXpos() {
-                return xpos;
-            }
-
-            /**
-             * Sets the value of the xpos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setXpos(Integer value) {
-                this.xpos = value;
-            }
-
-            /**
-             * Gets the value of the ypos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getYpos() {
-                return ypos;
-            }
-
-            /**
-             * Sets the value of the ypos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setYpos(Integer value) {
-                this.ypos = value;
-            }
-
-
-            /**
-             * <p>Java class for anonymous complex type.
-             * 
-             * <p>The following schema fragment specifies the expected content contained within this class.
-             * 
-             * <pre>
-             * &lt;complexType>
-             *   &lt;complexContent>
-             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     &lt;/restriction>
-             *   &lt;/complexContent>
-             * &lt;/complexType>
-             * </pre>
-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "")
-            public static class SecondaryStructure {
-
-                @XmlAttribute(name = "title")
-                protected String title;
-                @XmlAttribute(name = "annotationId", required = true)
-                protected String annotationId;
-                @XmlAttribute(name = "gapped")
-                protected Boolean gapped;
-                @XmlAttribute(name = "viewerState")
-                protected String viewerState;
-
-                /**
-                 * Gets the value of the title property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getTitle() {
-                    return title;
-                }
-
-                /**
-                 * Sets the value of the title property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setTitle(String value) {
-                    this.title = value;
-                }
-
-                /**
-                 * Gets the value of the annotationId property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getAnnotationId() {
-                    return annotationId;
-                }
-
-                /**
-                 * Sets the value of the annotationId property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setAnnotationId(String value) {
-                    this.annotationId = value;
-                }
-
-                /**
-                 * Gets the value of the gapped property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public Boolean isGapped() {
-                    return gapped;
-                }
-
-                /**
-                 * Sets the value of the gapped property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setGapped(Boolean value) {
-                    this.gapped = value;
-                }
-
-                /**
-                 * Gets the value of the viewerState property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getViewerState() {
-                    return viewerState;
-                }
-
-                /**
-                 * Sets the value of the viewerState property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setViewerState(String value) {
-                    this.viewerState = value;
-                }
-
-            }
+    /**
+     * Gets the value of the xpos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXpos()
+    {
+      return xpos;
+    }
 
-        }
+    /**
+     * Sets the value of the xpos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setXpos(Integer value)
+    {
+      this.xpos = value;
+    }
 
+    /**
+     * Gets the value of the ypos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getYpos()
+    {
+      return ypos;
     }
 
+    /**
+     * Sets the value of the ypos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setYpos(Integer value)
+    {
+      this.ypos = value;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * <p>
+     * Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
      * 
      * <pre>
      * &lt;complexType>
      *   &lt;complexContent>
      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="sequencePoint" maxOccurs="unbounded">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="seqPointMin">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="seqPointMax">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attGroup ref="{www.jalview.org}position"/>
      *     &lt;/restriction>
      *   &lt;/complexContent>
      * &lt;/complexType>
@@ -3145,3670 +3859,3130 @@ public class JalviewModel {
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "sequencePoint",
-        "axis",
-        "seqPointMin",
-        "seqPointMax",
-        "pcaData"
-    })
-    public static class PcaViewer {
-
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List<JalviewModel.PcaViewer.Axis> axis;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected PcaDataType pcaData;
-        @XmlAttribute(name = "title")
-        protected String title;
-        @XmlAttribute(name = "scoreModelName")
-        protected String scoreModelName;
-        @XmlAttribute(name = "xDim")
-        protected Integer xDim;
-        @XmlAttribute(name = "yDim")
-        protected Integer yDim;
-        @XmlAttribute(name = "zDim")
-        protected Integer zDim;
-        @XmlAttribute(name = "bgColour")
-        protected Integer bgColour;
-        @XmlAttribute(name = "scaleFactor")
-        protected Float scaleFactor;
-        @XmlAttribute(name = "showLabels")
-        protected Boolean showLabels;
-        @XmlAttribute(name = "linkToAllViews")
-        protected Boolean linkToAllViews;
-        @XmlAttribute(name = "includeGaps")
-        protected Boolean includeGaps;
-        @XmlAttribute(name = "matchGaps")
-        protected Boolean matchGaps;
-        @XmlAttribute(name = "includeGappedColumns")
-        protected Boolean includeGappedColumns;
-        @XmlAttribute(name = "denominateByShortestLength")
-        protected Boolean denominateByShortestLength;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
-
-        /**
-         * Gets the value of the sequencePoint property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getSequencePoint().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.PcaViewer.SequencePoint }
-         * 
-         * 
-         */
-        public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
-            if (sequencePoint == null) {
-                sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
-            }
-            return this.sequencePoint;
-        }
-
-        /**
-         * Gets the value of the axis property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the axis property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getAxis().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.PcaViewer.Axis }
-         * 
-         * 
-         */
-        public List<JalviewModel.PcaViewer.Axis> getAxis() {
-            if (axis == null) {
-                axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
-            }
-            return this.axis;
-        }
-
-        /**
-         * Gets the value of the seqPointMin property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link JalviewModel.PcaViewer.SeqPointMin }
-         *     
-         */
-        public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
-            return seqPointMin;
-        }
-
-        /**
-         * Sets the value of the seqPointMin property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link JalviewModel.PcaViewer.SeqPointMin }
-         *     
-         */
-        public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
-            this.seqPointMin = value;
-        }
-
-        /**
-         * Gets the value of the seqPointMax property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link JalviewModel.PcaViewer.SeqPointMax }
-         *     
-         */
-        public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
-            return seqPointMax;
-        }
-
-        /**
-         * Sets the value of the seqPointMax property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link JalviewModel.PcaViewer.SeqPointMax }
-         *     
-         */
-        public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
-            this.seqPointMax = value;
-        }
-
-        /**
-         * Gets the value of the pcaData property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link PcaDataType }
-         *     
-         */
-        public PcaDataType getPcaData() {
-            return pcaData;
-        }
-
-        /**
-         * Sets the value of the pcaData property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link PcaDataType }
-         *     
-         */
-        public void setPcaData(PcaDataType value) {
-            this.pcaData = value;
-        }
-
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getTitle() {
-            return title;
-        }
-
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setTitle(String value) {
-            this.title = value;
-        }
-
-        /**
-         * Gets the value of the scoreModelName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getScoreModelName() {
-            return scoreModelName;
-        }
-
-        /**
-         * Sets the value of the scoreModelName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setScoreModelName(String value) {
-            this.scoreModelName = value;
-        }
-
-        /**
-         * Gets the value of the xDim property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getXDim() {
-            return xDim;
-        }
-
-        /**
-         * Sets the value of the xDim property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setXDim(Integer value) {
-            this.xDim = value;
-        }
-
-        /**
-         * Gets the value of the yDim property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getYDim() {
-            return yDim;
-        }
+    @XmlType(name = "")
+    public static class Axis
+    {
+
+      @XmlAttribute(name = "xPos")
+      protected Float xPos;
+
+      @XmlAttribute(name = "yPos")
+      protected Float yPos;
+
+      @XmlAttribute(name = "zPos")
+      protected Float zPos;
+
+      /**
+       * Gets the value of the xPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getXPos()
+      {
+        return xPos;
+      }
+
+      /**
+       * Sets the value of the xPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setXPos(Float value)
+      {
+        this.xPos = value;
+      }
+
+      /**
+       * Gets the value of the yPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getYPos()
+      {
+        return yPos;
+      }
+
+      /**
+       * Sets the value of the yPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setYPos(Float value)
+      {
+        this.yPos = value;
+      }
+
+      /**
+       * Gets the value of the zPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getZPos()
+      {
+        return zPos;
+      }
+
+      /**
+       * Sets the value of the zPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setZPos(Float value)
+      {
+        this.zPos = value;
+      }
 
-        /**
-         * Sets the value of the yDim property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setYDim(Integer value) {
-            this.yDim = value;
-        }
+    }
 
-        /**
-         * Gets the value of the zDim property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getZDim() {
-            return zDim;
-        }
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attGroup ref="{www.jalview.org}position"/>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SeqPointMax
+    {
+
+      @XmlAttribute(name = "xPos")
+      protected Float xPos;
+
+      @XmlAttribute(name = "yPos")
+      protected Float yPos;
+
+      @XmlAttribute(name = "zPos")
+      protected Float zPos;
+
+      /**
+       * Gets the value of the xPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getXPos()
+      {
+        return xPos;
+      }
+
+      /**
+       * Sets the value of the xPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setXPos(Float value)
+      {
+        this.xPos = value;
+      }
+
+      /**
+       * Gets the value of the yPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getYPos()
+      {
+        return yPos;
+      }
+
+      /**
+       * Sets the value of the yPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setYPos(Float value)
+      {
+        this.yPos = value;
+      }
+
+      /**
+       * Gets the value of the zPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getZPos()
+      {
+        return zPos;
+      }
+
+      /**
+       * Sets the value of the zPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setZPos(Float value)
+      {
+        this.zPos = value;
+      }
 
-        /**
-         * Sets the value of the zDim property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setZDim(Integer value) {
-            this.zDim = value;
-        }
+    }
 
-        /**
-         * Gets the value of the bgColour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getBgColour() {
-            return bgColour;
-        }
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attGroup ref="{www.jalview.org}position"/>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SeqPointMin
+    {
+
+      @XmlAttribute(name = "xPos")
+      protected Float xPos;
+
+      @XmlAttribute(name = "yPos")
+      protected Float yPos;
+
+      @XmlAttribute(name = "zPos")
+      protected Float zPos;
+
+      /**
+       * Gets the value of the xPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getXPos()
+      {
+        return xPos;
+      }
+
+      /**
+       * Sets the value of the xPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setXPos(Float value)
+      {
+        this.xPos = value;
+      }
+
+      /**
+       * Gets the value of the yPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getYPos()
+      {
+        return yPos;
+      }
+
+      /**
+       * Sets the value of the yPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setYPos(Float value)
+      {
+        this.yPos = value;
+      }
+
+      /**
+       * Gets the value of the zPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getZPos()
+      {
+        return zPos;
+      }
+
+      /**
+       * Sets the value of the zPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setZPos(Float value)
+      {
+        this.zPos = value;
+      }
 
-        /**
-         * Sets the value of the bgColour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setBgColour(Integer value) {
-            this.bgColour = value;
-        }
+    }
 
-        /**
-         * Gets the value of the scaleFactor property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getScaleFactor() {
-            return scaleFactor;
-        }
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attGroup ref="{www.jalview.org}position"/>
+     *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SequencePoint
+    {
+
+      @XmlAttribute(name = "sequenceRef")
+      protected String sequenceRef;
+
+      @XmlAttribute(name = "xPos")
+      protected Float xPos;
+
+      @XmlAttribute(name = "yPos")
+      protected Float yPos;
+
+      @XmlAttribute(name = "zPos")
+      protected Float zPos;
+
+      /**
+       * Gets the value of the sequenceRef property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getSequenceRef()
+      {
+        return sequenceRef;
+      }
+
+      /**
+       * Sets the value of the sequenceRef property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setSequenceRef(String value)
+      {
+        this.sequenceRef = value;
+      }
+
+      /**
+       * Gets the value of the xPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getXPos()
+      {
+        return xPos;
+      }
+
+      /**
+       * Sets the value of the xPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setXPos(Float value)
+      {
+        this.xPos = value;
+      }
+
+      /**
+       * Gets the value of the yPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getYPos()
+      {
+        return yPos;
+      }
+
+      /**
+       * Sets the value of the yPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setYPos(Float value)
+      {
+        this.yPos = value;
+      }
+
+      /**
+       * Gets the value of the zPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getZPos()
+      {
+        return zPos;
+      }
+
+      /**
+       * Sets the value of the zPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setZPos(Float value)
+      {
+        this.zPos = value;
+      }
 
-        /**
-         * Sets the value of the scaleFactor property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setScaleFactor(Float value) {
-            this.scaleFactor = value;
-        }
+    }
 
-        /**
-         * Gets the value of the showLabels property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowLabels() {
-            return showLabels;
-        }
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence minOccurs="0">
+   *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *       &lt;/sequence>
+   *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+   *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "title", "newick" })
+  public static class Tree
+  {
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected String title;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected String newick;
+
+    @XmlAttribute(name = "fontName")
+    protected String fontName;
+
+    @XmlAttribute(name = "fontSize")
+    protected Integer fontSize;
+
+    @XmlAttribute(name = "fontStyle")
+    protected Integer fontStyle;
+
+    @XmlAttribute(name = "threshold")
+    protected Float threshold;
+
+    @XmlAttribute(name = "showBootstrap")
+    protected Boolean showBootstrap;
+
+    @XmlAttribute(name = "showDistances")
+    protected Boolean showDistances;
+
+    @XmlAttribute(name = "markUnlinked")
+    protected Boolean markUnlinked;
+
+    @XmlAttribute(name = "fitToWindow")
+    protected Boolean fitToWindow;
+
+    @XmlAttribute(name = "currentTree")
+    protected Boolean currentTree;
+
+    @XmlAttribute(name = "columnWise")
+    protected Boolean columnWise;
+
+    @XmlAttribute(name = "columnReference")
+    protected String columnReference;
+
+    @XmlAttribute(name = "id")
+    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+    @XmlID
+    @XmlSchemaType(name = "ID")
+    protected String id;
+
+    @XmlAttribute(name = "linkToAllViews")
+    protected Boolean linkToAllViews;
+
+    @XmlAttribute(name = "width")
+    protected Integer width;
+
+    @XmlAttribute(name = "height")
+    protected Integer height;
+
+    @XmlAttribute(name = "xpos")
+    protected Integer xpos;
+
+    @XmlAttribute(name = "ypos")
+    protected Integer ypos;
 
-        /**
-         * Sets the value of the showLabels property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowLabels(Boolean value) {
-            this.showLabels = value;
-        }
+    /**
+     * Gets the value of the title property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getTitle()
+    {
+      return title;
+    }
 
-        /**
-         * Gets the value of the linkToAllViews property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isLinkToAllViews() {
-            return linkToAllViews;
-        }
+    /**
+     * Sets the value of the title property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setTitle(String value)
+    {
+      this.title = value;
+    }
 
-        /**
-         * Sets the value of the linkToAllViews property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setLinkToAllViews(Boolean value) {
-            this.linkToAllViews = value;
-        }
+    /**
+     * Gets the value of the newick property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getNewick()
+    {
+      return newick;
+    }
 
-        /**
-         * Gets the value of the includeGaps property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isIncludeGaps() {
-            return includeGaps;
-        }
+    /**
+     * Sets the value of the newick property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setNewick(String value)
+    {
+      this.newick = value;
+    }
 
-        /**
-         * Sets the value of the includeGaps property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setIncludeGaps(Boolean value) {
-            this.includeGaps = value;
-        }
+    /**
+     * Gets the value of the fontName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getFontName()
+    {
+      return fontName;
+    }
 
-        /**
-         * Gets the value of the matchGaps property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isMatchGaps() {
-            return matchGaps;
-        }
+    /**
+     * Sets the value of the fontName property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setFontName(String value)
+    {
+      this.fontName = value;
+    }
 
-        /**
-         * Sets the value of the matchGaps property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setMatchGaps(Boolean value) {
-            this.matchGaps = value;
-        }
+    /**
+     * Gets the value of the fontSize property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontSize()
+    {
+      return fontSize;
+    }
 
-        /**
-         * Gets the value of the includeGappedColumns property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isIncludeGappedColumns() {
-            return includeGappedColumns;
-        }
+    /**
+     * Sets the value of the fontSize property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setFontSize(Integer value)
+    {
+      this.fontSize = value;
+    }
 
-        /**
-         * Sets the value of the includeGappedColumns property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setIncludeGappedColumns(Boolean value) {
-            this.includeGappedColumns = value;
-        }
+    /**
+     * Gets the value of the fontStyle property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontStyle()
+    {
+      return fontStyle;
+    }
 
-        /**
-         * Gets the value of the denominateByShortestLength property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isDenominateByShortestLength() {
-            return denominateByShortestLength;
-        }
+    /**
+     * Sets the value of the fontStyle property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setFontStyle(Integer value)
+    {
+      this.fontStyle = value;
+    }
 
-        /**
-         * Sets the value of the denominateByShortestLength property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setDenominateByShortestLength(Boolean value) {
-            this.denominateByShortestLength = value;
-        }
+    /**
+     * Gets the value of the threshold property.
+     * 
+     * @return possible object is {@link Float }
+     * 
+     */
+    public Float getThreshold()
+    {
+      return threshold;
+    }
 
-        /**
-         * Gets the value of the width property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getWidth() {
-            return width;
-        }
+    /**
+     * Sets the value of the threshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Float }
+     * 
+     */
+    public void setThreshold(Float value)
+    {
+      this.threshold = value;
+    }
 
-        /**
-         * Sets the value of the width property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setWidth(Integer value) {
-            this.width = value;
-        }
+    /**
+     * Gets the value of the showBootstrap property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowBootstrap()
+    {
+      return showBootstrap;
+    }
 
-        /**
-         * Gets the value of the height property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getHeight() {
-            return height;
-        }
+    /**
+     * Sets the value of the showBootstrap property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowBootstrap(Boolean value)
+    {
+      this.showBootstrap = value;
+    }
 
-        /**
-         * Sets the value of the height property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setHeight(Integer value) {
-            this.height = value;
-        }
+    /**
+     * Gets the value of the showDistances property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowDistances()
+    {
+      return showDistances;
+    }
 
-        /**
-         * Gets the value of the xpos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getXpos() {
-            return xpos;
-        }
+    /**
+     * Sets the value of the showDistances property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowDistances(Boolean value)
+    {
+      this.showDistances = value;
+    }
 
-        /**
-         * Sets the value of the xpos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setXpos(Integer value) {
-            this.xpos = value;
-        }
+    /**
+     * Gets the value of the markUnlinked property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isMarkUnlinked()
+    {
+      return markUnlinked;
+    }
 
-        /**
-         * Gets the value of the ypos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getYpos() {
-            return ypos;
-        }
+    /**
+     * Sets the value of the markUnlinked property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setMarkUnlinked(Boolean value)
+    {
+      this.markUnlinked = value;
+    }
 
-        /**
-         * Sets the value of the ypos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setYpos(Integer value) {
-            this.ypos = value;
-        }
+    /**
+     * Gets the value of the fitToWindow property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isFitToWindow()
+    {
+      return fitToWindow;
+    }
 
+    /**
+     * Sets the value of the fitToWindow property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setFitToWindow(Boolean value)
+    {
+      this.fitToWindow = value;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Axis {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * Gets the value of the currentTree property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isCurrentTree()
+    {
+      return currentTree;
+    }
 
-        }
+    /**
+     * Sets the value of the currentTree property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setCurrentTree(Boolean value)
+    {
+      this.currentTree = value;
+    }
 
+    /**
+     * Gets the value of the columnWise property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isColumnWise()
+    {
+      if (columnWise == null)
+      {
+        return false;
+      }
+      else
+      {
+        return columnWise;
+      }
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SeqPointMax {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * Sets the value of the columnWise property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setColumnWise(Boolean value)
+    {
+      this.columnWise = value;
+    }
+
+    /**
+     * Gets the value of the columnReference property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getColumnReference()
+    {
+      return columnReference;
+    }
+
+    /**
+     * Sets the value of the columnReference property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setColumnReference(String value)
+    {
+      this.columnReference = 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;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SeqPointMin {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * Gets the value of the linkToAllViews property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isLinkToAllViews()
+    {
+      if (linkToAllViews == null)
+      {
+        return false;
+      }
+      else
+      {
+        return linkToAllViews;
+      }
+    }
 
-        }
+    /**
+     * Sets the value of the linkToAllViews property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setLinkToAllViews(Boolean value)
+    {
+      this.linkToAllViews = value;
+    }
 
+    /**
+     * Gets the value of the width property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getWidth()
+    {
+      return width;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SequencePoint {
-
-            @XmlAttribute(name = "sequenceRef")
-            protected String sequenceRef;
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the sequenceRef property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getSequenceRef() {
-                return sequenceRef;
-            }
-
-            /**
-             * Sets the value of the sequenceRef property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setSequenceRef(String value) {
-                this.sequenceRef = value;
-            }
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * Sets the value of the width property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setWidth(Integer value)
+    {
+      this.width = value;
+    }
 
-        }
+    /**
+     * Gets the value of the height property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getHeight()
+    {
+      return height;
+    }
 
+    /**
+     * Sets the value of the height property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setHeight(Integer value)
+    {
+      this.height = value;
     }
 
+    /**
+     * Gets the value of the xpos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXpos()
+    {
+      return xpos;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Sets the value of the xpos property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Integer }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence minOccurs="0">
-     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public void setXpos(Integer value)
+    {
+      this.xpos = value;
+    }
+
+    /**
+     * Gets the value of the ypos property.
      * 
+     * @return possible object is {@link Integer }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "title",
-        "newick"
-    })
-    public static class Tree {
+    public Integer getYpos()
+    {
+      return ypos;
+    }
 
-        @XmlElement(namespace = "www.jalview.org")
-        protected String title;
-        @XmlElement(namespace = "www.jalview.org")
-        protected String newick;
-        @XmlAttribute(name = "fontName")
-        protected String fontName;
-        @XmlAttribute(name = "fontSize")
-        protected Integer fontSize;
-        @XmlAttribute(name = "fontStyle")
-        protected Integer fontStyle;
-        @XmlAttribute(name = "threshold")
-        protected Float threshold;
-        @XmlAttribute(name = "showBootstrap")
-        protected Boolean showBootstrap;
-        @XmlAttribute(name = "showDistances")
-        protected Boolean showDistances;
-        @XmlAttribute(name = "markUnlinked")
-        protected Boolean markUnlinked;
-        @XmlAttribute(name = "fitToWindow")
-        protected Boolean fitToWindow;
-        @XmlAttribute(name = "currentTree")
-        protected Boolean currentTree;
-        @XmlAttribute(name = "columnWise")
-        protected Boolean columnWise;
-        @XmlAttribute(name = "columnReference")
-        protected String columnReference;
-        @XmlAttribute(name = "id")
-        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-        @XmlID
-        @XmlSchemaType(name = "ID")
-        protected String id;
-        @XmlAttribute(name = "linkToAllViews")
-        protected Boolean linkToAllViews;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
+    /**
+     * Sets the value of the ypos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setYpos(Integer value)
+    {
+      this.ypos = value;
+    }
 
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getTitle() {
-            return title;
-        }
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "userColourScheme" })
+  public static class UserColours
+  {
+
+    @XmlElement(
+      name = "UserColourScheme",
+      namespace = "www.jalview.org",
+      required = true)
+    protected JalviewUserColours userColourScheme;
+
+    @XmlAttribute(name = "id")
+    protected String id;
 
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setTitle(String value) {
-            this.title = value;
-        }
+    /**
+     * Gets the value of the userColourScheme property.
+     * 
+     * @return possible object is {@link JalviewUserColours }
+     * 
+     */
+    public JalviewUserColours getUserColourScheme()
+    {
+      return userColourScheme;
+    }
 
-        /**
-         * Gets the value of the newick property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getNewick() {
-            return newick;
-        }
+    /**
+     * Sets the value of the userColourScheme property.
+     * 
+     * @param value
+     *          allowed object is {@link JalviewUserColours }
+     * 
+     */
+    public void setUserColourScheme(JalviewUserColours value)
+    {
+      this.userColourScheme = value;
+    }
 
-        /**
-         * Sets the value of the newick property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setNewick(String value) {
-            this.newick = value;
-        }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
 
-        /**
-         * Gets the value of the fontName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getFontName() {
-            return fontName;
-        }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setId(String value)
+    {
+      this.id = value;
+    }
 
-        /**
-         * Sets the value of the fontName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setFontName(String value) {
-            this.fontName = value;
-        }
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+   *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               &lt;/extension>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *         &lt;element name="overview" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *       &lt;/sequence>
+   *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+   *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
+  public static class Viewport
+  {
+
+    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+    protected AnnotationColourScheme annotationColours;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected JalviewModel.Viewport.Overview overview;
+
+    @XmlAttribute(name = "conservationSelected")
+    protected Boolean conservationSelected;
+
+    @XmlAttribute(name = "pidSelected")
+    protected Boolean pidSelected;
+
+    @XmlAttribute(name = "bgColour")
+    protected String bgColour;
+
+    @XmlAttribute(name = "consThreshold")
+    protected Integer consThreshold;
+
+    @XmlAttribute(name = "pidThreshold")
+    protected Integer pidThreshold;
+
+    @XmlAttribute(name = "title")
+    protected String title;
+
+    @XmlAttribute(name = "showFullId")
+    protected Boolean showFullId;
+
+    @XmlAttribute(name = "rightAlignIds")
+    protected Boolean rightAlignIds;
+
+    @XmlAttribute(name = "showText")
+    protected Boolean showText;
+
+    @XmlAttribute(name = "showColourText")
+    protected Boolean showColourText;
+
+    @XmlAttribute(name = "showUnconserved")
+    protected Boolean showUnconserved;
+
+    @XmlAttribute(name = "showBoxes")
+    protected Boolean showBoxes;
+
+    @XmlAttribute(name = "wrapAlignment")
+    protected Boolean wrapAlignment;
 
-        /**
-         * Gets the value of the fontSize property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontSize() {
-            return fontSize;
-        }
+    @XmlAttribute(name = "renderGaps")
+    protected Boolean renderGaps;
 
-        /**
-         * Sets the value of the fontSize property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontSize(Integer value) {
-            this.fontSize = value;
-        }
+    @XmlAttribute(name = "showSequenceFeatures")
+    protected Boolean showSequenceFeatures;
 
-        /**
-         * Gets the value of the fontStyle property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontStyle() {
-            return fontStyle;
-        }
+    @XmlAttribute(name = "showNPfeatureTooltip")
+    protected Boolean showNPfeatureTooltip;
 
-        /**
-         * Sets the value of the fontStyle property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontStyle(Integer value) {
-            this.fontStyle = value;
-        }
+    @XmlAttribute(name = "showDbRefTooltip")
+    protected Boolean showDbRefTooltip;
 
-        /**
-         * Gets the value of the threshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getThreshold() {
-            return threshold;
-        }
+    @XmlAttribute(name = "followHighlight")
+    protected Boolean followHighlight;
 
-        /**
-         * Sets the value of the threshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setThreshold(Float value) {
-            this.threshold = value;
-        }
+    @XmlAttribute(name = "followSelection")
+    protected Boolean followSelection;
 
-        /**
-         * Gets the value of the showBootstrap property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowBootstrap() {
-            return showBootstrap;
-        }
+    @XmlAttribute(name = "showAnnotation")
+    protected Boolean showAnnotation;
 
-        /**
-         * Sets the value of the showBootstrap property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowBootstrap(Boolean value) {
-            this.showBootstrap = value;
-        }
+    @XmlAttribute(name = "centreColumnLabels")
+    protected Boolean centreColumnLabels;
 
-        /**
-         * Gets the value of the showDistances property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowDistances() {
-            return showDistances;
-        }
+    @XmlAttribute(name = "showGroupConservation")
+    protected Boolean showGroupConservation;
 
-        /**
-         * Sets the value of the showDistances property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowDistances(Boolean value) {
-            this.showDistances = value;
-        }
+    @XmlAttribute(name = "showGroupConsensus")
+    protected Boolean showGroupConsensus;
 
-        /**
-         * Gets the value of the markUnlinked property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isMarkUnlinked() {
-            return markUnlinked;
-        }
+    @XmlAttribute(name = "showConsensusHistogram")
+    protected Boolean showConsensusHistogram;
 
-        /**
-         * Sets the value of the markUnlinked property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setMarkUnlinked(Boolean value) {
-            this.markUnlinked = value;
-        }
+    @XmlAttribute(name = "showSequenceLogo")
+    protected Boolean showSequenceLogo;
 
-        /**
-         * Gets the value of the fitToWindow property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isFitToWindow() {
-            return fitToWindow;
-        }
+    @XmlAttribute(name = "normaliseSequenceLogo")
+    protected Boolean normaliseSequenceLogo;
 
-        /**
-         * Sets the value of the fitToWindow property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setFitToWindow(Boolean value) {
-            this.fitToWindow = value;
-        }
+    @XmlAttribute(name = "ignoreGapsinConsensus")
+    protected Boolean ignoreGapsinConsensus;
 
-        /**
-         * Gets the value of the currentTree property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isCurrentTree() {
-            return currentTree;
-        }
+    @XmlAttribute(name = "startRes")
+    protected Integer startRes;
 
-        /**
-         * Sets the value of the currentTree property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setCurrentTree(Boolean value) {
-            this.currentTree = value;
-        }
+    @XmlAttribute(name = "startSeq")
+    protected Integer startSeq;
 
-        /**
-         * Gets the value of the columnWise property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isColumnWise() {
-            if (columnWise == null) {
-                return false;
-            } else {
-                return columnWise;
-            }
-        }
+    @XmlAttribute(name = "charWidth")
+    protected Integer charWidth;
 
-        /**
-         * Sets the value of the columnWise property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setColumnWise(Boolean value) {
-            this.columnWise = value;
-        }
+    @XmlAttribute(name = "charHeight")
+    protected Integer charHeight;
 
-        /**
-         * Gets the value of the columnReference property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getColumnReference() {
-            return columnReference;
-        }
+    @XmlAttribute(name = "fontName")
+    protected String fontName;
 
-        /**
-         * Sets the value of the columnReference property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setColumnReference(String value) {
-            this.columnReference = value;
-        }
+    @XmlAttribute(name = "fontSize")
+    protected Integer fontSize;
 
-        /**
-         * Gets the value of the id property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getId() {
-            return id;
-        }
+    @XmlAttribute(name = "fontStyle")
+    protected Integer fontStyle;
 
-        /**
-         * Sets the value of the id property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
+    @XmlAttribute(name = "scaleProteinAsCdna")
+    protected Boolean scaleProteinAsCdna;
 
-        /**
-         * Gets the value of the linkToAllViews property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isLinkToAllViews() {
-            if (linkToAllViews == null) {
-                return false;
-            } else {
-                return linkToAllViews;
-            }
-        }
+    @XmlAttribute(name = "viewName")
+    protected String viewName;
 
-        /**
-         * Sets the value of the linkToAllViews property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setLinkToAllViews(Boolean value) {
-            this.linkToAllViews = value;
-        }
+    @XmlAttribute(name = "sequenceSetId")
+    protected String sequenceSetId;
+
+    @XmlAttribute(name = "gatheredViews")
+    protected Boolean gatheredViews;
 
-        /**
-         * Gets the value of the width property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getWidth() {
-            return width;
-        }
+    @XmlAttribute(name = "textCol1")
+    protected Integer textCol1;
 
-        /**
-         * Sets the value of the width property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setWidth(Integer value) {
-            this.width = value;
-        }
+    @XmlAttribute(name = "textCol2")
+    protected Integer textCol2;
 
-        /**
-         * Gets the value of the height property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getHeight() {
-            return height;
-        }
+    @XmlAttribute(name = "textColThreshold")
+    protected Integer textColThreshold;
 
-        /**
-         * Sets the value of the height property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setHeight(Integer value) {
-            this.height = value;
-        }
+    @XmlAttribute(name = "id")
+    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+    @XmlID
+    @XmlSchemaType(name = "ID")
+    protected String id;
 
-        /**
-         * Gets the value of the xpos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getXpos() {
-            return xpos;
-        }
+    @XmlAttribute(name = "complementId")
+    protected String complementId;
 
-        /**
-         * Sets the value of the xpos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setXpos(Integer value) {
-            this.xpos = value;
-        }
+    @XmlAttribute(name = "showComplementFeatures")
+    protected Boolean showComplementFeatures;
 
-        /**
-         * Gets the value of the ypos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getYpos() {
-            return ypos;
-        }
+    @XmlAttribute(name = "showComplementFeaturesOnTop")
+    protected Boolean showComplementFeaturesOnTop;
 
-        /**
-         * Sets the value of the ypos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setYpos(Integer value) {
-            this.ypos = value;
-        }
+    @XmlAttribute(name = "width")
+    protected Integer width;
 
+    @XmlAttribute(name = "height")
+    protected Integer height;
+
+    @XmlAttribute(name = "xpos")
+    protected Integer xpos;
+
+    @XmlAttribute(name = "ypos")
+    protected Integer ypos;
+
+    /**
+     * Gets the value of the annotationColours property.
+     * 
+     * @return possible object is {@link AnnotationColourScheme }
+     * 
+     */
+    public AnnotationColourScheme getAnnotationColours()
+    {
+      return annotationColours;
     }
 
+    /**
+     * Sets the value of the annotationColours property.
+     * 
+     * @param value
+     *          allowed object is {@link AnnotationColourScheme }
+     * 
+     */
+    public void setAnnotationColours(AnnotationColourScheme value)
+    {
+      this.annotationColours = value;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the hiddenColumns property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the hiddenColumns property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getHiddenColumns().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Viewport.HiddenColumns }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "userColourScheme"
-    })
-    public static class UserColours {
-
-        @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
-        protected JalviewUserColours userColourScheme;
-        @XmlAttribute(name = "id")
-        protected String id;
-
-        /**
-         * Gets the value of the userColourScheme property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link JalviewUserColours }
-         *     
-         */
-        public JalviewUserColours getUserColourScheme() {
-            return userColourScheme;
-        }
-
-        /**
-         * Sets the value of the userColourScheme property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link JalviewUserColours }
-         *     
-         */
-        public void setUserColourScheme(JalviewUserColours value) {
-            this.userColourScheme = value;
-        }
-
-        /**
-         * Gets the value of the id property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getId() {
-            return id;
-        }
-
-        /**
-         * Sets the value of the id property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
-
+    public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns()
+    {
+      if (hiddenColumns == null)
+      {
+        hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+      }
+      return this.hiddenColumns;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the calcIdParam property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the calcIdParam property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/extension>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="overview" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getCalcIdParam().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Viewport.CalcIdParam }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "annotationColours",
-        "hiddenColumns",
-        "calcIdParam",
-        "overview"
-    })
-    public static class Viewport {
-
-        @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
-        protected AnnotationColourScheme annotationColours;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
-        @XmlElement(namespace = "www.jalview.org")
-        protected JalviewModel.Viewport.Overview overview;
-        @XmlAttribute(name = "conservationSelected")
-        protected Boolean conservationSelected;
-        @XmlAttribute(name = "pidSelected")
-        protected Boolean pidSelected;
-        @XmlAttribute(name = "bgColour")
-        protected String bgColour;
-        @XmlAttribute(name = "consThreshold")
-        protected Integer consThreshold;
-        @XmlAttribute(name = "pidThreshold")
-        protected Integer pidThreshold;
-        @XmlAttribute(name = "title")
-        protected String title;
-        @XmlAttribute(name = "showFullId")
-        protected Boolean showFullId;
-        @XmlAttribute(name = "rightAlignIds")
-        protected Boolean rightAlignIds;
-        @XmlAttribute(name = "showText")
-        protected Boolean showText;
-        @XmlAttribute(name = "showColourText")
-        protected Boolean showColourText;
-        @XmlAttribute(name = "showUnconserved")
-        protected Boolean showUnconserved;
-        @XmlAttribute(name = "showBoxes")
-        protected Boolean showBoxes;
-        @XmlAttribute(name = "wrapAlignment")
-        protected Boolean wrapAlignment;
-        @XmlAttribute(name = "renderGaps")
-        protected Boolean renderGaps;
-        @XmlAttribute(name = "showSequenceFeatures")
-        protected Boolean showSequenceFeatures;
-        @XmlAttribute(name = "showNPfeatureTooltip")
-        protected Boolean showNPfeatureTooltip;
-        @XmlAttribute(name = "showDbRefTooltip")
-        protected Boolean showDbRefTooltip;
-        @XmlAttribute(name = "followHighlight")
-        protected Boolean followHighlight;
-        @XmlAttribute(name = "followSelection")
-        protected Boolean followSelection;
-        @XmlAttribute(name = "showAnnotation")
-        protected Boolean showAnnotation;
-        @XmlAttribute(name = "centreColumnLabels")
-        protected Boolean centreColumnLabels;
-        @XmlAttribute(name = "showGroupConservation")
-        protected Boolean showGroupConservation;
-        @XmlAttribute(name = "showGroupConsensus")
-        protected Boolean showGroupConsensus;
-        @XmlAttribute(name = "showConsensusHistogram")
-        protected Boolean showConsensusHistogram;
-        @XmlAttribute(name = "showSequenceLogo")
-        protected Boolean showSequenceLogo;
-        @XmlAttribute(name = "normaliseSequenceLogo")
-        protected Boolean normaliseSequenceLogo;
-        @XmlAttribute(name = "ignoreGapsinConsensus")
-        protected Boolean ignoreGapsinConsensus;
-        @XmlAttribute(name = "startRes")
-        protected Integer startRes;
-        @XmlAttribute(name = "startSeq")
-        protected Integer startSeq;
-        @XmlAttribute(name = "charWidth")
-        protected Integer charWidth;
-        @XmlAttribute(name = "charHeight")
-        protected Integer charHeight;
-        @XmlAttribute(name = "fontName")
-        protected String fontName;
-        @XmlAttribute(name = "fontSize")
-        protected Integer fontSize;
-        @XmlAttribute(name = "fontStyle")
-        protected Integer fontStyle;
-        @XmlAttribute(name = "scaleProteinAsCdna")
-        protected Boolean scaleProteinAsCdna;
-        @XmlAttribute(name = "viewName")
-        protected String viewName;
-        @XmlAttribute(name = "sequenceSetId")
-        protected String sequenceSetId;
-        @XmlAttribute(name = "gatheredViews")
-        protected Boolean gatheredViews;
-        @XmlAttribute(name = "textCol1")
-        protected Integer textCol1;
-        @XmlAttribute(name = "textCol2")
-        protected Integer textCol2;
-        @XmlAttribute(name = "textColThreshold")
-        protected Integer textColThreshold;
-        @XmlAttribute(name = "id")
-        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-        @XmlID
-        @XmlSchemaType(name = "ID")
-        protected String id;
-        @XmlAttribute(name = "complementId")
-        protected String complementId;
-        @XmlAttribute(name = "showComplementFeatures")
-        protected Boolean showComplementFeatures;
-        @XmlAttribute(name = "showComplementFeaturesOnTop")
-        protected Boolean showComplementFeaturesOnTop;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
-
-        /**
-         * Gets the value of the annotationColours property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link AnnotationColourScheme }
-         *     
-         */
-        public AnnotationColourScheme getAnnotationColours() {
-            return annotationColours;
-        }
-
-        /**
-         * Sets the value of the annotationColours property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link AnnotationColourScheme }
-         *     
-         */
-        public void setAnnotationColours(AnnotationColourScheme value) {
-            this.annotationColours = value;
-        }
-
-        /**
-         * Gets the value of the hiddenColumns property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getHiddenColumns().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.Viewport.HiddenColumns }
-         * 
-         * 
-         */
-        public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
-            if (hiddenColumns == null) {
-                hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
-            }
-            return this.hiddenColumns;
-        }
-
-        /**
-         * Gets the value of the calcIdParam property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getCalcIdParam().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.Viewport.CalcIdParam }
-         * 
-         * 
-         */
-        public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
-            if (calcIdParam == null) {
-                calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
-            }
-            return this.calcIdParam;
-        }
-
-        /**
-         * Gets the value of the overview property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link JalviewModel.Viewport.Overview }
-         *     
-         */
-        public JalviewModel.Viewport.Overview getOverview() {
-            return overview;
-        }
-
-        /**
-         * Sets the value of the overview property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link JalviewModel.Viewport.Overview }
-         *     
-         */
-        public void setOverview(JalviewModel.Viewport.Overview value) {
-            this.overview = value;
-        }
-
-        /**
-         * Gets the value of the conservationSelected property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isConservationSelected() {
-            return conservationSelected;
-        }
-
-        /**
-         * Sets the value of the conservationSelected property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setConservationSelected(Boolean value) {
-            this.conservationSelected = value;
-        }
-
-        /**
-         * Gets the value of the pidSelected property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isPidSelected() {
-            return pidSelected;
-        }
-
-        /**
-         * Sets the value of the pidSelected property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setPidSelected(Boolean value) {
-            this.pidSelected = value;
-        }
-
-        /**
-         * Gets the value of the bgColour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getBgColour() {
-            return bgColour;
-        }
+    public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam()
+    {
+      if (calcIdParam == null)
+      {
+        calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+      }
+      return this.calcIdParam;
+    }
 
-        /**
-         * Sets the value of the bgColour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setBgColour(String value) {
-            this.bgColour = value;
-        }
+    /**
+     * Gets the value of the overview property.
+     * 
+     * @return possible object is {@link JalviewModel.Viewport.Overview }
+     * 
+     */
+    public JalviewModel.Viewport.Overview getOverview()
+    {
+      return overview;
+    }
 
-        /**
-         * Gets the value of the consThreshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getConsThreshold() {
-            return consThreshold;
-        }
+    /**
+     * Sets the value of the overview property.
+     * 
+     * @param value
+     *          allowed object is {@link JalviewModel.Viewport.Overview }
+     * 
+     */
+    public void setOverview(JalviewModel.Viewport.Overview value)
+    {
+      this.overview = value;
+    }
 
-        /**
-         * Sets the value of the consThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setConsThreshold(Integer value) {
-            this.consThreshold = value;
-        }
+    /**
+     * Gets the value of the conservationSelected property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isConservationSelected()
+    {
+      return conservationSelected;
+    }
 
-        /**
-         * Gets the value of the pidThreshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getPidThreshold() {
-            return pidThreshold;
-        }
+    /**
+     * Sets the value of the conservationSelected property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setConservationSelected(Boolean value)
+    {
+      this.conservationSelected = value;
+    }
 
-        /**
-         * Sets the value of the pidThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setPidThreshold(Integer value) {
-            this.pidThreshold = value;
-        }
+    /**
+     * Gets the value of the pidSelected property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isPidSelected()
+    {
+      return pidSelected;
+    }
 
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getTitle() {
-            return title;
-        }
+    /**
+     * Sets the value of the pidSelected property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setPidSelected(Boolean value)
+    {
+      this.pidSelected = value;
+    }
 
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setTitle(String value) {
-            this.title = value;
-        }
+    /**
+     * Gets the value of the bgColour property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getBgColour()
+    {
+      return bgColour;
+    }
 
-        /**
-         * Gets the value of the showFullId property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowFullId() {
-            return showFullId;
-        }
+    /**
+     * Sets the value of the bgColour property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setBgColour(String value)
+    {
+      this.bgColour = value;
+    }
 
-        /**
-         * Sets the value of the showFullId property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowFullId(Boolean value) {
-            this.showFullId = value;
-        }
+    /**
+     * Gets the value of the consThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getConsThreshold()
+    {
+      return consThreshold;
+    }
 
-        /**
-         * Gets the value of the rightAlignIds property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isRightAlignIds() {
-            return rightAlignIds;
-        }
+    /**
+     * Sets the value of the consThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setConsThreshold(Integer value)
+    {
+      this.consThreshold = value;
+    }
 
-        /**
-         * Sets the value of the rightAlignIds property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setRightAlignIds(Boolean value) {
-            this.rightAlignIds = value;
-        }
+    /**
+     * Gets the value of the pidThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getPidThreshold()
+    {
+      return pidThreshold;
+    }
 
-        /**
-         * Gets the value of the showText property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowText() {
-            return showText;
-        }
+    /**
+     * Sets the value of the pidThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setPidThreshold(Integer value)
+    {
+      this.pidThreshold = value;
+    }
 
-        /**
-         * Sets the value of the showText property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowText(Boolean value) {
-            this.showText = value;
-        }
+    /**
+     * Gets the value of the title property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getTitle()
+    {
+      return title;
+    }
 
-        /**
-         * Gets the value of the showColourText property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowColourText() {
-            return showColourText;
-        }
+    /**
+     * Sets the value of the title property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setTitle(String value)
+    {
+      this.title = value;
+    }
 
-        /**
-         * Sets the value of the showColourText property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowColourText(Boolean value) {
-            this.showColourText = value;
-        }
+    /**
+     * Gets the value of the showFullId property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowFullId()
+    {
+      return showFullId;
+    }
 
-        /**
-         * Gets the value of the showUnconserved property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowUnconserved() {
-            if (showUnconserved == null) {
-                return false;
-            } else {
-                return showUnconserved;
-            }
-        }
+    /**
+     * Sets the value of the showFullId property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowFullId(Boolean value)
+    {
+      this.showFullId = value;
+    }
 
-        /**
-         * Sets the value of the showUnconserved property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowUnconserved(Boolean value) {
-            this.showUnconserved = value;
-        }
+    /**
+     * Gets the value of the rightAlignIds property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isRightAlignIds()
+    {
+      return rightAlignIds;
+    }
 
-        /**
-         * Gets the value of the showBoxes property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowBoxes() {
-            return showBoxes;
-        }
+    /**
+     * Sets the value of the rightAlignIds property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setRightAlignIds(Boolean value)
+    {
+      this.rightAlignIds = value;
+    }
 
-        /**
-         * Sets the value of the showBoxes property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowBoxes(Boolean value) {
-            this.showBoxes = value;
-        }
+    /**
+     * Gets the value of the showText property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowText()
+    {
+      return showText;
+    }
 
-        /**
-         * Gets the value of the wrapAlignment property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isWrapAlignment() {
-            return wrapAlignment;
-        }
+    /**
+     * Sets the value of the showText property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowText(Boolean value)
+    {
+      this.showText = value;
+    }
 
-        /**
-         * Sets the value of the wrapAlignment property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setWrapAlignment(Boolean value) {
-            this.wrapAlignment = value;
-        }
+    /**
+     * Gets the value of the showColourText property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowColourText()
+    {
+      return showColourText;
+    }
 
-        /**
-         * Gets the value of the renderGaps property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isRenderGaps() {
-            return renderGaps;
-        }
+    /**
+     * Sets the value of the showColourText property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowColourText(Boolean value)
+    {
+      this.showColourText = value;
+    }
 
-        /**
-         * Sets the value of the renderGaps property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setRenderGaps(Boolean value) {
-            this.renderGaps = value;
-        }
+    /**
+     * Gets the value of the showUnconserved property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowUnconserved()
+    {
+      if (showUnconserved == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showUnconserved;
+      }
+    }
 
-        /**
-         * Gets the value of the showSequenceFeatures property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowSequenceFeatures() {
-            return showSequenceFeatures;
-        }
+    /**
+     * Sets the value of the showUnconserved property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowUnconserved(Boolean value)
+    {
+      this.showUnconserved = value;
+    }
 
-        /**
-         * Sets the value of the showSequenceFeatures property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowSequenceFeatures(Boolean value) {
-            this.showSequenceFeatures = value;
-        }
+    /**
+     * Gets the value of the showBoxes property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowBoxes()
+    {
+      return showBoxes;
+    }
 
-        /**
-         * Gets the value of the showNPfeatureTooltip property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowNPfeatureTooltip() {
-            return showNPfeatureTooltip;
-        }
+    /**
+     * Sets the value of the showBoxes property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowBoxes(Boolean value)
+    {
+      this.showBoxes = value;
+    }
 
-        /**
-         * Sets the value of the showNPfeatureTooltip property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowNPfeatureTooltip(Boolean value) {
-            this.showNPfeatureTooltip = value;
-        }
+    /**
+     * Gets the value of the wrapAlignment property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isWrapAlignment()
+    {
+      return wrapAlignment;
+    }
 
-        /**
-         * Gets the value of the showDbRefTooltip property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowDbRefTooltip() {
-            return showDbRefTooltip;
-        }
+    /**
+     * Sets the value of the wrapAlignment property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setWrapAlignment(Boolean value)
+    {
+      this.wrapAlignment = value;
+    }
 
-        /**
-         * Sets the value of the showDbRefTooltip property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowDbRefTooltip(Boolean value) {
-            this.showDbRefTooltip = value;
-        }
+    /**
+     * Gets the value of the renderGaps property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isRenderGaps()
+    {
+      return renderGaps;
+    }
 
-        /**
-         * Gets the value of the followHighlight property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isFollowHighlight() {
-            if (followHighlight == null) {
-                return true;
-            } else {
-                return followHighlight;
-            }
-        }
+    /**
+     * Sets the value of the renderGaps property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setRenderGaps(Boolean value)
+    {
+      this.renderGaps = value;
+    }
 
-        /**
-         * Sets the value of the followHighlight property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setFollowHighlight(Boolean value) {
-            this.followHighlight = value;
-        }
+    /**
+     * Gets the value of the showSequenceFeatures property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowSequenceFeatures()
+    {
+      return showSequenceFeatures;
+    }
 
-        /**
-         * Gets the value of the followSelection property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isFollowSelection() {
-            if (followSelection == null) {
-                return true;
-            } else {
-                return followSelection;
-            }
-        }
+    /**
+     * Sets the value of the showSequenceFeatures property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowSequenceFeatures(Boolean value)
+    {
+      this.showSequenceFeatures = value;
+    }
 
-        /**
-         * Sets the value of the followSelection property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setFollowSelection(Boolean value) {
-            this.followSelection = value;
-        }
+    /**
+     * Gets the value of the showNPfeatureTooltip property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowNPfeatureTooltip()
+    {
+      return showNPfeatureTooltip;
+    }
 
-        /**
-         * Gets the value of the showAnnotation property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowAnnotation() {
-            return showAnnotation;
-        }
+    /**
+     * Sets the value of the showNPfeatureTooltip property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowNPfeatureTooltip(Boolean value)
+    {
+      this.showNPfeatureTooltip = value;
+    }
 
-        /**
-         * Sets the value of the showAnnotation property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowAnnotation(Boolean value) {
-            this.showAnnotation = value;
-        }
+    /**
+     * Gets the value of the showDbRefTooltip property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowDbRefTooltip()
+    {
+      return showDbRefTooltip;
+    }
 
-        /**
-         * Gets the value of the centreColumnLabels property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isCentreColumnLabels() {
-            if (centreColumnLabels == null) {
-                return false;
-            } else {
-                return centreColumnLabels;
-            }
-        }
+    /**
+     * Sets the value of the showDbRefTooltip property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowDbRefTooltip(Boolean value)
+    {
+      this.showDbRefTooltip = value;
+    }
 
-        /**
-         * Sets the value of the centreColumnLabels property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setCentreColumnLabels(Boolean value) {
-            this.centreColumnLabels = value;
-        }
+    /**
+     * Gets the value of the followHighlight property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isFollowHighlight()
+    {
+      if (followHighlight == null)
+      {
+        return true;
+      }
+      else
+      {
+        return followHighlight;
+      }
+    }
 
-        /**
-         * Gets the value of the showGroupConservation property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowGroupConservation() {
-            if (showGroupConservation == null) {
-                return false;
-            } else {
-                return showGroupConservation;
-            }
-        }
+    /**
+     * Sets the value of the followHighlight property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setFollowHighlight(Boolean value)
+    {
+      this.followHighlight = value;
+    }
 
-        /**
-         * Sets the value of the showGroupConservation property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowGroupConservation(Boolean value) {
-            this.showGroupConservation = value;
-        }
+    /**
+     * Gets the value of the followSelection property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isFollowSelection()
+    {
+      if (followSelection == null)
+      {
+        return true;
+      }
+      else
+      {
+        return followSelection;
+      }
+    }
 
-        /**
-         * Gets the value of the showGroupConsensus property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowGroupConsensus() {
-            if (showGroupConsensus == null) {
-                return false;
-            } else {
-                return showGroupConsensus;
-            }
-        }
+    /**
+     * Sets the value of the followSelection property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setFollowSelection(Boolean value)
+    {
+      this.followSelection = value;
+    }
 
-        /**
-         * Sets the value of the showGroupConsensus property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowGroupConsensus(Boolean value) {
-            this.showGroupConsensus = value;
-        }
+    /**
+     * Gets the value of the showAnnotation property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowAnnotation()
+    {
+      return showAnnotation;
+    }
 
-        /**
-         * Gets the value of the showConsensusHistogram property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowConsensusHistogram() {
-            if (showConsensusHistogram == null) {
-                return true;
-            } else {
-                return showConsensusHistogram;
-            }
-        }
+    /**
+     * Sets the value of the showAnnotation property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowAnnotation(Boolean value)
+    {
+      this.showAnnotation = value;
+    }
 
-        /**
-         * Sets the value of the showConsensusHistogram property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowConsensusHistogram(Boolean value) {
-            this.showConsensusHistogram = value;
-        }
+    /**
+     * Gets the value of the centreColumnLabels property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isCentreColumnLabels()
+    {
+      if (centreColumnLabels == null)
+      {
+        return false;
+      }
+      else
+      {
+        return centreColumnLabels;
+      }
+    }
 
-        /**
-         * Gets the value of the showSequenceLogo property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowSequenceLogo() {
-            if (showSequenceLogo == null) {
-                return false;
-            } else {
-                return showSequenceLogo;
-            }
-        }
+    /**
+     * Sets the value of the centreColumnLabels property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setCentreColumnLabels(Boolean value)
+    {
+      this.centreColumnLabels = value;
+    }
 
-        /**
-         * Sets the value of the showSequenceLogo property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowSequenceLogo(Boolean value) {
-            this.showSequenceLogo = value;
-        }
+    /**
+     * Gets the value of the showGroupConservation property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowGroupConservation()
+    {
+      if (showGroupConservation == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showGroupConservation;
+      }
+    }
 
-        /**
-         * Gets the value of the normaliseSequenceLogo property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isNormaliseSequenceLogo() {
-            if (normaliseSequenceLogo == null) {
-                return false;
-            } else {
-                return normaliseSequenceLogo;
-            }
-        }
+    /**
+     * Sets the value of the showGroupConservation property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowGroupConservation(Boolean value)
+    {
+      this.showGroupConservation = value;
+    }
 
-        /**
-         * Sets the value of the normaliseSequenceLogo property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setNormaliseSequenceLogo(Boolean value) {
-            this.normaliseSequenceLogo = value;
-        }
+    /**
+     * Gets the value of the showGroupConsensus property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowGroupConsensus()
+    {
+      if (showGroupConsensus == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showGroupConsensus;
+      }
+    }
 
-        /**
-         * Gets the value of the ignoreGapsinConsensus property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isIgnoreGapsinConsensus() {
-            if (ignoreGapsinConsensus == null) {
-                return true;
-            } else {
-                return ignoreGapsinConsensus;
-            }
-        }
+    /**
+     * Sets the value of the showGroupConsensus property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowGroupConsensus(Boolean value)
+    {
+      this.showGroupConsensus = value;
+    }
 
-        /**
-         * Sets the value of the ignoreGapsinConsensus property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setIgnoreGapsinConsensus(Boolean value) {
-            this.ignoreGapsinConsensus = value;
-        }
+    /**
+     * Gets the value of the showConsensusHistogram property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowConsensusHistogram()
+    {
+      if (showConsensusHistogram == null)
+      {
+        return true;
+      }
+      else
+      {
+        return showConsensusHistogram;
+      }
+    }
 
-        /**
-         * Gets the value of the startRes property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getStartRes() {
-            return startRes;
-        }
+    /**
+     * Sets the value of the showConsensusHistogram property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowConsensusHistogram(Boolean value)
+    {
+      this.showConsensusHistogram = value;
+    }
 
-        /**
-         * Sets the value of the startRes property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setStartRes(Integer value) {
-            this.startRes = value;
-        }
+    /**
+     * Gets the value of the showSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowSequenceLogo()
+    {
+      if (showSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showSequenceLogo;
+      }
+    }
 
-        /**
-         * Gets the value of the startSeq property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getStartSeq() {
-            return startSeq;
-        }
+    /**
+     * Sets the value of the showSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowSequenceLogo(Boolean value)
+    {
+      this.showSequenceLogo = value;
+    }
 
-        /**
-         * Sets the value of the startSeq property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setStartSeq(Integer value) {
-            this.startSeq = value;
-        }
+    /**
+     * Gets the value of the normaliseSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isNormaliseSequenceLogo()
+    {
+      if (normaliseSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return normaliseSequenceLogo;
+      }
+    }
 
-        /**
-         * Gets the value of the charWidth property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getCharWidth() {
-            return charWidth;
-        }
+    /**
+     * Sets the value of the normaliseSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setNormaliseSequenceLogo(Boolean value)
+    {
+      this.normaliseSequenceLogo = value;
+    }
+
+    /**
+     * Gets the value of the ignoreGapsinConsensus property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isIgnoreGapsinConsensus()
+    {
+      if (ignoreGapsinConsensus == null)
+      {
+        return true;
+      }
+      else
+      {
+        return ignoreGapsinConsensus;
+      }
+    }
 
-        /**
-         * Sets the value of the charWidth property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setCharWidth(Integer value) {
-            this.charWidth = value;
-        }
+    /**
+     * Sets the value of the ignoreGapsinConsensus property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIgnoreGapsinConsensus(Boolean value)
+    {
+      this.ignoreGapsinConsensus = value;
+    }
 
-        /**
-         * Gets the value of the charHeight property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getCharHeight() {
-            return charHeight;
-        }
+    /**
+     * Gets the value of the startRes property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getStartRes()
+    {
+      return startRes;
+    }
 
-        /**
-         * Sets the value of the charHeight property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setCharHeight(Integer value) {
-            this.charHeight = value;
-        }
+    /**
+     * Sets the value of the startRes property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setStartRes(Integer value)
+    {
+      this.startRes = value;
+    }
 
-        /**
-         * Gets the value of the fontName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getFontName() {
-            return fontName;
-        }
+    /**
+     * Gets the value of the startSeq property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getStartSeq()
+    {
+      return startSeq;
+    }
 
-        /**
-         * Sets the value of the fontName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setFontName(String value) {
-            this.fontName = value;
-        }
+    /**
+     * Sets the value of the startSeq property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setStartSeq(Integer value)
+    {
+      this.startSeq = value;
+    }
 
-        /**
-         * Gets the value of the fontSize property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontSize() {
-            return fontSize;
-        }
+    /**
+     * Gets the value of the charWidth property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getCharWidth()
+    {
+      return charWidth;
+    }
 
-        /**
-         * Sets the value of the fontSize property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontSize(Integer value) {
-            this.fontSize = value;
-        }
+    /**
+     * Sets the value of the charWidth property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setCharWidth(Integer value)
+    {
+      this.charWidth = value;
+    }
 
-        /**
-         * Gets the value of the fontStyle property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontStyle() {
-            return fontStyle;
-        }
+    /**
+     * Gets the value of the charHeight property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getCharHeight()
+    {
+      return charHeight;
+    }
 
-        /**
-         * Sets the value of the fontStyle property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontStyle(Integer value) {
-            this.fontStyle = value;
-        }
+    /**
+     * Sets the value of the charHeight property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setCharHeight(Integer value)
+    {
+      this.charHeight = value;
+    }
 
-        /**
-         * Gets the value of the scaleProteinAsCdna property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isScaleProteinAsCdna() {
-            if (scaleProteinAsCdna == null) {
-                return true;
-            } else {
-                return scaleProteinAsCdna;
-            }
-        }
+    /**
+     * Gets the value of the fontName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getFontName()
+    {
+      return fontName;
+    }
 
-        /**
-         * Sets the value of the scaleProteinAsCdna property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setScaleProteinAsCdna(Boolean value) {
-            this.scaleProteinAsCdna = value;
-        }
+    /**
+     * Sets the value of the fontName property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setFontName(String value)
+    {
+      this.fontName = value;
+    }
 
-        /**
-         * Gets the value of the viewName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getViewName() {
-            return viewName;
-        }
+    /**
+     * Gets the value of the fontSize property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontSize()
+    {
+      return fontSize;
+    }
 
-        /**
-         * Sets the value of the viewName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setViewName(String value) {
-            this.viewName = value;
-        }
+    /**
+     * Sets the value of the fontSize property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setFontSize(Integer value)
+    {
+      this.fontSize = value;
+    }
 
-        /**
-         * Gets the value of the sequenceSetId property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getSequenceSetId() {
-            return sequenceSetId;
-        }
+    /**
+     * Gets the value of the fontStyle property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontStyle()
+    {
+      return fontStyle;
+    }
 
-        /**
-         * Sets the value of the sequenceSetId property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setSequenceSetId(String value) {
-            this.sequenceSetId = value;
-        }
+    /**
+     * Sets the value of the fontStyle property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setFontStyle(Integer value)
+    {
+      this.fontStyle = value;
+    }
 
-        /**
-         * Gets the value of the gatheredViews property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isGatheredViews() {
-            return gatheredViews;
-        }
+    /**
+     * Gets the value of the scaleProteinAsCdna property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isScaleProteinAsCdna()
+    {
+      if (scaleProteinAsCdna == null)
+      {
+        return true;
+      }
+      else
+      {
+        return scaleProteinAsCdna;
+      }
+    }
 
-        /**
-         * Sets the value of the gatheredViews property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setGatheredViews(Boolean value) {
-            this.gatheredViews = value;
-        }
+    /**
+     * Sets the value of the scaleProteinAsCdna property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setScaleProteinAsCdna(Boolean value)
+    {
+      this.scaleProteinAsCdna = value;
+    }
 
-        /**
-         * Gets the value of the textCol1 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextCol1() {
-            return textCol1;
-        }
+    /**
+     * Gets the value of the viewName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getViewName()
+    {
+      return viewName;
+    }
 
-        /**
-         * Sets the value of the textCol1 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setTextCol1(Integer value) {
-            this.textCol1 = value;
-        }
+    /**
+     * Sets the value of the viewName property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setViewName(String value)
+    {
+      this.viewName = value;
+    }
 
-        /**
-         * Gets the value of the textCol2 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextCol2() {
-            return textCol2;
-        }
+    /**
+     * Gets the value of the sequenceSetId property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getSequenceSetId()
+    {
+      return sequenceSetId;
+    }
 
-        /**
-         * Sets the value of the textCol2 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setTextCol2(Integer value) {
-            this.textCol2 = value;
-        }
+    /**
+     * Sets the value of the sequenceSetId property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setSequenceSetId(String value)
+    {
+      this.sequenceSetId = value;
+    }
 
-        /**
-         * Gets the value of the textColThreshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextColThreshold() {
-            return textColThreshold;
-        }
+    /**
+     * Gets the value of the gatheredViews property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isGatheredViews()
+    {
+      return gatheredViews;
+    }
 
-        /**
-         * Sets the value of the textColThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setTextColThreshold(Integer value) {
-            this.textColThreshold = value;
-        }
+    /**
+     * Sets the value of the gatheredViews property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setGatheredViews(Boolean value)
+    {
+      this.gatheredViews = value;
+    }
 
-        /**
-         * Gets the value of the id property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getId() {
-            return id;
-        }
+    /**
+     * Gets the value of the textCol1 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol1()
+    {
+      return textCol1;
+    }
 
-        /**
-         * Sets the value of the id property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
+    /**
+     * Sets the value of the textCol1 property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextCol1(Integer value)
+    {
+      this.textCol1 = value;
+    }
 
-        /**
-         * Gets the value of the complementId property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getComplementId() {
-            return complementId;
-        }
+    /**
+     * Gets the value of the textCol2 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol2()
+    {
+      return textCol2;
+    }
 
-        /**
-         * Sets the value of the complementId property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setComplementId(String value) {
-            this.complementId = value;
-        }
+    /**
+     * Sets the value of the textCol2 property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextCol2(Integer value)
+    {
+      this.textCol2 = value;
+    }
 
-        /**
-         * Gets the value of the showComplementFeatures property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowComplementFeatures() {
-            if (showComplementFeatures == null) {
-                return false;
-            } else {
-                return showComplementFeatures;
-            }
-        }
+    /**
+     * Gets the value of the textColThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextColThreshold()
+    {
+      return textColThreshold;
+    }
 
-        /**
-         * Sets the value of the showComplementFeatures property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowComplementFeatures(Boolean value) {
-            this.showComplementFeatures = value;
-        }
+    /**
+     * Sets the value of the textColThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextColThreshold(Integer value)
+    {
+      this.textColThreshold = value;
+    }
 
-        /**
-         * Gets the value of the showComplementFeaturesOnTop property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowComplementFeaturesOnTop() {
-            if (showComplementFeaturesOnTop == null) {
-                return false;
-            } else {
-                return showComplementFeaturesOnTop;
-            }
-        }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
 
-        /**
-         * Sets the value of the showComplementFeaturesOnTop property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowComplementFeaturesOnTop(Boolean value) {
-            this.showComplementFeaturesOnTop = value;
-        }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setId(String value)
+    {
+      this.id = value;
+    }
 
-        /**
-         * Gets the value of the width property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getWidth() {
-            return width;
-        }
+    /**
+     * Gets the value of the complementId property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getComplementId()
+    {
+      return complementId;
+    }
 
-        /**
-         * Sets the value of the width property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setWidth(Integer value) {
-            this.width = value;
-        }
+    /**
+     * Sets the value of the complementId property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setComplementId(String value)
+    {
+      this.complementId = value;
+    }
 
-        /**
-         * Gets the value of the height property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getHeight() {
-            return height;
-        }
+    /**
+     * Gets the value of the showComplementFeatures property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowComplementFeatures()
+    {
+      if (showComplementFeatures == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showComplementFeatures;
+      }
+    }
 
-        /**
-         * Sets the value of the height property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setHeight(Integer value) {
-            this.height = value;
-        }
+    /**
+     * Sets the value of the showComplementFeatures property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowComplementFeatures(Boolean value)
+    {
+      this.showComplementFeatures = value;
+    }
 
-        /**
-         * Gets the value of the xpos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getXpos() {
-            return xpos;
-        }
+    /**
+     * Gets the value of the showComplementFeaturesOnTop property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowComplementFeaturesOnTop()
+    {
+      if (showComplementFeaturesOnTop == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showComplementFeaturesOnTop;
+      }
+    }
 
-        /**
-         * Sets the value of the xpos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setXpos(Integer value) {
-            this.xpos = value;
-        }
+    /**
+     * Sets the value of the showComplementFeaturesOnTop property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowComplementFeaturesOnTop(Boolean value)
+    {
+      this.showComplementFeaturesOnTop = value;
+    }
 
-        /**
-         * Gets the value of the ypos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getYpos() {
-            return ypos;
-        }
+    /**
+     * Gets the value of the width property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getWidth()
+    {
+      return width;
+    }
 
-        /**
-         * Sets the value of the ypos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setYpos(Integer value) {
-            this.ypos = value;
-        }
+    /**
+     * Sets the value of the width property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setWidth(Integer value)
+    {
+      this.width = value;
+    }
 
+    /**
+     * Gets the value of the height property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getHeight()
+    {
+      return height;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-         *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/extension>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class CalcIdParam
-            extends WebServiceParameterSet
-        {
+    /**
+     * Sets the value of the height property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setHeight(Integer value)
+    {
+      this.height = value;
+    }
 
-            @XmlAttribute(name = "calcId", required = true)
-            protected String calcId;
-            @XmlAttribute(name = "needsUpdate")
-            protected Boolean needsUpdate;
-            @XmlAttribute(name = "autoUpdate", required = true)
-            protected boolean autoUpdate;
-
-            /**
-             * Gets the value of the calcId property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getCalcId() {
-                return calcId;
-            }
-
-            /**
-             * Sets the value of the calcId property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setCalcId(String value) {
-                this.calcId = value;
-            }
-
-            /**
-             * Gets the value of the needsUpdate property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public boolean isNeedsUpdate() {
-                if (needsUpdate == null) {
-                    return false;
-                } else {
-                    return needsUpdate;
-                }
-            }
-
-            /**
-             * Sets the value of the needsUpdate property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setNeedsUpdate(Boolean value) {
-                this.needsUpdate = value;
-            }
-
-            /**
-             * Gets the value of the autoUpdate property.
-             * 
-             */
-            public boolean isAutoUpdate() {
-                return autoUpdate;
-            }
-
-            /**
-             * Sets the value of the autoUpdate property.
-             * 
-             */
-            public void setAutoUpdate(boolean value) {
-                this.autoUpdate = value;
-            }
+    /**
+     * Gets the value of the xpos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXpos()
+    {
+      return xpos;
+    }
 
-        }
+    /**
+     * Sets the value of the xpos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setXpos(Integer value)
+    {
+      this.xpos = value;
+    }
 
+    /**
+     * Gets the value of the ypos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getYpos()
+    {
+      return ypos;
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class HiddenColumns {
-
-            @XmlAttribute(name = "start")
-            protected Integer start;
-            @XmlAttribute(name = "end")
-            protected Integer end;
-
-            /**
-             * Gets the value of the start property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getStart() {
-                return start;
-            }
-
-            /**
-             * Sets the value of the start property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setStart(Integer value) {
-                this.start = value;
-            }
-
-            /**
-             * Gets the value of the end property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getEnd() {
-                return end;
-            }
-
-            /**
-             * Sets the value of the end property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setEnd(Integer value) {
-                this.end = value;
-            }
+    /**
+     * Sets the value of the ypos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setYpos(Integer value)
+    {
+      this.ypos = value;
+    }
 
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/extension>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class CalcIdParam extends WebServiceParameterSet
+    {
+
+      @XmlAttribute(name = "calcId", required = true)
+      protected String calcId;
+
+      @XmlAttribute(name = "needsUpdate")
+      protected Boolean needsUpdate;
+
+      @XmlAttribute(name = "autoUpdate", required = true)
+      protected boolean autoUpdate;
+
+      /**
+       * Gets the value of the calcId property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getCalcId()
+      {
+        return calcId;
+      }
+
+      /**
+       * Sets the value of the calcId property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setCalcId(String value)
+      {
+        this.calcId = value;
+      }
+
+      /**
+       * Gets the value of the needsUpdate property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public boolean isNeedsUpdate()
+      {
+        if (needsUpdate == null)
+        {
+          return false;
         }
+        else
+        {
+          return needsUpdate;
+        }
+      }
+
+      /**
+       * Sets the value of the needsUpdate property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setNeedsUpdate(Boolean value)
+      {
+        this.needsUpdate = value;
+      }
+
+      /**
+       * Gets the value of the autoUpdate property.
+       * 
+       */
+      public boolean isAutoUpdate()
+      {
+        return autoUpdate;
+      }
+
+      /**
+       * Sets the value of the autoUpdate property.
+       * 
+       */
+      public void setAutoUpdate(boolean value)
+      {
+        this.autoUpdate = value;
+      }
 
+    }
 
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-         *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Overview {
-
-            @XmlAttribute(name = "showHidden")
-            protected Boolean showHidden;
-            @XmlAttribute(name = "residueColour")
-            protected Integer residueColour;
-            @XmlAttribute(name = "gapColour")
-            protected Integer gapColour;
-            @XmlAttribute(name = "hiddenColour")
-            protected Integer hiddenColour;
-            @XmlAttribute(name = "title")
-            protected String title;
-            @XmlAttribute(name = "width")
-            protected Integer width;
-            @XmlAttribute(name = "height")
-            protected Integer height;
-            @XmlAttribute(name = "xpos")
-            protected Integer xpos;
-            @XmlAttribute(name = "ypos")
-            protected Integer ypos;
-
-            /**
-             * Gets the value of the showHidden property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isShowHidden() {
-                return showHidden;
-            }
-
-            /**
-             * Sets the value of the showHidden property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setShowHidden(Boolean value) {
-                this.showHidden = value;
-            }
-
-            /**
-             * Gets the value of the residueColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getResidueColour() {
-                return residueColour;
-            }
-
-            /**
-             * Sets the value of the residueColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setResidueColour(Integer value) {
-                this.residueColour = value;
-            }
-
-            /**
-             * Gets the value of the gapColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getGapColour() {
-                return gapColour;
-            }
-
-            /**
-             * Sets the value of the gapColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setGapColour(Integer value) {
-                this.gapColour = value;
-            }
-
-            /**
-             * Gets the value of the hiddenColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getHiddenColour() {
-                return hiddenColour;
-            }
-
-            /**
-             * Sets the value of the hiddenColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setHiddenColour(Integer value) {
-                this.hiddenColour = value;
-            }
-
-            /**
-             * Gets the value of the title property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getTitle() {
-                return title;
-            }
-
-            /**
-             * Sets the value of the title property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setTitle(String value) {
-                this.title = value;
-            }
-
-            /**
-             * Gets the value of the width property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getWidth() {
-                return width;
-            }
-
-            /**
-             * Sets the value of the width property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setWidth(Integer value) {
-                this.width = value;
-            }
-
-            /**
-             * Gets the value of the height property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getHeight() {
-                return height;
-            }
-
-            /**
-             * Sets the value of the height property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setHeight(Integer value) {
-                this.height = value;
-            }
-
-            /**
-             * Gets the value of the xpos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getXpos() {
-                return xpos;
-            }
-
-            /**
-             * Sets the value of the xpos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setXpos(Integer value) {
-                this.xpos = value;
-            }
-
-            /**
-             * Gets the value of the ypos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getYpos() {
-                return ypos;
-            }
-
-            /**
-             * Sets the value of the ypos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setYpos(Integer value) {
-                this.ypos = value;
-            }
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class HiddenColumns
+    {
+
+      @XmlAttribute(name = "start")
+      protected Integer start;
+
+      @XmlAttribute(name = "end")
+      protected Integer end;
+
+      /**
+       * Gets the value of the start property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getStart()
+      {
+        return start;
+      }
+
+      /**
+       * Sets the value of the start property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setStart(Integer value)
+      {
+        this.start = value;
+      }
+
+      /**
+       * Gets the value of the end property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getEnd()
+      {
+        return end;
+      }
+
+      /**
+       * Sets the value of the end property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setEnd(Integer value)
+      {
+        this.end = value;
+      }
 
-        }
+    }
+
+    /**
+     * <p>
+     * Java class for anonymous complex type.
+     * 
+     * <p>
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Overview
+    {
+
+      @XmlAttribute(name = "showHidden")
+      protected Boolean showHidden;
+
+      @XmlAttribute(name = "residueColour")
+      protected Integer residueColour;
+
+      @XmlAttribute(name = "gapColour")
+      protected Integer gapColour;
+
+      @XmlAttribute(name = "hiddenColour")
+      protected Integer hiddenColour;
+
+      @XmlAttribute(name = "title")
+      protected String title;
+
+      @XmlAttribute(name = "width")
+      protected Integer width;
+
+      @XmlAttribute(name = "height")
+      protected Integer height;
+
+      @XmlAttribute(name = "xpos")
+      protected Integer xpos;
+
+      @XmlAttribute(name = "ypos")
+      protected Integer ypos;
+
+      /**
+       * Gets the value of the showHidden property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public Boolean isShowHidden()
+      {
+        return showHidden;
+      }
+
+      /**
+       * Sets the value of the showHidden property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setShowHidden(Boolean value)
+      {
+        this.showHidden = value;
+      }
+
+      /**
+       * Gets the value of the residueColour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getResidueColour()
+      {
+        return residueColour;
+      }
+
+      /**
+       * Sets the value of the residueColour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setResidueColour(Integer value)
+      {
+        this.residueColour = value;
+      }
+
+      /**
+       * Gets the value of the gapColour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getGapColour()
+      {
+        return gapColour;
+      }
+
+      /**
+       * Sets the value of the gapColour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setGapColour(Integer value)
+      {
+        this.gapColour = value;
+      }
+
+      /**
+       * Gets the value of the hiddenColour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getHiddenColour()
+      {
+        return hiddenColour;
+      }
+
+      /**
+       * Sets the value of the hiddenColour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setHiddenColour(Integer value)
+      {
+        this.hiddenColour = value;
+      }
+
+      /**
+       * Gets the value of the title property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getTitle()
+      {
+        return title;
+      }
+
+      /**
+       * Sets the value of the title property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setTitle(String value)
+      {
+        this.title = value;
+      }
+
+      /**
+       * Gets the value of the width property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getWidth()
+      {
+        return width;
+      }
+
+      /**
+       * Sets the value of the width property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setWidth(Integer value)
+      {
+        this.width = value;
+      }
+
+      /**
+       * Gets the value of the height property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getHeight()
+      {
+        return height;
+      }
+
+      /**
+       * Sets the value of the height property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setHeight(Integer value)
+      {
+        this.height = value;
+      }
+
+      /**
+       * Gets the value of the xpos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getXpos()
+      {
+        return xpos;
+      }
+
+      /**
+       * Sets the value of the xpos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setXpos(Integer value)
+      {
+        this.xpos = value;
+      }
+
+      /**
+       * Gets the value of the ypos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getYpos()
+      {
+        return ypos;
+      }
+
+      /**
+       * Sets the value of the ypos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setYpos(Integer value)
+      {
+        this.ypos = value;
+      }
 
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index b62cf15..8a9f681 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for JalviewUserColours complex type.
+ * <p>
+ * Java class for JalviewUserColours complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="JalviewUserColours">
@@ -71,542 +72,556 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
-    "version",
-    "colour",
-    "filter"
-})
-public class JalviewUserColours {
-
-    @XmlElement(name = "Version", namespace = "")
-    protected String version;
-    @XmlElement(namespace = "")
-    protected List<JalviewUserColours.Colour> colour;
+@XmlType(
+  name = "JalviewUserColours",
+  namespace = "www.jalview.org/colours",
+  propOrder =
+  { "version", "colour", "filter" })
+public class JalviewUserColours
+{
+
+  @XmlElement(name = "Version", namespace = "")
+  protected String version;
+
+  @XmlElement(namespace = "")
+  protected List<JalviewUserColours.Colour> colour;
+
+  @XmlElement(namespace = "")
+  protected List<JalviewUserColours.Filter> filter;
+
+  @XmlAttribute(name = "schemeName")
+  protected String schemeName;
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the colour property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the colour property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getColour().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewUserColours.Colour }
+   * 
+   * 
+   */
+  public List<JalviewUserColours.Colour> getColour()
+  {
+    if (colour == null)
+    {
+      colour = new ArrayList<JalviewUserColours.Colour>();
+    }
+    return this.colour;
+  }
+
+  /**
+   * Gets the value of the filter property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the filter property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getFilter().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link JalviewUserColours.Filter }
+   * 
+   * 
+   */
+  public List<JalviewUserColours.Filter> getFilter()
+  {
+    if (filter == null)
+    {
+      filter = new ArrayList<JalviewUserColours.Filter>();
+    }
+    return this.filter;
+  }
+
+  /**
+   * Gets the value of the schemeName property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSchemeName()
+  {
+    return schemeName;
+  }
+
+  /**
+   * Sets the value of the schemeName property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSchemeName(String value)
+  {
+    this.schemeName = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+   *       &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+   *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "attributeName" })
+  public static class Colour
+  {
+
     @XmlElement(namespace = "")
-    protected List<JalviewUserColours.Filter> filter;
-    @XmlAttribute(name = "schemeName")
-    protected String schemeName;
+    protected List<String> attributeName;
+
+    @XmlAttribute(name = "Name")
+    protected String name;
+
+    @XmlAttribute(name = "RGB", required = true)
+    protected String rgb;
+
+    @XmlAttribute(name = "minRGB")
+    protected String minRGB;
+
+    @XmlAttribute(name = "noValueColour")
+    protected NoValueColour noValueColour;
+
+    @XmlAttribute(name = "threshType")
+    protected ThresholdType threshType;
+
+    @XmlAttribute(name = "threshold")
+    protected Float threshold;
+
+    @XmlAttribute(name = "max")
+    protected Float max;
+
+    @XmlAttribute(name = "min")
+    protected Float min;
+
+    @XmlAttribute(name = "colourByLabel")
+    protected Boolean colourByLabel;
+
+    @XmlAttribute(name = "autoScale")
+    protected Boolean autoScale;
 
     /**
-     * Gets the value of the version property.
+     * Gets the value of the attributeName property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the attributeName property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getAttributeName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link String }
+     * 
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getVersion() {
-        return version;
+    public List<String> getAttributeName()
+    {
+      if (attributeName == null)
+      {
+        attributeName = new ArrayList<String>();
+      }
+      return this.attributeName;
     }
 
     /**
-     * Sets the value of the version property.
+     * 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 }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setVersion(String value) {
-        this.version = value;
+    public void setName(String value)
+    {
+      this.name = value;
     }
 
     /**
-     * Gets the value of the colour property.
+     * Gets the value of the rgb property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the colour property.
+     * @return possible object is {@link String }
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getColour().add(newItem);
-     * </pre>
+     */
+    public String getRGB()
+    {
+      return rgb;
+    }
+
+    /**
+     * Sets the value of the rgb property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewUserColours.Colour }
+     */
+    public void setRGB(String value)
+    {
+      this.rgb = value;
+    }
+
+    /**
+     * Gets the value of the minRGB property.
      * 
+     * @return possible object is {@link String }
      * 
      */
-    public List<JalviewUserColours.Colour> getColour() {
-        if (colour == null) {
-            colour = new ArrayList<JalviewUserColours.Colour>();
-        }
-        return this.colour;
+    public String getMinRGB()
+    {
+      return minRGB;
     }
 
     /**
-     * Gets the value of the filter property.
+     * Sets the value of the minRGB property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the filter property.
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getFilter().add(newItem);
-     * </pre>
+     */
+    public void setMinRGB(String value)
+    {
+      this.minRGB = value;
+    }
+
+    /**
+     * Gets the value of the noValueColour property.
      * 
+     * @return possible object is {@link NoValueColour }
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewUserColours.Filter }
+     */
+    public NoValueColour getNoValueColour()
+    {
+      if (noValueColour == null)
+      {
+        return NoValueColour.MIN;
+      }
+      else
+      {
+        return noValueColour;
+      }
+    }
+
+    /**
+     * Sets the value of the noValueColour property.
      * 
+     * @param value
+     *          allowed object is {@link NoValueColour }
      * 
      */
-    public List<JalviewUserColours.Filter> getFilter() {
-        if (filter == null) {
-            filter = new ArrayList<JalviewUserColours.Filter>();
-        }
-        return this.filter;
+    public void setNoValueColour(NoValueColour value)
+    {
+      this.noValueColour = value;
     }
 
     /**
-     * Gets the value of the schemeName property.
+     * Gets the value of the threshType property.
+     * 
+     * @return possible object is {@link ThresholdType }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getSchemeName() {
-        return schemeName;
+    public ThresholdType getThreshType()
+    {
+      return threshType;
     }
 
     /**
-     * Sets the value of the schemeName property.
+     * Sets the value of the threshType property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link ThresholdType }
+     * 
      */
-    public void setSchemeName(String value) {
-        this.schemeName = value;
+    public void setThreshType(ThresholdType value)
+    {
+      this.threshType = value;
     }
 
+    /**
+     * Gets the value of the threshold property.
+     * 
+     * @return possible object is {@link Float }
+     * 
+     */
+    public Float getThreshold()
+    {
+      return threshold;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Sets the value of the threshold property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Float }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
-     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public void setThreshold(Float value)
+    {
+      this.threshold = value;
+    }
+
+    /**
+     * Gets the value of the max property.
+     * 
+     * @return possible object is {@link Float }
+     * 
+     */
+    public Float getMax()
+    {
+      return max;
+    }
+
+    /**
+     * Sets the value of the max property.
+     * 
+     * @param value
+     *          allowed object is {@link Float }
+     * 
+     */
+    public void setMax(Float value)
+    {
+      this.max = value;
+    }
+
+    /**
+     * Gets the value of the min property.
      * 
+     * @return possible object is {@link Float }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "attributeName"
-    })
-    public static class Colour {
-
-        @XmlElement(namespace = "")
-        protected List<String> attributeName;
-        @XmlAttribute(name = "Name")
-        protected String name;
-        @XmlAttribute(name = "RGB", required = true)
-        protected String rgb;
-        @XmlAttribute(name = "minRGB")
-        protected String minRGB;
-        @XmlAttribute(name = "noValueColour")
-        protected NoValueColour noValueColour;
-        @XmlAttribute(name = "threshType")
-        protected ThresholdType threshType;
-        @XmlAttribute(name = "threshold")
-        protected Float threshold;
-        @XmlAttribute(name = "max")
-        protected Float max;
-        @XmlAttribute(name = "min")
-        protected Float min;
-        @XmlAttribute(name = "colourByLabel")
-        protected Boolean colourByLabel;
-        @XmlAttribute(name = "autoScale")
-        protected Boolean autoScale;
-
-        /**
-         * Gets the value of the attributeName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the attributeName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getAttributeName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List<String> getAttributeName() {
-            if (attributeName == null) {
-                attributeName = new ArrayList<String>();
-            }
-            return this.attributeName;
-        }
-
-        /**
-         * Gets the value of the name property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getName() {
-            return name;
-        }
-
-        /**
-         * Sets the value of the name property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setName(String value) {
-            this.name = value;
-        }
-
-        /**
-         * Gets the value of the rgb property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getRGB() {
-            return rgb;
-        }
-
-        /**
-         * Sets the value of the rgb property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setRGB(String value) {
-            this.rgb = value;
-        }
-
-        /**
-         * Gets the value of the minRGB property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getMinRGB() {
-            return minRGB;
-        }
-
-        /**
-         * Sets the value of the minRGB property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setMinRGB(String value) {
-            this.minRGB = value;
-        }
-
-        /**
-         * Gets the value of the noValueColour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link NoValueColour }
-         *     
-         */
-        public NoValueColour getNoValueColour() {
-            if (noValueColour == null) {
-                return NoValueColour.MIN;
-            } else {
-                return noValueColour;
-            }
-        }
-
-        /**
-         * Sets the value of the noValueColour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link NoValueColour }
-         *     
-         */
-        public void setNoValueColour(NoValueColour value) {
-            this.noValueColour = value;
-        }
-
-        /**
-         * Gets the value of the threshType property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link ThresholdType }
-         *     
-         */
-        public ThresholdType getThreshType() {
-            return threshType;
-        }
-
-        /**
-         * Sets the value of the threshType property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link ThresholdType }
-         *     
-         */
-        public void setThreshType(ThresholdType value) {
-            this.threshType = value;
-        }
-
-        /**
-         * Gets the value of the threshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getThreshold() {
-            return threshold;
-        }
-
-        /**
-         * Sets the value of the threshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setThreshold(Float value) {
-            this.threshold = value;
-        }
-
-        /**
-         * Gets the value of the max property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getMax() {
-            return max;
-        }
-
-        /**
-         * Sets the value of the max property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setMax(Float value) {
-            this.max = value;
-        }
-
-        /**
-         * Gets the value of the min property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getMin() {
-            return min;
-        }
-
-        /**
-         * Sets the value of the min property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setMin(Float value) {
-            this.min = value;
-        }
-
-        /**
-         * Gets the value of the colourByLabel property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isColourByLabel() {
-            return colourByLabel;
-        }
-
-        /**
-         * Sets the value of the colourByLabel property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setColourByLabel(Boolean value) {
-            this.colourByLabel = value;
-        }
-
-        /**
-         * Gets the value of the autoScale property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isAutoScale() {
-            return autoScale;
-        }
-
-        /**
-         * Sets the value of the autoScale property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setAutoScale(Boolean value) {
-            this.autoScale = value;
-        }
+    public Float getMin()
+    {
+      return min;
+    }
 
+    /**
+     * Sets the value of the min property.
+     * 
+     * @param value
+     *          allowed object is {@link Float }
+     * 
+     */
+    public void setMin(Float value)
+    {
+      this.min = value;
     }
 
+    /**
+     * Gets the value of the colourByLabel property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isColourByLabel()
+    {
+      return colourByLabel;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Sets the value of the colourByLabel property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Boolean }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public void setColourByLabel(Boolean value)
+    {
+      this.colourByLabel = value;
+    }
+
+    /**
+     * Gets the value of the autoScale property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isAutoScale()
+    {
+      return autoScale;
+    }
+
+    /**
+     * Sets the value of the autoScale property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setAutoScale(Boolean value)
+    {
+      this.autoScale = value;
+    }
+
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "matcherSet" })
+  public static class Filter
+  {
+
+    @XmlElement(namespace = "", required = true)
+    protected FeatureMatcherSet matcherSet;
+
+    @XmlAttribute(name = "featureType", required = true)
+    protected String featureType;
+
+    /**
+     * Gets the value of the matcherSet property.
+     * 
+     * @return possible object is {@link FeatureMatcherSet }
+     * 
+     */
+    public FeatureMatcherSet getMatcherSet()
+    {
+      return matcherSet;
+    }
+
+    /**
+     * Sets the value of the matcherSet property.
+     * 
+     * @param value
+     *          allowed object is {@link FeatureMatcherSet }
+     * 
+     */
+    public void setMatcherSet(FeatureMatcherSet value)
+    {
+      this.matcherSet = value;
+    }
+
+    /**
+     * Gets the value of the featureType property.
      * 
+     * @return possible object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "matcherSet"
-    })
-    public static class Filter {
-
-        @XmlElement(namespace = "", required = true)
-        protected FeatureMatcherSet matcherSet;
-        @XmlAttribute(name = "featureType", required = true)
-        protected String featureType;
-
-        /**
-         * Gets the value of the matcherSet property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link FeatureMatcherSet }
-         *     
-         */
-        public FeatureMatcherSet getMatcherSet() {
-            return matcherSet;
-        }
-
-        /**
-         * Sets the value of the matcherSet property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link FeatureMatcherSet }
-         *     
-         */
-        public void setMatcherSet(FeatureMatcherSet value) {
-            this.matcherSet = value;
-        }
-
-        /**
-         * Gets the value of the featureType property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getFeatureType() {
-            return featureType;
-        }
-
-        /**
-         * Sets the value of the featureType property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setFeatureType(String value) {
-            this.featureType = value;
-        }
+    public String getFeatureType()
+    {
+      return featureType;
+    }
 
+    /**
+     * Sets the value of the featureType property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setFeatureType(String value)
+    {
+      this.featureType = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
index 7a86123..6d7f5f2 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -18,15 +17,17 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * 
- * 				This effectively represents a java.util.MapList object
- * 			
+ * This effectively represents a java.util.MapList object
  * 
- * <p>Java class for mapListType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * Java class for mapListType complex type.
+ * 
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="mapListType">
@@ -64,252 +65,271 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = {
-    "mapListFrom",
-    "mapListTo"
-})
-@XmlSeeAlso({
-    Mapping.class
-})
-public class MapListType {
+@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
+@XmlSeeAlso({ Mapping.class })
+public class MapListType
+{
+
+  protected List<MapListType.MapListFrom> mapListFrom;
+
+  protected List<MapListType.MapListTo> mapListTo;
+
+  @XmlAttribute(name = "mapFromUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapFromUnit;
+
+  @XmlAttribute(name = "mapToUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapToUnit;
+
+  /**
+   * Gets the value of the mapListFrom property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the mapListFrom property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getMapListFrom().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link MapListType.MapListFrom }
+   * 
+   * 
+   */
+  public List<MapListType.MapListFrom> getMapListFrom()
+  {
+    if (mapListFrom == null)
+    {
+      mapListFrom = new ArrayList<MapListType.MapListFrom>();
+    }
+    return this.mapListFrom;
+  }
+
+  /**
+   * Gets the value of the mapListTo property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the mapListTo property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getMapListTo().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link MapListType.MapListTo }
+   * 
+   * 
+   */
+  public List<MapListType.MapListTo> getMapListTo()
+  {
+    if (mapListTo == null)
+    {
+      mapListTo = new ArrayList<MapListType.MapListTo>();
+    }
+    return this.mapListTo;
+  }
+
+  /**
+   * Gets the value of the mapFromUnit property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getMapFromUnit()
+  {
+    return mapFromUnit;
+  }
+
+  /**
+   * Sets the value of the mapFromUnit property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setMapFromUnit(BigInteger value)
+  {
+    this.mapFromUnit = value;
+  }
 
-    protected List<MapListType.MapListFrom> mapListFrom;
-    protected List<MapListType.MapListTo> mapListTo;
-    @XmlAttribute(name = "mapFromUnit", required = true)
-    @XmlSchemaType(name = "positiveInteger")
-    protected BigInteger mapFromUnit;
-    @XmlAttribute(name = "mapToUnit", required = true)
-    @XmlSchemaType(name = "positiveInteger")
-    protected BigInteger mapToUnit;
+  /**
+   * Gets the value of the mapToUnit property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getMapToUnit()
+  {
+    return mapToUnit;
+  }
+
+  /**
+   * Sets the value of the mapToUnit property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setMapToUnit(BigInteger value)
+  {
+    this.mapToUnit = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class MapListFrom
+  {
+
+    @XmlAttribute(name = "start", required = true)
+    protected int start;
+
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
 
     /**
-     * Gets the value of the mapListFrom property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getMapListFrom().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link MapListType.MapListFrom }
-     * 
+     * Gets the value of the start property.
      * 
      */
-    public List<MapListType.MapListFrom> getMapListFrom() {
-        if (mapListFrom == null) {
-            mapListFrom = new ArrayList<MapListType.MapListFrom>();
-        }
-        return this.mapListFrom;
+    public int getStart()
+    {
+      return start;
     }
 
     /**
-     * Gets the value of the mapListTo property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getMapListTo().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link MapListType.MapListTo }
-     * 
+     * Sets the value of the start property.
      * 
      */
-    public List<MapListType.MapListTo> getMapListTo() {
-        if (mapListTo == null) {
-            mapListTo = new ArrayList<MapListType.MapListTo>();
-        }
-        return this.mapListTo;
+    public void setStart(int value)
+    {
+      this.start = value;
     }
 
     /**
-     * Gets the value of the mapFromUnit property.
+     * Gets the value of the end property.
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
      */
-    public BigInteger getMapFromUnit() {
-        return mapFromUnit;
+    public int getEnd()
+    {
+      return end;
     }
 
     /**
-     * Sets the value of the mapFromUnit property.
+     * Sets the value of the end property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
      */
-    public void setMapFromUnit(BigInteger value) {
-        this.mapFromUnit = value;
+    public void setEnd(int value)
+    {
+      this.end = value;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class MapListTo
+  {
+
+    @XmlAttribute(name = "start", required = true)
+    protected int start;
+
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
+
     /**
-     * Gets the value of the mapToUnit property.
+     * Gets the value of the start property.
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
      */
-    public BigInteger getMapToUnit() {
-        return mapToUnit;
+    public int getStart()
+    {
+      return start;
     }
 
     /**
-     * Sets the value of the mapToUnit property.
+     * Sets the value of the start property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
      */
-    public void setMapToUnit(BigInteger value) {
-        this.mapToUnit = value;
+    public void setStart(int value)
+    {
+      this.start = value;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
+     * Gets the value of the end property.
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class MapListFrom {
-
-        @XmlAttribute(name = "start", required = true)
-        protected int start;
-        @XmlAttribute(name = "end", required = true)
-        protected int end;
-
-        /**
-         * Gets the value of the start property.
-         * 
-         */
-        public int getStart() {
-            return start;
-        }
-
-        /**
-         * Sets the value of the start property.
-         * 
-         */
-        public void setStart(int value) {
-            this.start = value;
-        }
-
-        /**
-         * Gets the value of the end property.
-         * 
-         */
-        public int getEnd() {
-            return end;
-        }
-
-        /**
-         * Sets the value of the end property.
-         * 
-         */
-        public void setEnd(int value) {
-            this.end = value;
-        }
-
+    public int getEnd()
+    {
+      return end;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
+     * Sets the value of the end property.
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class MapListTo {
-
-        @XmlAttribute(name = "start", required = true)
-        protected int start;
-        @XmlAttribute(name = "end", required = true)
-        protected int end;
-
-        /**
-         * Gets the value of the start property.
-         * 
-         */
-        public int getStart() {
-            return start;
-        }
-
-        /**
-         * Sets the value of the start property.
-         * 
-         */
-        public void setStart(int value) {
-            this.start = value;
-        }
-
-        /**
-         * Gets the value of the end property.
-         * 
-         */
-        public int getEnd() {
-            return end;
-        }
-
-        /**
-         * Sets the value of the end property.
-         * 
-         */
-        public void setEnd(int value) {
-            this.end = value;
-        }
-
+    public void setEnd(int value)
+    {
+      this.end = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index 10d3d5b..0d5acfb 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -15,17 +14,19 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * 
- * 					Represent the jalview.datamodel.Mapping object - it also provides
- * 					a way of storing sequences that are mapped 'to' without adding them
- * 					to the sequence set (which will mean they are then added to the alignment too).
- * 				
+ * Represent the jalview.datamodel.Mapping object - it also provides a way of
+ * storing sequences that are mapped 'to' without adding them to the sequence
+ * set (which will mean they are then added to the alignment too).
+ * 
  * 
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -51,91 +52,86 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "sequence",
-    "dseqFor"
-})
+@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
 @XmlRootElement(name = "Mapping")
-public class Mapping
-    extends MapListType
+public class Mapping extends MapListType
 {
 
-    @XmlElement(name = "Sequence")
-    protected Sequence sequence;
-    protected String dseqFor;
-    @XmlAttribute(name = "mappingType")
-    protected String mappingType;
+  @XmlElement(name = "Sequence")
+  protected Sequence sequence;
+
+  protected String dseqFor;
+
+  @XmlAttribute(name = "mappingType")
+  protected String mappingType;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Sequence }
-     *     
-     */
-    public Sequence getSequence() {
-        return sequence;
-    }
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link Sequence }
+   * 
+   */
+  public Sequence getSequence()
+  {
+    return sequence;
+  }
 
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Sequence }
-     *     
-     */
-    public void setSequence(Sequence value) {
-        this.sequence = value;
-    }
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link Sequence }
+   * 
+   */
+  public void setSequence(Sequence value)
+  {
+    this.sequence = value;
+  }
 
-    /**
-     * Gets the value of the dseqFor property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDseqFor() {
-        return dseqFor;
-    }
+  /**
+   * Gets the value of the dseqFor property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDseqFor()
+  {
+    return dseqFor;
+  }
 
-    /**
-     * Sets the value of the dseqFor property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDseqFor(String value) {
-        this.dseqFor = value;
-    }
+  /**
+   * Sets the value of the dseqFor property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDseqFor(String value)
+  {
+    this.dseqFor = value;
+  }
 
-    /**
-     * Gets the value of the mappingType property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getMappingType() {
-        return mappingType;
-    }
+  /**
+   * Gets the value of the mappingType property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getMappingType()
+  {
+    return mappingType;
+  }
 
-    /**
-     * Sets the value of the mappingType property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setMappingType(String value) {
-        this.mappingType = value;
-    }
+  /**
+   * Sets the value of the mappingType property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setMappingType(String value)
+  {
+    this.mappingType = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java
index d884100..23aa9ac 100644
--- a/src/jalview/xml/binding/jalview/MatrixType.java
+++ b/src/jalview/xml/binding/jalview/MatrixType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for MatrixType complex type.
+ * <p>
+ * Java class for MatrixType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="MatrixType">
@@ -47,285 +48,292 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MatrixType", propOrder = {
-    "elements",
-    "groups",
-    "newick",
-    "property"
-})
-public class MatrixType {
+@XmlType(
+  name = "MatrixType",
+  propOrder =
+  { "elements", "groups", "newick", "property" })
+public class MatrixType
+{
 
-    @XmlElement(required = true)
-    protected String elements;
-    protected List<String> groups;
-    protected List<String> newick;
-    protected List<Property> 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;
+  @XmlElement(required = true)
+  protected String elements;
 
-    /**
-     * Gets the value of the elements property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getElements() {
-        return elements;
-    }
+  protected List<String> groups;
 
-    /**
-     * Sets the value of the elements property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setElements(String value) {
-        this.elements = value;
-    }
+  protected List<String> newick;
 
-    /**
-     * Gets the value of the groups property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the groups property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getGroups().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getGroups() {
-        if (groups == null) {
-            groups = new ArrayList<String>();
-        }
-        return this.groups;
-    }
+  protected List<Property> property;
 
-    /**
-     * Gets the value of the newick property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the newick property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getNewick().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getNewick() {
-        if (newick == null) {
-            newick = new ArrayList<String>();
-        }
-        return this.newick;
-    }
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the property property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the property property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getProperty().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Property }
-     * 
-     * 
-     */
-    public List<Property> getProperty() {
-        if (property == null) {
-            property = new ArrayList<Property>();
-        }
-        return this.property;
-    }
+  @XmlAttribute(name = "rows", required = true)
+  protected BigInteger rows;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  @XmlAttribute(name = "cols", required = true)
+  protected BigInteger cols;
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  @XmlAttribute(name = "treeMethod")
+  protected String treeMethod;
 
-    /**
-     * Gets the value of the rows property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getRows() {
-        return rows;
-    }
+  @XmlAttribute(name = "cutHeight")
+  protected Double cutHeight;
 
-    /**
-     * Sets the value of the rows property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setRows(BigInteger value) {
-        this.rows = value;
-    }
+  @XmlAttribute(name = "id")
+  protected String id;
 
-    /**
-     * Gets the value of the cols property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getCols() {
-        return cols;
-    }
+  /**
+   * Gets the value of the elements property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getElements()
+  {
+    return elements;
+  }
 
-    /**
-     * Sets the value of the cols property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setCols(BigInteger value) {
-        this.cols = value;
-    }
+  /**
+   * Sets the value of the elements property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setElements(String value)
+  {
+    this.elements = value;
+  }
 
-    /**
-     * Gets the value of the treeMethod property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getTreeMethod() {
-        return treeMethod;
+  /**
+   * Gets the value of the groups property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the groups property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getGroups().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getGroups()
+  {
+    if (groups == null)
+    {
+      groups = new ArrayList<String>();
     }
+    return this.groups;
+  }
 
-    /**
-     * 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 newick property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the newick property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getNewick().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getNewick()
+  {
+    if (newick == null)
+    {
+      newick = new ArrayList<String>();
     }
+    return this.newick;
+  }
 
-    /**
-     * Gets the value of the cutHeight property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Double }
-     *     
-     */
-    public Double getCutHeight() {
-        return cutHeight;
+  /**
+   * Gets the value of the property property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the property property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getProperty().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Property }
+   * 
+   * 
+   */
+  public List<Property> getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList<Property>();
     }
+    return this.property;
+  }
 
-    /**
-     * 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 type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Gets the value of the rows property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getRows()
+  {
+    return rows;
+  }
+
+  /**
+   * Sets the value of the rows property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setRows(BigInteger value)
+  {
+    this.rows = value;
+  }
+
+  /**
+   * Gets the value of the cols property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getCols()
+  {
+    return cols;
+  }
+
+  /**
+   * Sets the value of the cols property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setCols(BigInteger value)
+  {
+    this.cols = value;
+  }
+
+  /**
+   * 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 22b78a5..77074d1 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -5,19 +5,21 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for NoValueColour.
+ * <p>
+ * Java class for NoValueColour.
  * 
- * <p>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.
+ * <p>
+ * 
  * <pre>
  * &lt;simpleType name="NoValueColour">
  *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -31,31 +33,36 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum NoValueColour {
-
-    @XmlEnumValue("None")
-    NONE("None"),
-    @XmlEnumValue("Min")
-    MIN("Min"),
-    @XmlEnumValue("Max")
-    MAX("Max");
-    private final String value;
-
-    NoValueColour(String v) {
-        value = v;
-    }
+public enum NoValueColour
+{
 
-    public String value() {
-        return value;
-    }
+  @XmlEnumValue("None")
+  NONE("None"), @XmlEnumValue("Min")
+  MIN("Min"), @XmlEnumValue("Max")
+  MAX("Max");
+
+  private final String value;
+
+  NoValueColour(String v)
+  {
+    value = v;
+  }
+
+  public String value()
+  {
+    return value;
+  }
 
-    public static NoValueColour fromValue(String v) {
-        for (NoValueColour c: NoValueColour.values()) {
-            if (c.value.equals(v)) {
-                return c;
-            }
-        }
-        throw new IllegalArgumentException(v);
+  public static NoValueColour fromValue(String v)
+  {
+    for (NoValueColour c : NoValueColour.values())
+    {
+      if (c.value.equals(v))
+      {
+        return c;
+      }
     }
+    throw new IllegalArgumentException(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index f034a2a..448b35f 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.JAXBElement;
@@ -13,492 +12,567 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 import javax.xml.namespace.QName;
 
-
 /**
- * This object contains factory methods for each 
- * Java content interface and Java element interface 
- * generated in the jalview.xml.binding.jalview package. 
- * <p>An ObjectFactory allows you to programatically 
- * construct new instances of the Java representation 
- * for XML content. The Java representation of XML 
- * content can consist of schema derived interfaces 
- * and classes representing the binding of schema 
- * type definitions, element declarations and model 
- * groups.  Factory methods for each of these are 
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.jalview package.
+ * <p>
+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
  * 
  */
 @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");
-
-    /**
-     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
-     * 
-     */
-    public ObjectFactory() {
-    }
-
-    /**
-     * Create an instance of {@link AlcodonFrame }
-     * 
-     */
-    public AlcodonFrame createAlcodonFrame() {
-        return new AlcodonFrame();
-    }
-
-    /**
-     * Create an instance of {@link MapListType }
-     * 
-     */
-    public MapListType createMapListType() {
-        return new MapListType();
-    }
-
-    /**
-     * Create an instance of {@link Sequence }
-     * 
-     */
-    public Sequence createSequence() {
-        return new Sequence();
-    }
-
-    /**
-     * Create an instance of {@link Annotation }
-     * 
-     */
-    public Annotation createAnnotation() {
-        return new Annotation();
-    }
-
-    /**
-     * Create an instance of {@link SequenceSet }
-     * 
-     */
-    public SequenceSet createSequenceSet() {
-        return new SequenceSet();
-    }
-
-    /**
-     * Create an instance of {@link FeatureMatcherSet }
-     * 
-     */
-    public FeatureMatcherSet createFeatureMatcherSet() {
-        return new FeatureMatcherSet();
-    }
-
-    /**
-     * Create an instance of {@link JalviewUserColours }
-     * 
-     */
-    public JalviewUserColours createJalviewUserColours() {
-        return new JalviewUserColours();
-    }
-
-    /**
-     * Create an instance of {@link Pdbentry }
-     * 
-     */
-    public Pdbentry createPdbentry() {
-        return new Pdbentry();
-    }
-
-    /**
-     * Create an instance of {@link Feature }
-     * 
-     */
-    public Feature createFeature() {
-        return new Feature();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel }
-     * 
-     */
-    public JalviewModel createJalviewModel() {
-        return new JalviewModel();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.FeatureSettings }
-     * 
-     */
-    public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
-        return new JalviewModel.FeatureSettings();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer }
-     * 
-     */
-    public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
-        return new JalviewModel.PcaViewer();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport }
-     * 
-     */
-    public JalviewModel.Viewport createJalviewModelViewport() {
-        return new JalviewModel.Viewport();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq }
-     * 
-     */
-    public JalviewModel.JSeq createJalviewModelJSeq() {
-        return new JalviewModel.JSeq();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
-     * 
-     */
-    public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
-        return new JalviewModel.JSeq.RnaViewer();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.Pdbids }
-     * 
-     */
-    public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
-        return new JalviewModel.JSeq.Pdbids();
-    }
-
-    /**
-     * Create an instance of {@link DoubleMatrix }
-     * 
-     */
-    public DoubleMatrix createDoubleMatrix() {
-        return new DoubleMatrix();
-    }
-
-    /**
-     * Create an instance of {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme createAnnotationColourScheme() {
-        return new AnnotationColourScheme();
-    }
-
-    /**
-     * Create an instance of {@link PcaDataType }
-     * 
-     */
-    public PcaDataType createPcaDataType() {
-        return new PcaDataType();
-    }
-
-    /**
-     * Create an instance of {@link DoubleVector }
-     * 
-     */
-    public DoubleVector createDoubleVector() {
-        return new DoubleVector();
-    }
-
-    /**
-     * Create an instance of {@link AlcodonFrame.Alcodon }
-     * 
-     */
-    public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
-        return new AlcodonFrame.Alcodon();
-    }
-
-    /**
-     * Create an instance of {@link AlcodonFrame.AlcodMap }
-     * 
-     */
-    public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
-        return new AlcodonFrame.AlcodMap();
-    }
-
-    /**
-     * Create an instance of {@link AnnotationElement }
-     * 
-     */
-    public AnnotationElement createAnnotationElement() {
-        return new AnnotationElement();
-    }
-
-    /**
-     * Create an instance of {@link Mapping }
-     * 
-     */
-    public Mapping createMapping() {
-        return new Mapping();
-    }
-
-    /**
-     * Create an instance of {@link MapListType.MapListFrom }
-     * 
-     */
-    public MapListType.MapListFrom createMapListTypeMapListFrom() {
-        return new MapListType.MapListFrom();
-    }
-
-    /**
-     * Create an instance of {@link MapListType.MapListTo }
-     * 
-     */
-    public MapListType.MapListTo createMapListTypeMapListTo() {
-        return new MapListType.MapListTo();
-    }
-
-    /**
-     * Create an instance of {@link SequenceType }
-     * 
-     */
-    public SequenceType createSequenceType() {
-        return new SequenceType();
-    }
-
-    /**
-     * Create an instance of {@link Sequence.DBRef }
-     * 
-     */
-    public Sequence.DBRef createSequenceDBRef() {
-        return new Sequence.DBRef();
-    }
-
-    /**
-     * Create an instance of {@link Annotation.ThresholdLine }
-     * 
-     */
-    public Annotation.ThresholdLine createAnnotationThresholdLine() {
-        return new Annotation.ThresholdLine();
-    }
-
-    /**
-     * Create an instance of {@link MatrixType }
-     * 
-     */
-    public MatrixType createMatrixType() {
-        return new MatrixType();
-    }
-
-    /**
-     * Create an instance of {@link jalview.xml.binding.jalview.Property }
-     * 
-     */
-    public jalview.xml.binding.jalview.Property createProperty() {
-        return new jalview.xml.binding.jalview.Property();
-    }
-
-    /**
-     * Create an instance of {@link SequenceSet.SequenceSetProperties }
-     * 
-     */
-    public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
-        return new SequenceSet.SequenceSetProperties();
-    }
-
-    /**
-     * Create an instance of {@link VAMSAS }
-     * 
-     */
-    public VAMSAS createVAMSAS() {
-        return new VAMSAS();
-    }
-
-    /**
-     * Create an instance of {@link FeatureMatcher }
-     * 
-     */
-    public FeatureMatcher createFeatureMatcher() {
-        return new FeatureMatcher();
-    }
-
-    /**
-     * Create an instance of {@link WebServiceParameterSet }
-     * 
-     */
-    public WebServiceParameterSet createWebServiceParameterSet() {
-        return new WebServiceParameterSet();
-    }
-
-    /**
-     * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
-     * 
-     */
-    public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
-        return new FeatureMatcherSet.CompoundMatcher();
-    }
-
-    /**
-     * Create an instance of {@link JalviewUserColours.Colour }
-     * 
-     */
-    public JalviewUserColours.Colour createJalviewUserColoursColour() {
-        return new JalviewUserColours.Colour();
-    }
-
-    /**
-     * Create an instance of {@link JalviewUserColours.Filter }
-     * 
-     */
-    public JalviewUserColours.Filter createJalviewUserColoursFilter() {
-        return new JalviewUserColours.Filter();
-    }
-
-    /**
-     * Create an instance of {@link Pdbentry.Property }
-     * 
-     */
-    public Pdbentry.Property createPdbentryProperty() {
-        return new Pdbentry.Property();
-    }
-
-    /**
-     * Create an instance of {@link Feature.OtherData }
-     * 
-     */
-    public Feature.OtherData createFeatureOtherData() {
-        return new Feature.OtherData();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JGroup }
-     * 
-     */
-    public JalviewModel.JGroup createJalviewModelJGroup() {
-        return new JalviewModel.JGroup();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.UserColours }
-     * 
-     */
-    public JalviewModel.UserColours createJalviewModelUserColours() {
-        return new JalviewModel.UserColours();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Tree }
-     * 
-     */
-    public JalviewModel.Tree createJalviewModelTree() {
-        return new JalviewModel.Tree();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
-     * 
-     */
-    public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
-        return new JalviewModel.FeatureSettings.Setting();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.FeatureSettings.Group }
-     * 
-     */
-    public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
-        return new JalviewModel.FeatureSettings.Group();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
-     * 
-     */
-    public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
-        return new JalviewModel.PcaViewer.SequencePoint();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.Axis }
-     * 
-     */
-    public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
-        return new JalviewModel.PcaViewer.Axis();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
-        return new JalviewModel.PcaViewer.SeqPointMin();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
-        return new JalviewModel.PcaViewer.SeqPointMax();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
-     * 
-     */
-    public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
-        return new JalviewModel.Viewport.HiddenColumns();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
-     * 
-     */
-    public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
-        return new JalviewModel.Viewport.CalcIdParam();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport.Overview }
-     * 
-     */
-    public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
-        return new JalviewModel.Viewport.Overview();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-     * 
-     */
-    public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
-        return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
-     * 
-     */
-    public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
-        return new JalviewModel.JSeq.Pdbids.StructureState();
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
-     * 
-     */
-    @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
-    public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
-        return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
-     * 
-     */
-    @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
-    public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
-        return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
-     * 
-     */
-    @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
-    public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
-        return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
-    }
+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");
+
+  /**
+   * Create a new ObjectFactory that can be used to create new instances of
+   * schema derived classes for package: jalview.xml.binding.jalview
+   * 
+   */
+  public ObjectFactory()
+  {
+  }
+
+  /**
+   * Create an instance of {@link AlcodonFrame }
+   * 
+   */
+  public AlcodonFrame createAlcodonFrame()
+  {
+    return new AlcodonFrame();
+  }
+
+  /**
+   * Create an instance of {@link MapListType }
+   * 
+   */
+  public MapListType createMapListType()
+  {
+    return new MapListType();
+  }
+
+  /**
+   * Create an instance of {@link Sequence }
+   * 
+   */
+  public Sequence createSequence()
+  {
+    return new Sequence();
+  }
+
+  /**
+   * Create an instance of {@link Annotation }
+   * 
+   */
+  public Annotation createAnnotation()
+  {
+    return new Annotation();
+  }
+
+  /**
+   * Create an instance of {@link SequenceSet }
+   * 
+   */
+  public SequenceSet createSequenceSet()
+  {
+    return new SequenceSet();
+  }
+
+  /**
+   * Create an instance of {@link FeatureMatcherSet }
+   * 
+   */
+  public FeatureMatcherSet createFeatureMatcherSet()
+  {
+    return new FeatureMatcherSet();
+  }
+
+  /**
+   * Create an instance of {@link JalviewUserColours }
+   * 
+   */
+  public JalviewUserColours createJalviewUserColours()
+  {
+    return new JalviewUserColours();
+  }
+
+  /**
+   * Create an instance of {@link Pdbentry }
+   * 
+   */
+  public Pdbentry createPdbentry()
+  {
+    return new Pdbentry();
+  }
+
+  /**
+   * Create an instance of {@link Feature }
+   * 
+   */
+  public Feature createFeature()
+  {
+    return new Feature();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel }
+   * 
+   */
+  public JalviewModel createJalviewModel()
+  {
+    return new JalviewModel();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.FeatureSettings }
+   * 
+   */
+  public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
+  {
+    return new JalviewModel.FeatureSettings();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer }
+   * 
+   */
+  public JalviewModel.PcaViewer createJalviewModelPcaViewer()
+  {
+    return new JalviewModel.PcaViewer();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport }
+   * 
+   */
+  public JalviewModel.Viewport createJalviewModelViewport()
+  {
+    return new JalviewModel.Viewport();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq }
+   * 
+   */
+  public JalviewModel.JSeq createJalviewModelJSeq()
+  {
+    return new JalviewModel.JSeq();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+   * 
+   */
+  public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
+  {
+    return new JalviewModel.JSeq.RnaViewer();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+   * 
+   */
+  public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
+  {
+    return new JalviewModel.JSeq.Pdbids();
+  }
+
+  /**
+   * Create an instance of {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix createDoubleMatrix()
+  {
+    return new DoubleMatrix();
+  }
+
+  /**
+   * Create an instance of {@link AnnotationColourScheme }
+   * 
+   */
+  public AnnotationColourScheme createAnnotationColourScheme()
+  {
+    return new AnnotationColourScheme();
+  }
+
+  /**
+   * Create an instance of {@link PcaDataType }
+   * 
+   */
+  public PcaDataType createPcaDataType()
+  {
+    return new PcaDataType();
+  }
+
+  /**
+   * Create an instance of {@link DoubleVector }
+   * 
+   */
+  public DoubleVector createDoubleVector()
+  {
+    return new DoubleVector();
+  }
+
+  /**
+   * Create an instance of {@link AlcodonFrame.Alcodon }
+   * 
+   */
+  public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
+  {
+    return new AlcodonFrame.Alcodon();
+  }
+
+  /**
+   * Create an instance of {@link AlcodonFrame.AlcodMap }
+   * 
+   */
+  public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
+  {
+    return new AlcodonFrame.AlcodMap();
+  }
+
+  /**
+   * Create an instance of {@link AnnotationElement }
+   * 
+   */
+  public AnnotationElement createAnnotationElement()
+  {
+    return new AnnotationElement();
+  }
+
+  /**
+   * Create an instance of {@link Mapping }
+   * 
+   */
+  public Mapping createMapping()
+  {
+    return new Mapping();
+  }
+
+  /**
+   * Create an instance of {@link MapListType.MapListFrom }
+   * 
+   */
+  public MapListType.MapListFrom createMapListTypeMapListFrom()
+  {
+    return new MapListType.MapListFrom();
+  }
+
+  /**
+   * Create an instance of {@link MapListType.MapListTo }
+   * 
+   */
+  public MapListType.MapListTo createMapListTypeMapListTo()
+  {
+    return new MapListType.MapListTo();
+  }
+
+  /**
+   * Create an instance of {@link SequenceType }
+   * 
+   */
+  public SequenceType createSequenceType()
+  {
+    return new SequenceType();
+  }
+
+  /**
+   * Create an instance of {@link Sequence.DBRef }
+   * 
+   */
+  public Sequence.DBRef createSequenceDBRef()
+  {
+    return new Sequence.DBRef();
+  }
+
+  /**
+   * Create an instance of {@link Annotation.ThresholdLine }
+   * 
+   */
+  public Annotation.ThresholdLine createAnnotationThresholdLine()
+  {
+    return new Annotation.ThresholdLine();
+  }
+
+  /**
+   * Create an instance of {@link MatrixType }
+   * 
+   */
+  public MatrixType createMatrixType()
+  {
+    return new MatrixType();
+  }
+
+  /**
+   * Create an instance of {@link jalview.xml.binding.jalview.Property }
+   * 
+   */
+  public jalview.xml.binding.jalview.Property createProperty()
+  {
+    return new jalview.xml.binding.jalview.Property();
+  }
+
+  /**
+   * Create an instance of {@link SequenceSet.SequenceSetProperties }
+   * 
+   */
+  public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
+  {
+    return new SequenceSet.SequenceSetProperties();
+  }
+
+  /**
+   * Create an instance of {@link VAMSAS }
+   * 
+   */
+  public VAMSAS createVAMSAS()
+  {
+    return new VAMSAS();
+  }
+
+  /**
+   * Create an instance of {@link FeatureMatcher }
+   * 
+   */
+  public FeatureMatcher createFeatureMatcher()
+  {
+    return new FeatureMatcher();
+  }
+
+  /**
+   * Create an instance of {@link WebServiceParameterSet }
+   * 
+   */
+  public WebServiceParameterSet createWebServiceParameterSet()
+  {
+    return new WebServiceParameterSet();
+  }
+
+  /**
+   * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+   * 
+   */
+  public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
+  {
+    return new FeatureMatcherSet.CompoundMatcher();
+  }
+
+  /**
+   * Create an instance of {@link JalviewUserColours.Colour }
+   * 
+   */
+  public JalviewUserColours.Colour createJalviewUserColoursColour()
+  {
+    return new JalviewUserColours.Colour();
+  }
+
+  /**
+   * Create an instance of {@link JalviewUserColours.Filter }
+   * 
+   */
+  public JalviewUserColours.Filter createJalviewUserColoursFilter()
+  {
+    return new JalviewUserColours.Filter();
+  }
+
+  /**
+   * Create an instance of {@link Pdbentry.Property }
+   * 
+   */
+  public Pdbentry.Property createPdbentryProperty()
+  {
+    return new Pdbentry.Property();
+  }
+
+  /**
+   * Create an instance of {@link Feature.OtherData }
+   * 
+   */
+  public Feature.OtherData createFeatureOtherData()
+  {
+    return new Feature.OtherData();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JGroup }
+   * 
+   */
+  public JalviewModel.JGroup createJalviewModelJGroup()
+  {
+    return new JalviewModel.JGroup();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.UserColours }
+   * 
+   */
+  public JalviewModel.UserColours createJalviewModelUserColours()
+  {
+    return new JalviewModel.UserColours();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Tree }
+   * 
+   */
+  public JalviewModel.Tree createJalviewModelTree()
+  {
+    return new JalviewModel.Tree();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+   * 
+   */
+  public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
+  {
+    return new JalviewModel.FeatureSettings.Setting();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+   * 
+   */
+  public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
+  {
+    return new JalviewModel.FeatureSettings.Group();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+   * 
+   */
+  public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
+  {
+    return new JalviewModel.PcaViewer.SequencePoint();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+   * 
+   */
+  public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
+  {
+    return new JalviewModel.PcaViewer.Axis();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+   * 
+   */
+  public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
+  {
+    return new JalviewModel.PcaViewer.SeqPointMin();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+   * 
+   */
+  public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
+  {
+    return new JalviewModel.PcaViewer.SeqPointMax();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+   * 
+   */
+  public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
+  {
+    return new JalviewModel.Viewport.HiddenColumns();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+   * 
+   */
+  public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
+  {
+    return new JalviewModel.Viewport.CalcIdParam();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport.Overview }
+   * 
+   */
+  public JalviewModel.Viewport.Overview createJalviewModelViewportOverview()
+  {
+    return new JalviewModel.Viewport.Overview();
+  }
+
+  /**
+   * Create an instance of
+   * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+   * 
+   */
+  public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
+  {
+    return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+   * 
+   */
+  public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
+  {
+    return new JalviewModel.JSeq.Pdbids.StructureState();
+  }
+
+  /**
+   * Create an instance of {@link JAXBElement
+   * }{@code <}{@link WebServiceParameterSet }{@code >}}
+   * 
+   */
+  @XmlElementDecl(
+    namespace = "www.jalview.org/xml/wsparamset",
+    name = "WebServiceParameterSet")
+  public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
+          WebServiceParameterSet value)
+  {
+    return new JAXBElement<WebServiceParameterSet>(
+            _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
+            null, value);
+  }
+
+  /**
+   * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
+   * }{@code >}}
+   * 
+   */
+  @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+  public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
+  {
+    return new JAXBElement<JalviewModel>(_JalviewModel_QNAME,
+            JalviewModel.class, null, value);
+  }
+
+  /**
+   * Create an instance of {@link JAXBElement
+   * }{@code <}{@link JalviewUserColours }{@code >}}
+   * 
+   */
+  @XmlElementDecl(
+    namespace = "www.jalview.org/colours",
+    name = "JalviewUserColours")
+  public JAXBElement<JalviewUserColours> createJalviewUserColours(
+          JalviewUserColours value)
+  {
+    return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME,
+            JalviewUserColours.class, null, value);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
index 06aecab..8719689 100644
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,15 +12,17 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * 
- * 				The results of a PCA calculation
- * 			
+ * The results of a PCA calculation
+ * 
  * 
- * <p>Java class for PcaDataType complex type.
+ * <p>
+ * Java class for PcaDataType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="PcaDataType">
@@ -40,90 +41,90 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
-    "pairwiseMatrix",
-    "tridiagonalMatrix",
-    "eigenMatrix"
-})
-public class PcaDataType {
+@XmlType(
+  name = "PcaDataType",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
+public class PcaDataType
+{
+
+  @XmlElement(required = true)
+  protected DoubleMatrix pairwiseMatrix;
+
+  @XmlElement(required = true)
+  protected DoubleMatrix tridiagonalMatrix;
 
-    @XmlElement(required = true)
-    protected DoubleMatrix pairwiseMatrix;
-    @XmlElement(required = true)
-    protected DoubleMatrix tridiagonalMatrix;
-    @XmlElement(required = true)
-    protected DoubleMatrix eigenMatrix;
+  @XmlElement(required = true)
+  protected DoubleMatrix eigenMatrix;
 
-    /**
-     * Gets the value of the pairwiseMatrix property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public DoubleMatrix getPairwiseMatrix() {
-        return pairwiseMatrix;
-    }
+  /**
+   * Gets the value of the pairwiseMatrix property.
+   * 
+   * @return possible object is {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix getPairwiseMatrix()
+  {
+    return pairwiseMatrix;
+  }
 
-    /**
-     * Sets the value of the pairwiseMatrix property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public void setPairwiseMatrix(DoubleMatrix value) {
-        this.pairwiseMatrix = value;
-    }
+  /**
+   * Sets the value of the pairwiseMatrix property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleMatrix }
+   * 
+   */
+  public void setPairwiseMatrix(DoubleMatrix value)
+  {
+    this.pairwiseMatrix = value;
+  }
 
-    /**
-     * Gets the value of the tridiagonalMatrix property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public DoubleMatrix getTridiagonalMatrix() {
-        return tridiagonalMatrix;
-    }
+  /**
+   * Gets the value of the tridiagonalMatrix property.
+   * 
+   * @return possible object is {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix getTridiagonalMatrix()
+  {
+    return tridiagonalMatrix;
+  }
 
-    /**
-     * Sets the value of the tridiagonalMatrix property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public void setTridiagonalMatrix(DoubleMatrix value) {
-        this.tridiagonalMatrix = value;
-    }
+  /**
+   * Sets the value of the tridiagonalMatrix property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleMatrix }
+   * 
+   */
+  public void setTridiagonalMatrix(DoubleMatrix value)
+  {
+    this.tridiagonalMatrix = value;
+  }
 
-    /**
-     * Gets the value of the eigenMatrix property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public DoubleMatrix getEigenMatrix() {
-        return eigenMatrix;
-    }
+  /**
+   * Gets the value of the eigenMatrix property.
+   * 
+   * @return possible object is {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix getEigenMatrix()
+  {
+    return eigenMatrix;
+  }
 
-    /**
-     * Sets the value of the eigenMatrix property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public void setEigenMatrix(DoubleMatrix value) {
-        this.eigenMatrix = value;
-    }
+  /**
+   * Sets the value of the eigenMatrix property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleMatrix }
+   * 
+   */
+  public void setEigenMatrix(DoubleMatrix value)
+  {
+    this.eigenMatrix = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index 401022a..c0bedff 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for pdbentry complex type.
+ * <p>
+ * Java class for pdbentry complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="pdbentry">
@@ -49,199 +50,205 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
-    "property"
-})
-@XmlSeeAlso({
-    jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
-})
-public class Pdbentry {
-
-    protected List<Pdbentry.Property> property;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "type")
-    protected String type;
-    @XmlAttribute(name = "file")
-    protected String file;
-
-    /**
-     * Gets the value of the property property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the property property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getProperty().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Pdbentry.Property }
-     * 
-     * 
-     */
-    public List<Pdbentry.Property> getProperty() {
-        if (property == null) {
-            property = new ArrayList<Pdbentry.Property>();
-        }
-        return this.property;
+@XmlType(
+  name = "pdbentry",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "property" })
+@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
+public class Pdbentry
+{
+
+  protected List<Pdbentry.Property> property;
+
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
+
+  @XmlAttribute(name = "type")
+  protected String type;
+
+  @XmlAttribute(name = "file")
+  protected String file;
+
+  /**
+   * Gets the value of the property property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the property property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getProperty().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link Pdbentry.Property }
+   * 
+   * 
+   */
+  public List<Pdbentry.Property> getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList<Pdbentry.Property>();
     }
+    return this.property;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the file property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getFile()
+  {
+    return file;
+  }
+
+  /**
+   * Sets the value of the file property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setFile(String value)
+  {
+    this.file = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Property
+  {
+
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
+
+    @XmlAttribute(name = "value", required = true)
+    protected String value;
 
     /**
-     * Gets the value of the id property.
+     * Gets the value of the name property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getId() {
-        return id;
+    public String getName()
+    {
+      return name;
     }
 
     /**
-     * Sets the value of the id property.
+     * Sets the value of the name property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
-
-    /**
-     * Gets the value of the type property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getType() {
-        return type;
+    public void setName(String value)
+    {
+      this.name = value;
     }
 
     /**
-     * Sets the value of the type property.
+     * Gets the value of the value property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
-
-    /**
-     * Gets the value of the file property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getFile() {
-        return file;
+    public String getValue()
+    {
+      return value;
     }
 
     /**
-     * Sets the value of the file property.
+     * Sets the value of the value property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setFile(String value) {
-        this.file = value;
-    }
-
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Property {
-
-        @XmlAttribute(name = "name", required = true)
-        protected String name;
-        @XmlAttribute(name = "value", required = true)
-        protected String value;
-
-        /**
-         * Gets the value of the name property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getName() {
-            return name;
-        }
-
-        /**
-         * Sets the value of the name property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setName(String value) {
-            this.name = value;
-        }
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
+    public void setValue(String value)
+    {
+      this.value = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/Property.java b/src/jalview/xml/binding/jalview/Property.java
index 3c0879d..ed57889 100644
--- a/src/jalview/xml/binding/jalview/Property.java
+++ b/src/jalview/xml/binding/jalview/Property.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for property complex type.
+ * <p>
+ * Java class for property complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="property">
@@ -34,59 +35,59 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "property")
-public class Property {
+public class Property
+{
+
+  @XmlAttribute(name = "name")
+  protected String name;
 
-    @XmlAttribute(name = "name")
-    protected String name;
-    @XmlAttribute(name = "value")
-    protected String value;
+  @XmlAttribute(name = "value")
+  protected String value;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index d02fd03..15893d8 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -55,294 +56,300 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "dbRef"
-})
+@XmlType(name = "", propOrder = { "dbRef" })
 @XmlRootElement(name = "Sequence")
-public class Sequence
-    extends SequenceType
+public class Sequence extends SequenceType
 {
 
-    @XmlElement(name = "DBRef")
-    protected List<Sequence.DBRef> dbRef;
-    @XmlAttribute(name = "dsseqid")
-    protected String dsseqid;
-    @XmlAttribute(name = "biotype")
-    protected String biotype;
+  @XmlElement(name = "DBRef")
+  protected List<Sequence.DBRef> dbRef;
+
+  @XmlAttribute(name = "dsseqid")
+  protected String dsseqid;
+
+  @XmlAttribute(name = "biotype")
+  protected String biotype;
+
+  /**
+   * Gets the value of the dbRef property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the dbRef property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getDBRef().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link Sequence.DBRef }
+   * 
+   * 
+   */
+  public List<Sequence.DBRef> getDBRef()
+  {
+    if (dbRef == null)
+    {
+      dbRef = new ArrayList<Sequence.DBRef>();
+    }
+    return this.dbRef;
+  }
+
+  /**
+   * Gets the value of the dsseqid property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDsseqid()
+  {
+    return dsseqid;
+  }
+
+  /**
+   * Sets the value of the dsseqid property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDsseqid(String value)
+  {
+    this.dsseqid = value;
+  }
+
+  /**
+   * Gets the value of the biotype property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getBiotype()
+  {
+    return biotype;
+  }
+
+  /**
+   * Sets the value of the biotype property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setBiotype(String value)
+  {
+    this.biotype = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "mapping" })
+  public static class DBRef
+  {
+
+    @XmlElement(name = "Mapping")
+    protected Mapping mapping;
+
+    @XmlAttribute(name = "source")
+    protected String source;
+
+    @XmlAttribute(name = "version")
+    protected String version;
+
+    @XmlAttribute(name = "accessionId")
+    protected String accessionId;
+
+    @XmlAttribute(name = "locus")
+    protected Boolean locus;
+
+    @XmlAttribute(name = "canonical")
+    protected Boolean canonical;
 
     /**
-     * Gets the value of the dbRef property.
+     * Gets the value of the mapping property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the dbRef property.
+     * @return possible object is {@link Mapping }
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getDBRef().add(newItem);
-     * </pre>
+     */
+    public Mapping getMapping()
+    {
+      return mapping;
+    }
+
+    /**
+     * Sets the value of the mapping property.
+     * 
+     * @param value
+     *          allowed object is {@link Mapping }
+     * 
+     */
+    public void setMapping(Mapping value)
+    {
+      this.mapping = value;
+    }
+
+    /**
+     * Gets the value of the source property.
      * 
+     * @return possible object is {@link String }
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Sequence.DBRef }
+     */
+    public String getSource()
+    {
+      return source;
+    }
+
+    /**
+     * Sets the value of the source property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    public List<Sequence.DBRef> getDBRef() {
-        if (dbRef == null) {
-            dbRef = new ArrayList<Sequence.DBRef>();
-        }
-        return this.dbRef;
+    public void setSource(String value)
+    {
+      this.source = value;
     }
 
     /**
-     * Gets the value of the dsseqid property.
+     * Gets the value of the version property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getDsseqid() {
-        return dsseqid;
+    public String getVersion()
+    {
+      return version;
     }
 
     /**
-     * Sets the value of the dsseqid property.
+     * Sets the value of the version property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setDsseqid(String value) {
-        this.dsseqid = value;
+    public void setVersion(String value)
+    {
+      this.version = value;
     }
 
     /**
-     * Gets the value of the biotype property.
+     * Gets the value of the accessionId property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getBiotype() {
-        return biotype;
+    public String getAccessionId()
+    {
+      return accessionId;
     }
 
     /**
-     * Sets the value of the biotype property.
+     * Sets the value of the accessionId property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setBiotype(String value) {
-        this.biotype = value;
+    public void setAccessionId(String value)
+    {
+      this.accessionId = value;
     }
 
+    /**
+     * Gets the value of the locus property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isLocus()
+    {
+      if (locus == null)
+      {
+        return false;
+      }
+      else
+      {
+        return locus;
+      }
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Sets the value of the locus property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Boolean }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public void setLocus(Boolean value)
+    {
+      this.locus = value;
+    }
+
+    /**
+     * Gets the value of the canonical property.
      * 
+     * @return possible object is {@link Boolean }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "mapping"
-    })
-    public static class DBRef {
-
-        @XmlElement(name = "Mapping")
-        protected Mapping mapping;
-        @XmlAttribute(name = "source")
-        protected String source;
-        @XmlAttribute(name = "version")
-        protected String version;
-        @XmlAttribute(name = "accessionId")
-        protected String accessionId;
-        @XmlAttribute(name = "locus")
-        protected Boolean locus;
-        @XmlAttribute(name = "canonical")
-        protected Boolean canonical;
-
-        /**
-         * Gets the value of the mapping property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Mapping }
-         *     
-         */
-        public Mapping getMapping() {
-            return mapping;
-        }
-
-        /**
-         * Sets the value of the mapping property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Mapping }
-         *     
-         */
-        public void setMapping(Mapping value) {
-            this.mapping = value;
-        }
-
-        /**
-         * Gets the value of the source property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getSource() {
-            return source;
-        }
-
-        /**
-         * Sets the value of the source property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setSource(String value) {
-            this.source = value;
-        }
-
-        /**
-         * Gets the value of the version property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getVersion() {
-            return version;
-        }
-
-        /**
-         * Sets the value of the version property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setVersion(String value) {
-            this.version = value;
-        }
-
-        /**
-         * Gets the value of the accessionId property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getAccessionId() {
-            return accessionId;
-        }
-
-        /**
-         * Sets the value of the accessionId property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setAccessionId(String value) {
-            this.accessionId = value;
-        }
-
-        /**
-         * Gets the value of the locus property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isLocus() {
-            if (locus == null) {
-                return false;
-            } else {
-                return locus;
-            }
-        }
-
-        /**
-         * Sets the value of the locus property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setLocus(Boolean value) {
-            this.locus = value;
-        }
-
-        /**
-         * Gets the value of the canonical property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isCanonical() {
-            if (canonical == null) {
-                return false;
-            } else {
-                return canonical;
-            }
-        }
-
-        /**
-         * Sets the value of the canonical property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setCanonical(Boolean value) {
-            this.canonical = value;
-        }
+    public boolean isCanonical()
+    {
+      if (canonical == null)
+      {
+        return false;
+      }
+      else
+      {
+        return canonical;
+      }
+    }
 
+    /**
+     * Sets the value of the canonical property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setCanonical(Boolean value)
+    {
+      this.canonical = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index a915d94..6676f7b 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -52,267 +53,282 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "sequence",
-    "annotation",
-    "sequenceSetProperties",
-    "alcodonFrame"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet {
+public class SequenceSet
+{
 
-    @XmlElement(name = "Sequence")
-    protected List<Sequence> sequence;
-    @XmlElement(name = "Annotation")
-    protected List<Annotation> annotation;
-    protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
-    @XmlElement(name = "AlcodonFrame")
-    protected List<AlcodonFrame> alcodonFrame;
-    @XmlAttribute(name = "gapChar", required = true)
-    protected String gapChar;
-    @XmlAttribute(name = "datasetId")
-    protected String datasetId;
+  @XmlElement(name = "Sequence")
+  protected List<Sequence> sequence;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the sequence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getSequence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Sequence }
-     * 
-     * 
-     */
-    public List<Sequence> getSequence() {
-        if (sequence == null) {
-            sequence = new ArrayList<Sequence>();
-        }
-        return this.sequence;
+  @XmlElement(name = "Annotation")
+  protected List<Annotation> annotation;
+
+  protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+
+  @XmlElement(name = "AlcodonFrame")
+  protected List<AlcodonFrame> alcodonFrame;
+
+  @XmlAttribute(name = "gapChar", required = true)
+  protected String gapChar;
+
+  @XmlAttribute(name = "datasetId")
+  protected String datasetId;
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the sequence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getSequence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Sequence }
+   * 
+   * 
+   */
+  public List<Sequence> getSequence()
+  {
+    if (sequence == null)
+    {
+      sequence = new ArrayList<Sequence>();
     }
+    return this.sequence;
+  }
 
-    /**
-     * Gets the value of the annotation property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the annotation property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getAnnotation().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Annotation }
-     * 
-     * 
-     */
-    public List<Annotation> getAnnotation() {
-        if (annotation == null) {
-            annotation = new ArrayList<Annotation>();
-        }
-        return this.annotation;
+  /**
+   * Gets the value of the annotation property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the annotation property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAnnotation().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Annotation
+   * }
+   * 
+   * 
+   */
+  public List<Annotation> getAnnotation()
+  {
+    if (annotation == null)
+    {
+      annotation = new ArrayList<Annotation>();
     }
+    return this.annotation;
+  }
 
-    /**
-     * Gets the value of the sequenceSetProperties property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getSequenceSetProperties().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link SequenceSet.SequenceSetProperties }
-     * 
-     * 
-     */
-    public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
-        if (sequenceSetProperties == null) {
-            sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
-        }
-        return this.sequenceSetProperties;
+  /**
+   * Gets the value of the sequenceSetProperties property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the sequenceSetProperties property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getSequenceSetProperties().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link SequenceSet.SequenceSetProperties }
+   * 
+   * 
+   */
+  public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties()
+  {
+    if (sequenceSetProperties == null)
+    {
+      sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
     }
+    return this.sequenceSetProperties;
+  }
 
-    /**
-     * Gets the value of the alcodonFrame property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getAlcodonFrame().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link AlcodonFrame }
-     * 
-     * 
-     */
-    public List<AlcodonFrame> getAlcodonFrame() {
-        if (alcodonFrame == null) {
-            alcodonFrame = new ArrayList<AlcodonFrame>();
-        }
-        return this.alcodonFrame;
+  /**
+   * Gets the value of the alcodonFrame property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the alcodonFrame property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAlcodonFrame().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link AlcodonFrame }
+   * 
+   * 
+   */
+  public List<AlcodonFrame> getAlcodonFrame()
+  {
+    if (alcodonFrame == null)
+    {
+      alcodonFrame = new ArrayList<AlcodonFrame>();
     }
+    return this.alcodonFrame;
+  }
+
+  /**
+   * Gets the value of the gapChar property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getGapChar()
+  {
+    return gapChar;
+  }
+
+  /**
+   * Sets the value of the gapChar property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setGapChar(String value)
+  {
+    this.gapChar = value;
+  }
+
+  /**
+   * Gets the value of the datasetId property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDatasetId()
+  {
+    return datasetId;
+  }
+
+  /**
+   * Sets the value of the datasetId property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDatasetId(String value)
+  {
+    this.datasetId = value;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class SequenceSetProperties
+  {
+
+    @XmlAttribute(name = "key")
+    protected String key;
+
+    @XmlAttribute(name = "value")
+    protected String value;
 
     /**
-     * Gets the value of the gapChar property.
+     * Gets the value of the key property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getGapChar() {
-        return gapChar;
+    public String getKey()
+    {
+      return key;
     }
 
     /**
-     * Sets the value of the gapChar property.
+     * Sets the value of the key property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setGapChar(String value) {
-        this.gapChar = value;
-    }
-
-    /**
-     * Gets the value of the datasetId property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getDatasetId() {
-        return datasetId;
+    public void setKey(String value)
+    {
+      this.key = value;
     }
 
     /**
-     * Sets the value of the datasetId property.
+     * Gets the value of the value property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
      */
-    public void setDatasetId(String value) {
-        this.datasetId = value;
+    public String getValue()
+    {
+      return value;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * Sets the value of the value property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SequenceSetProperties {
-
-        @XmlAttribute(name = "key")
-        protected String key;
-        @XmlAttribute(name = "value")
-        protected String value;
-
-        /**
-         * Gets the value of the key property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getKey() {
-            return key;
-        }
-
-        /**
-         * Sets the value of the key property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setKey(String value) {
-            this.key = value;
-        }
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
+    public void setValue(String value)
+    {
+      this.value = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java
index fa65d58..3de52d2 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,11 +13,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for SequenceType complex type.
+ * <p>
+ * Java class for SequenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="SequenceType">
@@ -38,116 +39,111 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = {
-    "sequence",
-    "name"
-})
-@XmlSeeAlso({
-    Sequence.class
-})
-public class SequenceType {
-
-    protected String sequence;
-    protected String name;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "description")
-    protected String description;
-
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSequence() {
-        return sequence;
-    }
-
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSequence(String value) {
-        this.sequence = value;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
+@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
+@XmlSeeAlso({ Sequence.class })
+public class SequenceType
+{
+
+  protected String sequence;
+
+  protected String name;
+
+  @XmlAttribute(name = "id")
+  protected String id;
+
+  @XmlAttribute(name = "description")
+  protected String description;
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSequence(String value)
+  {
+    this.sequence = value;
+  }
+
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index 192caf8..6c9cbce 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -5,18 +5,20 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for ThresholdType.
+ * <p>
+ * Java class for ThresholdType.
  * 
- * <p>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.
+ * <p>
+ * 
  * <pre>
  * &lt;simpleType name="ThresholdType">
  *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -30,18 +32,19 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum ThresholdType {
+public enum ThresholdType
+{
 
-    NONE,
-    ABOVE,
-    BELOW;
+  NONE, ABOVE, BELOW;
 
-    public String value() {
-        return name();
-    }
+  public String value()
+  {
+    return name();
+  }
 
-    public static ThresholdType fromValue(String v) {
-        return valueOf(v);
-    }
+  public static ThresholdType fromValue(String v)
+  {
+    return valueOf(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index dd41877..10635e5 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for VAMSAS complex type.
+ * <p>
+ * Java class for VAMSAS complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="VAMSAS">
@@ -37,73 +38,77 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = {
-    "tree",
-    "sequenceSet"
-})
-public class VAMSAS {
+@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
+public class VAMSAS
+{
+
+  @XmlElement(name = "Tree")
+  protected List<String> tree;
 
-    @XmlElement(name = "Tree")
-    protected List<String> tree;
-    @XmlElement(name = "SequenceSet")
-    protected List<SequenceSet> sequenceSet;
+  @XmlElement(name = "SequenceSet")
+  protected List<SequenceSet> sequenceSet;
 
-    /**
-     * Gets the value of the tree property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the tree property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getTree().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getTree() {
-        if (tree == null) {
-            tree = new ArrayList<String>();
-        }
-        return this.tree;
+  /**
+   * Gets the value of the tree property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the tree property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getTree().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getTree()
+  {
+    if (tree == null)
+    {
+      tree = new ArrayList<String>();
     }
+    return this.tree;
+  }
 
-    /**
-     * Gets the value of the sequenceSet property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getSequenceSet().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link SequenceSet }
-     * 
-     * 
-     */
-    public List<SequenceSet> getSequenceSet() {
-        if (sequenceSet == null) {
-            sequenceSet = new ArrayList<SequenceSet>();
-        }
-        return this.sequenceSet;
+  /**
+   * Gets the value of the sequenceSet property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the sequenceSet property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getSequenceSet().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link SequenceSet
+   * }
+   * 
+   * 
+   */
+  public List<SequenceSet> getSequenceSet()
+  {
+    if (sequenceSet == null)
+    {
+      sequenceSet = new ArrayList<SequenceSet>();
     }
+    return this.sequenceSet;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index d3c2098..88f5a22 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -18,11 +17,13 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for WebServiceParameterSet complex type.
+ * <p>
+ * Java class for WebServiceParameterSet complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="WebServiceParameterSet">
@@ -43,152 +44,153 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
-    "version",
-    "description",
-    "serviceURL",
-    "parameters"
-})
+@XmlType(
+  name = "WebServiceParameterSet",
+  namespace = "www.jalview.org/xml/wsparamset",
+  propOrder =
+  { "version", "description", "serviceURL", "parameters" })
 @XmlSeeAlso({
-    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
-})
-public class WebServiceParameterSet {
-
-    @XmlElement(name = "Version", namespace = "")
-    protected String version;
-    @XmlElement(namespace = "")
-    protected String description;
-    @XmlElement(namespace = "", required = true)
-    @XmlSchemaType(name = "anyURI")
-    protected List<String> serviceURL;
-    @XmlElement(namespace = "", required = true)
-    protected String parameters;
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
-
-    /**
-     * Gets the value of the version property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getVersion() {
-        return version;
-    }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setVersion(String value) {
-        this.version = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * Gets the value of the serviceURL property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getServiceURL().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getServiceURL() {
-        if (serviceURL == null) {
-            serviceURL = new ArrayList<String>();
-        }
-        return this.serviceURL;
-    }
-
-    /**
-     * Gets the value of the parameters property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getParameters() {
-        return parameters;
-    }
-
-    /**
-     * Sets the value of the parameters property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setParameters(String value) {
-        this.parameters = value;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
+    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
+public class WebServiceParameterSet
+{
+
+  @XmlElement(name = "Version", namespace = "")
+  protected String version;
+
+  @XmlElement(namespace = "")
+  protected String description;
+
+  @XmlElement(namespace = "", required = true)
+  @XmlSchemaType(name = "anyURI")
+  protected List<String> serviceURL;
+
+  @XmlElement(namespace = "", required = true)
+  protected String parameters;
+
+  @XmlAttribute(name = "name", required = true)
+  protected String name;
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the serviceURL property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the serviceURL property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getServiceURL().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getServiceURL()
+  {
+    if (serviceURL == null)
+    {
+      serviceURL = new ArrayList<String>();
     }
+    return this.serviceURL;
+  }
+
+  /**
+   * Gets the value of the parameters property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getParameters()
+  {
+    return parameters;
+  }
+
+  /**
+   * Sets the value of the parameters property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setParameters(String value)
+  {
+    this.parameters = value;
+  }
+
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index 2cfefda..e5bd209 100644
--- a/src/jalview/xml/binding/jalview/package-info.java
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -5,5 +5,7 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+  namespace = "www.vamsas.ac.uk/jalview/version2",
+  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.jalview;
diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java
index de12eb2..2622784 100644
--- a/src/jalview/xml/binding/uniprot/CitationType.java
+++ b/src/jalview/xml/binding/uniprot/CitationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,14 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes different types of citations.
- *             Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
+ * Describes different types of citations. Equivalent to the flat file RX-, RG-,
+ * RA-, RT- and RL-lines.
  * 
- * <p>Java class for citationType complex type.
+ * <p>
+ * Java class for citationType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="citationType">
@@ -72,456 +73,457 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "citationType", propOrder = {
-    "title",
-    "editorList",
-    "authorList",
-    "locator",
-    "dbReference"
-})
-public class CitationType {
-
-    protected String title;
-    protected NameListType editorList;
-    protected NameListType authorList;
-    protected String locator;
-    protected List<DbReferenceType> dbReference;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "date")
-    protected String date;
-    @XmlAttribute(name = "name")
-    protected String name;
-    @XmlAttribute(name = "volume")
-    protected String volume;
-    @XmlAttribute(name = "first")
-    protected String first;
-    @XmlAttribute(name = "last")
-    protected String last;
-    @XmlAttribute(name = "publisher")
-    protected String publisher;
-    @XmlAttribute(name = "city")
-    protected String city;
-    @XmlAttribute(name = "db")
-    protected String db;
-    @XmlAttribute(name = "number")
-    protected String number;
-    @XmlAttribute(name = "institute")
-    protected String institute;
-    @XmlAttribute(name = "country")
-    protected String country;
-
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getTitle() {
-        return title;
-    }
-
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setTitle(String value) {
-        this.title = value;
-    }
-
-    /**
-     * Gets the value of the editorList property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link NameListType }
-     *     
-     */
-    public NameListType getEditorList() {
-        return editorList;
-    }
-
-    /**
-     * Sets the value of the editorList property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link NameListType }
-     *     
-     */
-    public void setEditorList(NameListType value) {
-        this.editorList = value;
-    }
-
-    /**
-     * Gets the value of the authorList property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link NameListType }
-     *     
-     */
-    public NameListType getAuthorList() {
-        return authorList;
-    }
-
-    /**
-     * Sets the value of the authorList property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link NameListType }
-     *     
-     */
-    public void setAuthorList(NameListType value) {
-        this.authorList = value;
-    }
-
-    /**
-     * Gets the value of the locator property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getLocator() {
-        return locator;
-    }
-
-    /**
-     * Sets the value of the locator property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setLocator(String value) {
-        this.locator = value;
-    }
-
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getDbReference().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link DbReferenceType }
-     * 
-     * 
-     */
-    public List<DbReferenceType> getDbReference() {
-        if (dbReference == null) {
-            dbReference = new ArrayList<DbReferenceType>();
-        }
-        return this.dbReference;
-    }
-
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
-
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
-
-    /**
-     * Gets the value of the date property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDate() {
-        return date;
-    }
-
-    /**
-     * Sets the value of the date property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDate(String value) {
-        this.date = 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 volume property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getVolume() {
-        return volume;
-    }
-
-    /**
-     * Sets the value of the volume property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setVolume(String value) {
-        this.volume = value;
-    }
-
-    /**
-     * Gets the value of the first property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getFirst() {
-        return first;
-    }
-
-    /**
-     * Sets the value of the first property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setFirst(String value) {
-        this.first = value;
-    }
-
-    /**
-     * Gets the value of the last property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getLast() {
-        return last;
-    }
-
-    /**
-     * Sets the value of the last property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setLast(String value) {
-        this.last = value;
-    }
-
-    /**
-     * Gets the value of the publisher property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getPublisher() {
-        return publisher;
-    }
-
-    /**
-     * Sets the value of the publisher property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setPublisher(String value) {
-        this.publisher = value;
-    }
-
-    /**
-     * Gets the value of the city property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getCity() {
-        return city;
-    }
-
-    /**
-     * Sets the value of the city property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setCity(String value) {
-        this.city = value;
-    }
-
-    /**
-     * Gets the value of the db property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDb() {
-        return db;
-    }
-
-    /**
-     * Sets the value of the db property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDb(String value) {
-        this.db = value;
-    }
-
-    /**
-     * Gets the value of the number property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getNumber() {
-        return number;
-    }
-
-    /**
-     * Sets the value of the number property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setNumber(String value) {
-        this.number = value;
-    }
-
-    /**
-     * Gets the value of the institute property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getInstitute() {
-        return institute;
-    }
-
-    /**
-     * Sets the value of the institute property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setInstitute(String value) {
-        this.institute = value;
-    }
-
-    /**
-     * Gets the value of the country property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getCountry() {
-        return country;
-    }
-
-    /**
-     * Sets the value of the country property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setCountry(String value) {
-        this.country = value;
-    }
+@XmlType(
+  name = "citationType",
+  propOrder =
+  { "title", "editorList", "authorList", "locator", "dbReference" })
+public class CitationType
+{
+
+  protected String title;
+
+  protected NameListType editorList;
+
+  protected NameListType authorList;
+
+  protected String locator;
+
+  protected List<DbReferenceType> dbReference;
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
+
+  @XmlAttribute(name = "date")
+  protected String date;
+
+  @XmlAttribute(name = "name")
+  protected String name;
+
+  @XmlAttribute(name = "volume")
+  protected String volume;
+
+  @XmlAttribute(name = "first")
+  protected String first;
+
+  @XmlAttribute(name = "last")
+  protected String last;
+
+  @XmlAttribute(name = "publisher")
+  protected String publisher;
+
+  @XmlAttribute(name = "city")
+  protected String city;
+
+  @XmlAttribute(name = "db")
+  protected String db;
+
+  @XmlAttribute(name = "number")
+  protected String number;
+
+  @XmlAttribute(name = "institute")
+  protected String institute;
+
+  @XmlAttribute(name = "country")
+  protected String country;
+
+  /**
+   * Gets the value of the title property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getTitle()
+  {
+    return title;
+  }
+
+  /**
+   * Sets the value of the title property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setTitle(String value)
+  {
+    this.title = value;
+  }
+
+  /**
+   * Gets the value of the editorList property.
+   * 
+   * @return possible object is {@link NameListType }
+   * 
+   */
+  public NameListType getEditorList()
+  {
+    return editorList;
+  }
+
+  /**
+   * Sets the value of the editorList property.
+   * 
+   * @param value
+   *          allowed object is {@link NameListType }
+   * 
+   */
+  public void setEditorList(NameListType value)
+  {
+    this.editorList = value;
+  }
+
+  /**
+   * Gets the value of the authorList property.
+   * 
+   * @return possible object is {@link NameListType }
+   * 
+   */
+  public NameListType getAuthorList()
+  {
+    return authorList;
+  }
+
+  /**
+   * Sets the value of the authorList property.
+   * 
+   * @param value
+   *          allowed object is {@link NameListType }
+   * 
+   */
+  public void setAuthorList(NameListType value)
+  {
+    this.authorList = value;
+  }
+
+  /**
+   * Gets the value of the locator property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getLocator()
+  {
+    return locator;
+  }
+
+  /**
+   * Sets the value of the locator property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setLocator(String value)
+  {
+    this.locator = value;
+  }
+
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the dbReference property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getDbReference().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List<DbReferenceType> getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList<DbReferenceType>();
+    }
+    return this.dbReference;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the date property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDate()
+  {
+    return date;
+  }
+
+  /**
+   * Sets the value of the date property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDate(String value)
+  {
+    this.date = 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 volume property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVolume()
+  {
+    return volume;
+  }
+
+  /**
+   * Sets the value of the volume property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVolume(String value)
+  {
+    this.volume = value;
+  }
+
+  /**
+   * Gets the value of the first property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getFirst()
+  {
+    return first;
+  }
+
+  /**
+   * Sets the value of the first property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setFirst(String value)
+  {
+    this.first = value;
+  }
+
+  /**
+   * Gets the value of the last property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getLast()
+  {
+    return last;
+  }
+
+  /**
+   * Sets the value of the last property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setLast(String value)
+  {
+    this.last = value;
+  }
+
+  /**
+   * Gets the value of the publisher property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getPublisher()
+  {
+    return publisher;
+  }
+
+  /**
+   * Sets the value of the publisher property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setPublisher(String value)
+  {
+    this.publisher = value;
+  }
+
+  /**
+   * Gets the value of the city property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getCity()
+  {
+    return city;
+  }
+
+  /**
+   * Sets the value of the city property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setCity(String value)
+  {
+    this.city = value;
+  }
+
+  /**
+   * Gets the value of the db property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDb()
+  {
+    return db;
+  }
+
+  /**
+   * Sets the value of the db property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDb(String value)
+  {
+    this.db = value;
+  }
+
+  /**
+   * Gets the value of the number property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getNumber()
+  {
+    return number;
+  }
+
+  /**
+   * Sets the value of the number property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setNumber(String value)
+  {
+    this.number = value;
+  }
+
+  /**
+   * Gets the value of the institute property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getInstitute()
+  {
+    return institute;
+  }
+
+  /**
+   * Sets the value of the institute property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setInstitute(String value)
+  {
+    this.institute = value;
+  }
+
+  /**
+   * Gets the value of the country property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getCountry()
+  {
+    return country;
+  }
+
+  /**
+   * Sets the value of the country property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setCountry(String value)
+  {
+    this.country = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java
index e9244e9..28e7220 100644
--- a/src/jalview/xml/binding/uniprot/CofactorType.java
+++ b/src/jalview/xml/binding/uniprot/CofactorType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Describes a cofactor.
  * 
- * <p>Java class for cofactorType complex type.
+ * <p>
+ * Java class for cofactorType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="cofactorType">
@@ -41,94 +42,94 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cofactorType", propOrder = {
-    "name",
-    "dbReference"
-})
-public class CofactorType {
+@XmlType(name = "cofactorType", propOrder = { "name", "dbReference" })
+public class CofactorType
+{
 
-    @XmlElement(required = true)
-    protected String name;
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+  @XmlElement(required = true)
+  protected String name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  @XmlElement(required = true)
+  protected DbReferenceType dbReference;
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
+
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
+
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java
index e0692c9..f26c12b 100644
--- a/src/jalview/xml/binding/uniprot/CommentType.java
+++ b/src/jalview/xml/binding/uniprot/CommentType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -17,14 +16,16 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes different types of general annotations.
- *             Equivalent to the flat file CC-line.
+ * Describes different types of general annotations. Equivalent to the flat file
+ * CC-line.
  * 
- * <p>Java class for commentType complex type.
+ * <p>
+ * Java class for commentType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="commentType">
@@ -173,1619 +174,1673 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "commentType", propOrder = {
-    "molecule",
-    "absorption",
-    "kinetics",
-    "phDependence",
-    "redoxPotential",
-    "temperatureDependence",
-    "reaction",
-    "physiologicalReaction",
-    "cofactor",
-    "subcellularLocation",
-    "conflict",
-    "link",
-    "event",
-    "isoform",
-    "interactant",
-    "organismsDiffer",
-    "experiments",
-    "disease",
-    "location",
-    "text"
-})
-public class CommentType {
-
-    protected MoleculeType molecule;
-    protected CommentType.Absorption absorption;
-    protected CommentType.Kinetics kinetics;
-    protected CommentType.PhDependence phDependence;
-    protected CommentType.RedoxPotential redoxPotential;
-    protected CommentType.TemperatureDependence temperatureDependence;
-    protected ReactionType reaction;
-    protected List<PhysiologicalReactionType> physiologicalReaction;
-    protected List<CofactorType> cofactor;
-    protected List<SubcellularLocationType> subcellularLocation;
-    protected CommentType.Conflict conflict;
-    protected List<CommentType.Link> link;
-    protected List<EventType> event;
-    protected List<IsoformType> isoform;
-    protected List<InteractantType> interactant;
-    @XmlElement(defaultValue = "false")
-    protected Boolean organismsDiffer;
-    protected Integer experiments;
-    protected CommentType.Disease disease;
-    protected List<LocationType> location;
-    protected List<EvidencedStringType> text;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "locationType")
-    protected String locationType;
-    @XmlAttribute(name = "name")
-    protected String name;
-    @XmlAttribute(name = "mass")
-    protected Float mass;
-    @XmlAttribute(name = "error")
-    protected String error;
-    @XmlAttribute(name = "method")
-    protected String method;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+@XmlType(
+  name = "commentType",
+  propOrder =
+  { "molecule", "absorption", "kinetics", "phDependence", "redoxPotential",
+      "temperatureDependence", "reaction", "physiologicalReaction",
+      "cofactor", "subcellularLocation", "conflict", "link", "event",
+      "isoform", "interactant", "organismsDiffer", "experiments", "disease",
+      "location", "text" })
+public class CommentType
+{
 
-    /**
-     * Gets the value of the molecule property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public MoleculeType getMolecule() {
-        return molecule;
-    }
+  protected MoleculeType molecule;
 
-    /**
-     * Sets the value of the molecule property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public void setMolecule(MoleculeType value) {
-        this.molecule = value;
-    }
+  protected CommentType.Absorption absorption;
 
-    /**
-     * Gets the value of the absorption property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.Absorption }
-     *     
-     */
-    public CommentType.Absorption getAbsorption() {
-        return absorption;
-    }
+  protected CommentType.Kinetics kinetics;
 
-    /**
-     * Sets the value of the absorption property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.Absorption }
-     *     
-     */
-    public void setAbsorption(CommentType.Absorption value) {
-        this.absorption = value;
-    }
+  protected CommentType.PhDependence phDependence;
 
-    /**
-     * Gets the value of the kinetics property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.Kinetics }
-     *     
-     */
-    public CommentType.Kinetics getKinetics() {
-        return kinetics;
-    }
+  protected CommentType.RedoxPotential redoxPotential;
 
-    /**
-     * Sets the value of the kinetics property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.Kinetics }
-     *     
-     */
-    public void setKinetics(CommentType.Kinetics value) {
-        this.kinetics = value;
-    }
+  protected CommentType.TemperatureDependence temperatureDependence;
 
-    /**
-     * Gets the value of the phDependence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.PhDependence }
-     *     
-     */
-    public CommentType.PhDependence getPhDependence() {
-        return phDependence;
-    }
+  protected ReactionType reaction;
 
-    /**
-     * Sets the value of the phDependence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.PhDependence }
-     *     
-     */
-    public void setPhDependence(CommentType.PhDependence value) {
-        this.phDependence = value;
-    }
+  protected List<PhysiologicalReactionType> physiologicalReaction;
 
-    /**
-     * Gets the value of the redoxPotential property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.RedoxPotential }
-     *     
-     */
-    public CommentType.RedoxPotential getRedoxPotential() {
-        return redoxPotential;
-    }
+  protected List<CofactorType> cofactor;
 
-    /**
-     * Sets the value of the redoxPotential property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.RedoxPotential }
-     *     
-     */
-    public void setRedoxPotential(CommentType.RedoxPotential value) {
-        this.redoxPotential = value;
-    }
+  protected List<SubcellularLocationType> subcellularLocation;
 
-    /**
-     * Gets the value of the temperatureDependence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.TemperatureDependence }
-     *     
-     */
-    public CommentType.TemperatureDependence getTemperatureDependence() {
-        return temperatureDependence;
-    }
+  protected CommentType.Conflict conflict;
 
-    /**
-     * Sets the value of the temperatureDependence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.TemperatureDependence }
-     *     
-     */
-    public void setTemperatureDependence(CommentType.TemperatureDependence value) {
-        this.temperatureDependence = value;
+  protected List<CommentType.Link> link;
+
+  protected List<EventType> event;
+
+  protected List<IsoformType> isoform;
+
+  protected List<InteractantType> interactant;
+
+  @XmlElement(defaultValue = "false")
+  protected Boolean organismsDiffer;
+
+  protected Integer experiments;
+
+  protected CommentType.Disease disease;
+
+  protected List<LocationType> location;
+
+  protected List<EvidencedStringType> text;
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
+
+  @XmlAttribute(name = "locationType")
+  protected String locationType;
+
+  @XmlAttribute(name = "name")
+  protected String name;
+
+  @XmlAttribute(name = "mass")
+  protected Float mass;
+
+  @XmlAttribute(name = "error")
+  protected String error;
+
+  @XmlAttribute(name = "method")
+  protected String method;
+
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
+
+  /**
+   * Gets the value of the molecule property.
+   * 
+   * @return possible object is {@link MoleculeType }
+   * 
+   */
+  public MoleculeType getMolecule()
+  {
+    return molecule;
+  }
+
+  /**
+   * Sets the value of the molecule property.
+   * 
+   * @param value
+   *          allowed object is {@link MoleculeType }
+   * 
+   */
+  public void setMolecule(MoleculeType value)
+  {
+    this.molecule = value;
+  }
+
+  /**
+   * Gets the value of the absorption property.
+   * 
+   * @return possible object is {@link CommentType.Absorption }
+   * 
+   */
+  public CommentType.Absorption getAbsorption()
+  {
+    return absorption;
+  }
+
+  /**
+   * Sets the value of the absorption property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.Absorption }
+   * 
+   */
+  public void setAbsorption(CommentType.Absorption value)
+  {
+    this.absorption = value;
+  }
+
+  /**
+   * Gets the value of the kinetics property.
+   * 
+   * @return possible object is {@link CommentType.Kinetics }
+   * 
+   */
+  public CommentType.Kinetics getKinetics()
+  {
+    return kinetics;
+  }
+
+  /**
+   * Sets the value of the kinetics property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.Kinetics }
+   * 
+   */
+  public void setKinetics(CommentType.Kinetics value)
+  {
+    this.kinetics = value;
+  }
+
+  /**
+   * Gets the value of the phDependence property.
+   * 
+   * @return possible object is {@link CommentType.PhDependence }
+   * 
+   */
+  public CommentType.PhDependence getPhDependence()
+  {
+    return phDependence;
+  }
+
+  /**
+   * Sets the value of the phDependence property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.PhDependence }
+   * 
+   */
+  public void setPhDependence(CommentType.PhDependence value)
+  {
+    this.phDependence = value;
+  }
+
+  /**
+   * Gets the value of the redoxPotential property.
+   * 
+   * @return possible object is {@link CommentType.RedoxPotential }
+   * 
+   */
+  public CommentType.RedoxPotential getRedoxPotential()
+  {
+    return redoxPotential;
+  }
+
+  /**
+   * Sets the value of the redoxPotential property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.RedoxPotential }
+   * 
+   */
+  public void setRedoxPotential(CommentType.RedoxPotential value)
+  {
+    this.redoxPotential = value;
+  }
+
+  /**
+   * Gets the value of the temperatureDependence property.
+   * 
+   * @return possible object is {@link CommentType.TemperatureDependence }
+   * 
+   */
+  public CommentType.TemperatureDependence getTemperatureDependence()
+  {
+    return temperatureDependence;
+  }
+
+  /**
+   * Sets the value of the temperatureDependence property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.TemperatureDependence }
+   * 
+   */
+  public void setTemperatureDependence(
+          CommentType.TemperatureDependence value)
+  {
+    this.temperatureDependence = value;
+  }
+
+  /**
+   * Gets the value of the reaction property.
+   * 
+   * @return possible object is {@link ReactionType }
+   * 
+   */
+  public ReactionType getReaction()
+  {
+    return reaction;
+  }
+
+  /**
+   * Sets the value of the reaction property.
+   * 
+   * @param value
+   *          allowed object is {@link ReactionType }
+   * 
+   */
+  public void setReaction(ReactionType value)
+  {
+    this.reaction = value;
+  }
+
+  /**
+   * Gets the value of the physiologicalReaction property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the physiologicalReaction property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getPhysiologicalReaction().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link PhysiologicalReactionType }
+   * 
+   * 
+   */
+  public List<PhysiologicalReactionType> getPhysiologicalReaction()
+  {
+    if (physiologicalReaction == null)
+    {
+      physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
+    }
+    return this.physiologicalReaction;
+  }
+
+  /**
+   * Gets the value of the cofactor property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the cofactor property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getCofactor().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link CofactorType }
+   * 
+   * 
+   */
+  public List<CofactorType> getCofactor()
+  {
+    if (cofactor == null)
+    {
+      cofactor = new ArrayList<CofactorType>();
+    }
+    return this.cofactor;
+  }
+
+  /**
+   * Gets the value of the subcellularLocation property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the subcellularLocation property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getSubcellularLocation().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link SubcellularLocationType }
+   * 
+   * 
+   */
+  public List<SubcellularLocationType> getSubcellularLocation()
+  {
+    if (subcellularLocation == null)
+    {
+      subcellularLocation = new ArrayList<SubcellularLocationType>();
+    }
+    return this.subcellularLocation;
+  }
+
+  /**
+   * Gets the value of the conflict property.
+   * 
+   * @return possible object is {@link CommentType.Conflict }
+   * 
+   */
+  public CommentType.Conflict getConflict()
+  {
+    return conflict;
+  }
+
+  /**
+   * Sets the value of the conflict property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.Conflict }
+   * 
+   */
+  public void setConflict(CommentType.Conflict value)
+  {
+    this.conflict = value;
+  }
+
+  /**
+   * Gets the value of the link property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the link property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getLink().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link CommentType.Link }
+   * 
+   * 
+   */
+  public List<CommentType.Link> getLink()
+  {
+    if (link == null)
+    {
+      link = new ArrayList<CommentType.Link>();
     }
+    return this.link;
+  }
+
+  /**
+   * Gets the value of the event property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the event property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvent().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link EventType }
+   * 
+   * 
+   */
+  public List<EventType> getEvent()
+  {
+    if (event == null)
+    {
+      event = new ArrayList<EventType>();
+    }
+    return this.event;
+  }
+
+  /**
+   * Gets the value of the isoform property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the isoform property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getIsoform().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link IsoformType
+   * }
+   * 
+   * 
+   */
+  public List<IsoformType> getIsoform()
+  {
+    if (isoform == null)
+    {
+      isoform = new ArrayList<IsoformType>();
+    }
+    return this.isoform;
+  }
+
+  /**
+   * Gets the value of the interactant property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the interactant property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getInteractant().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link InteractantType }
+   * 
+   * 
+   */
+  public List<InteractantType> getInteractant()
+  {
+    if (interactant == null)
+    {
+      interactant = new ArrayList<InteractantType>();
+    }
+    return this.interactant;
+  }
+
+  /**
+   * Gets the value of the organismsDiffer property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isOrganismsDiffer()
+  {
+    return organismsDiffer;
+  }
+
+  /**
+   * Sets the value of the organismsDiffer property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setOrganismsDiffer(Boolean value)
+  {
+    this.organismsDiffer = value;
+  }
+
+  /**
+   * Gets the value of the experiments property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getExperiments()
+  {
+    return experiments;
+  }
+
+  /**
+   * Sets the value of the experiments property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setExperiments(Integer value)
+  {
+    this.experiments = value;
+  }
+
+  /**
+   * Gets the value of the disease property.
+   * 
+   * @return possible object is {@link CommentType.Disease }
+   * 
+   */
+  public CommentType.Disease getDisease()
+  {
+    return disease;
+  }
+
+  /**
+   * Sets the value of the disease property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.Disease }
+   * 
+   */
+  public void setDisease(CommentType.Disease value)
+  {
+    this.disease = value;
+  }
+
+  /**
+   * Gets the value of the location property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the location property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getLocation().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link LocationType }
+   * 
+   * 
+   */
+  public List<LocationType> getLocation()
+  {
+    if (location == null)
+    {
+      location = new ArrayList<LocationType>();
+    }
+    return this.location;
+  }
+
+  /**
+   * Gets the value of the text property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the text property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getText().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List<EvidencedStringType> getText()
+  {
+    if (text == null)
+    {
+      text = new ArrayList<EvidencedStringType>();
+    }
+    return this.text;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the locationType property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getLocationType()
+  {
+    return locationType;
+  }
+
+  /**
+   * Sets the value of the locationType property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setLocationType(String value)
+  {
+    this.locationType = 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 mass property.
+   * 
+   * @return possible object is {@link Float }
+   * 
+   */
+  public Float getMass()
+  {
+    return mass;
+  }
+
+  /**
+   * Sets the value of the mass property.
+   * 
+   * @param value
+   *          allowed object is {@link Float }
+   * 
+   */
+  public void setMass(Float value)
+  {
+    this.mass = value;
+  }
+
+  /**
+   * Gets the value of the error property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getError()
+  {
+    return error;
+  }
+
+  /**
+   * Sets the value of the error property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setError(String value)
+  {
+    this.error = value;
+  }
+
+  /**
+   * Gets the value of the method property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getMethod()
+  {
+    return method;
+  }
+
+  /**
+   * Sets the value of the method property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setMethod(String value)
+  {
+    this.method = value;
+  }
+
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
+    }
+    return this.evidence;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "max", "text" })
+  public static class Absorption
+  {
+
+    protected EvidencedStringType max;
+
+    protected List<EvidencedStringType> text;
 
     /**
-     * Gets the value of the reaction property.
+     * Gets the value of the max property.
+     * 
+     * @return possible object is {@link EvidencedStringType }
      * 
-     * @return
-     *     possible object is
-     *     {@link ReactionType }
-     *     
      */
-    public ReactionType getReaction() {
-        return reaction;
+    public EvidencedStringType getMax()
+    {
+      return max;
     }
 
     /**
-     * Sets the value of the reaction property.
+     * Sets the value of the max property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link ReactionType }
-     *     
+     *          allowed object is {@link EvidencedStringType }
+     * 
      */
-    public void setReaction(ReactionType value) {
-        this.reaction = value;
+    public void setMax(EvidencedStringType value)
+    {
+      this.max = value;
     }
 
     /**
-     * Gets the value of the physiologicalReaction property.
+     * Gets the value of the text property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the physiologicalReaction 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
+     * <CODE>set</CODE> method for the text property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getPhysiologicalReaction().add(newItem);
+     * getText().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link PhysiologicalReactionType }
+     * {@link EvidencedStringType }
      * 
      * 
      */
-    public List<PhysiologicalReactionType> getPhysiologicalReaction() {
-        if (physiologicalReaction == null) {
-            physiologicalReaction = new ArrayList<PhysiologicalReactionType>();
-        }
-        return this.physiologicalReaction;
+    public List<EvidencedStringType> getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList<EvidencedStringType>();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="sequence" minOccurs="0">
+   *           &lt;complexType>
+   *             &lt;complexContent>
+   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 &lt;attribute name="resource" use="required">
+   *                   &lt;simpleType>
+   *                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *                       &lt;enumeration value="EMBL-CDS"/>
+   *                       &lt;enumeration value="EMBL"/>
+   *                     &lt;/restriction>
+   *                   &lt;/simpleType>
+   *                 &lt;/attribute>
+   *                 &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               &lt;/restriction>
+   *             &lt;/complexContent>
+   *           &lt;/complexType>
+   *         &lt;/element>
+   *       &lt;/sequence>
+   *       &lt;attribute name="type" use="required">
+   *         &lt;simpleType>
+   *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             &lt;enumeration value="frameshift"/>
+   *             &lt;enumeration value="erroneous initiation"/>
+   *             &lt;enumeration value="erroneous termination"/>
+   *             &lt;enumeration value="erroneous gene model prediction"/>
+   *             &lt;enumeration value="erroneous translation"/>
+   *             &lt;enumeration value="miscellaneous discrepancy"/>
+   *           &lt;/restriction>
+   *         &lt;/simpleType>
+   *       &lt;/attribute>
+   *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "sequence" })
+  public static class Conflict
+  {
+
+    protected CommentType.Conflict.Sequence sequence;
+
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+
+    @XmlAttribute(name = "ref")
+    protected String ref;
+
     /**
-     * Gets the value of the cofactor property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the cofactor property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getCofactor().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link CofactorType }
+     * Gets the value of the sequence property.
      * 
+     * @return possible object is {@link CommentType.Conflict.Sequence }
      * 
      */
-    public List<CofactorType> getCofactor() {
-        if (cofactor == null) {
-            cofactor = new ArrayList<CofactorType>();
-        }
-        return this.cofactor;
+    public CommentType.Conflict.Sequence getSequence()
+    {
+      return sequence;
     }
 
     /**
-     * Gets the value of the subcellularLocation property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getSubcellularLocation().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link SubcellularLocationType }
+     * Sets the value of the sequence property.
      * 
+     * @param value
+     *          allowed object is {@link CommentType.Conflict.Sequence }
      * 
      */
-    public List<SubcellularLocationType> getSubcellularLocation() {
-        if (subcellularLocation == null) {
-            subcellularLocation = new ArrayList<SubcellularLocationType>();
-        }
-        return this.subcellularLocation;
+    public void setSequence(CommentType.Conflict.Sequence value)
+    {
+      this.sequence = value;
     }
 
     /**
-     * Gets the value of the conflict property.
+     * Gets the value of the type property.
      * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.Conflict }
-     *     
-     */
-    public CommentType.Conflict getConflict() {
-        return conflict;
-    }
-
-    /**
-     * Sets the value of the conflict property.
+     * @return possible object is {@link String }
      * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.Conflict }
-     *     
      */
-    public void setConflict(CommentType.Conflict value) {
-        this.conflict = value;
+    public String getType()
+    {
+      return type;
     }
 
     /**
-     * Gets the value of the link property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the link property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getLink().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link CommentType.Link }
+     * Sets the value of the type property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    public List<CommentType.Link> getLink() {
-        if (link == null) {
-            link = new ArrayList<CommentType.Link>();
-        }
-        return this.link;
+    public void setType(String value)
+    {
+      this.type = value;
     }
 
     /**
-     * Gets the value of the event property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the event property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvent().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EventType }
+     * Gets the value of the ref property.
      * 
+     * @return possible object is {@link String }
      * 
      */
-    public List<EventType> getEvent() {
-        if (event == null) {
-            event = new ArrayList<EventType>();
-        }
-        return this.event;
+    public String getRef()
+    {
+      return ref;
     }
 
     /**
-     * Gets the value of the isoform property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the isoform property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getIsoform().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link IsoformType }
+     * Sets the value of the ref property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    public List<IsoformType> getIsoform() {
-        if (isoform == null) {
-            isoform = new ArrayList<IsoformType>();
-        }
-        return this.isoform;
+    public void setRef(String value)
+    {
+      this.ref = value;
     }
 
     /**
-     * Gets the value of the interactant property.
-     * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the interactant property.
+     * Java class for anonymous complex type.
      * 
      * <p>
-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * <pre>
-     *    getInteractant().add(newItem);
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="resource" use="required">
+     *         &lt;simpleType>
+     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             &lt;enumeration value="EMBL-CDS"/>
+     *             &lt;enumeration value="EMBL"/>
+     *           &lt;/restriction>
+     *         &lt;/simpleType>
+     *       &lt;/attribute>
+     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
      * </pre>
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link InteractantType }
-     * 
-     * 
      */
-    public List<InteractantType> getInteractant() {
-        if (interactant == null) {
-            interactant = new ArrayList<InteractantType>();
-        }
-        return this.interactant;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Sequence
+    {
+
+      @XmlAttribute(name = "resource", required = true)
+      protected String resource;
+
+      @XmlAttribute(name = "id", required = true)
+      protected String id;
+
+      @XmlAttribute(name = "version")
+      protected Integer version;
+
+      /**
+       * Gets the value of the resource property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getResource()
+      {
+        return resource;
+      }
+
+      /**
+       * Sets the value of the resource property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setResource(String value)
+      {
+        this.resource = value;
+      }
+
+      /**
+       * Gets the value of the id property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getId()
+      {
+        return id;
+      }
+
+      /**
+       * Sets the value of the id property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setId(String value)
+      {
+        this.id = value;
+      }
+
+      /**
+       * Gets the value of the version property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getVersion()
+      {
+        return version;
+      }
+
+      /**
+       * Sets the value of the version property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setVersion(Integer value)
+      {
+        this.version = value;
+      }
 
-    /**
-     * Gets the value of the organismsDiffer property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isOrganismsDiffer() {
-        return organismsDiffer;
     }
 
-    /**
-     * Sets the value of the organismsDiffer property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setOrganismsDiffer(Boolean value) {
-        this.organismsDiffer = value;
-    }
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+   *       &lt;/sequence>
+   *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "name", "acronym", "description", "dbReference" })
+  public static class Disease
+  {
+
+    @XmlElement(required = true)
+    protected String name;
 
-    /**
-     * Gets the value of the experiments property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getExperiments() {
-        return experiments;
-    }
+    @XmlElement(required = true)
+    protected String acronym;
 
-    /**
-     * Sets the value of the experiments property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setExperiments(Integer value) {
-        this.experiments = value;
-    }
+    @XmlElement(required = true)
+    protected String description;
 
-    /**
-     * Gets the value of the disease property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.Disease }
-     *     
-     */
-    public CommentType.Disease getDisease() {
-        return disease;
-    }
+    @XmlElement(required = true)
+    protected DbReferenceType dbReference;
 
-    /**
-     * Sets the value of the disease property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.Disease }
-     *     
-     */
-    public void setDisease(CommentType.Disease value) {
-        this.disease = value;
-    }
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
 
     /**
-     * Gets the value of the location property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the location property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getLocation().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link LocationType }
+     * Gets the value of the name property.
      * 
+     * @return possible object is {@link String }
      * 
      */
-    public List<LocationType> getLocation() {
-        if (location == null) {
-            location = new ArrayList<LocationType>();
-        }
-        return this.location;
+    public String getName()
+    {
+      return name;
     }
 
     /**
-     * Gets the value of the text property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the text property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getText().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     * Sets the value of the name property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    public List<EvidencedStringType> getText() {
-        if (text == null) {
-            text = new ArrayList<EvidencedStringType>();
-        }
-        return this.text;
+    public void setName(String value)
+    {
+      this.name = value;
     }
 
     /**
-     * Gets the value of the type property.
+     * Gets the value of the acronym property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getType() {
-        return type;
+    public String getAcronym()
+    {
+      return acronym;
     }
 
     /**
-     * Sets the value of the type property.
+     * Sets the value of the acronym property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
-
-    /**
-     * Gets the value of the locationType property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getLocationType() {
-        return locationType;
+    public void setAcronym(String value)
+    {
+      this.acronym = value;
     }
 
     /**
-     * Sets the value of the locationType property.
+     * Gets the value of the description property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setLocationType(String value) {
-        this.locationType = value;
-    }
-
-    /**
-     * Gets the value of the name property.
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getName() {
-        return name;
+    public String getDescription()
+    {
+      return description;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the description property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
-
-    /**
-     * Gets the value of the mass property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link Float }
-     *     
      */
-    public Float getMass() {
-        return mass;
+    public void setDescription(String value)
+    {
+      this.description = value;
     }
 
     /**
-     * Sets the value of the mass property.
+     * Gets the value of the dbReference property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link Float }
-     *     
-     */
-    public void setMass(Float value) {
-        this.mass = value;
-    }
-
-    /**
-     * Gets the value of the error property.
+     * @return possible object is {@link DbReferenceType }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getError() {
-        return error;
+    public DbReferenceType getDbReference()
+    {
+      return dbReference;
     }
 
     /**
-     * Sets the value of the error property.
+     * Sets the value of the dbReference property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link DbReferenceType }
+     * 
      */
-    public void setError(String value) {
-        this.error = value;
+    public void setDbReference(DbReferenceType value)
+    {
+      this.dbReference = value;
     }
 
     /**
-     * Gets the value of the method property.
+     * Gets the value of the id property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getMethod() {
-        return method;
+    public String getId()
+    {
+      return id;
     }
 
     /**
-     * Sets the value of the method property.
+     * Sets the value of the id property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setMethod(String value) {
-        this.method = value;
+    public void setId(String value)
+    {
+      this.id = value;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "km", "vmax", "text" })
+  public static class Kinetics
+  {
+
+    @XmlElement(name = "KM")
+    protected List<EvidencedStringType> km;
+
+    @XmlElement(name = "Vmax")
+    protected List<EvidencedStringType> vmax;
+
+    protected List<EvidencedStringType> text;
+
     /**
-     * Gets the value of the evidence property.
+     * Gets the value of the km property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence 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
+     * <CODE>set</CODE> method for the km property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getEvidence().add(newItem);
+     * getKM().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
+     * {@link EvidencedStringType }
      * 
      * 
      */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+    public List<EvidencedStringType> getKM()
+    {
+      if (km == null)
+      {
+        km = new ArrayList<EvidencedStringType>();
+      }
+      return this.km;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the vmax property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the vmax property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getVmax().add(newItem);
      * </pre>
      * 
      * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "max",
-        "text"
-    })
-    public static class Absorption {
-
-        protected EvidencedStringType max;
-        protected List<EvidencedStringType> text;
-
-        /**
-         * Gets the value of the max property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getMax() {
-            return max;
-        }
-
-        /**
-         * Sets the value of the max property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setMax(EvidencedStringType value) {
-            this.max = value;
-        }
-
-        /**
-         * Gets the value of the text property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the text property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getText().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getText() {
-            if (text == null) {
-                text = new ArrayList<EvidencedStringType>();
-            }
-            return this.text;
-        }
-
-    }
-
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="sequence" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="resource" use="required">
-     *                   &lt;simpleType>
-     *                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *                       &lt;enumeration value="EMBL-CDS"/>
-     *                       &lt;enumeration value="EMBL"/>
-     *                     &lt;/restriction>
-     *                   &lt;/simpleType>
-     *                 &lt;/attribute>
-     *                 &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attribute name="type" use="required">
-     *         &lt;simpleType>
-     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             &lt;enumeration value="frameshift"/>
-     *             &lt;enumeration value="erroneous initiation"/>
-     *             &lt;enumeration value="erroneous termination"/>
-     *             &lt;enumeration value="erroneous gene model prediction"/>
-     *             &lt;enumeration value="erroneous translation"/>
-     *             &lt;enumeration value="miscellaneous discrepancy"/>
-     *           &lt;/restriction>
-     *         &lt;/simpleType>
-     *       &lt;/attribute>
-     *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
      * 
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "sequence"
-    })
-    public static class Conflict {
-
-        protected CommentType.Conflict.Sequence sequence;
-        @XmlAttribute(name = "type", required = true)
-        protected String type;
-        @XmlAttribute(name = "ref")
-        protected String ref;
-
-        /**
-         * Gets the value of the sequence property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link CommentType.Conflict.Sequence }
-         *     
-         */
-        public CommentType.Conflict.Sequence getSequence() {
-            return sequence;
-        }
-
-        /**
-         * Sets the value of the sequence property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link CommentType.Conflict.Sequence }
-         *     
-         */
-        public void setSequence(CommentType.Conflict.Sequence value) {
-            this.sequence = value;
-        }
-
-        /**
-         * Gets the value of the type property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getType() {
-            return type;
-        }
-
-        /**
-         * Sets the value of the type property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setType(String value) {
-            this.type = value;
-        }
-
-        /**
-         * Gets the value of the ref property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getRef() {
-            return ref;
-        }
-
-        /**
-         * Sets the value of the ref property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setRef(String value) {
-            this.ref = value;
-        }
-
-
-        /**
-         * <p>Java class for anonymous complex type.
-         * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
-         * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="resource" use="required">
-         *         &lt;simpleType>
-         *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-         *             &lt;enumeration value="EMBL-CDS"/>
-         *             &lt;enumeration value="EMBL"/>
-         *           &lt;/restriction>
-         *         &lt;/simpleType>
-         *       &lt;/attribute>
-         *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Sequence {
-
-            @XmlAttribute(name = "resource", required = true)
-            protected String resource;
-            @XmlAttribute(name = "id", required = true)
-            protected String id;
-            @XmlAttribute(name = "version")
-            protected Integer version;
-
-            /**
-             * Gets the value of the resource property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getResource() {
-                return resource;
-            }
-
-            /**
-             * Sets the value of the resource property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setResource(String value) {
-                this.resource = value;
-            }
-
-            /**
-             * Gets the value of the id property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getId() {
-                return id;
-            }
-
-            /**
-             * Sets the value of the id property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setId(String value) {
-                this.id = value;
-            }
-
-            /**
-             * Gets the value of the version property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getVersion() {
-                return version;
-            }
-
-            /**
-             * Sets the value of the version property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setVersion(Integer value) {
-                this.version = value;
-            }
-
-        }
-
+    public List<EvidencedStringType> getVmax()
+    {
+      if (vmax == null)
+      {
+        vmax = new ArrayList<EvidencedStringType>();
+      }
+      return this.vmax;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the text property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the text property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getText().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "name",
-        "acronym",
-        "description",
-        "dbReference"
-    })
-    public static class Disease {
-
-        @XmlElement(required = true)
-        protected String name;
-        @XmlElement(required = true)
-        protected String acronym;
-        @XmlElement(required = true)
-        protected String description;
-        @XmlElement(required = true)
-        protected DbReferenceType dbReference;
-        @XmlAttribute(name = "id", required = true)
-        protected String id;
-
-        /**
-         * 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 acronym property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getAcronym() {
-            return acronym;
-        }
-
-        /**
-         * Sets the value of the acronym property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setAcronym(String value) {
-            this.acronym = value;
-        }
-
-        /**
-         * Gets the value of the description property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getDescription() {
-            return description;
-        }
-
-        /**
-         * Sets the value of the description property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setDescription(String value) {
-            this.description = value;
-        }
-
-        /**
-         * Gets the value of the dbReference property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link DbReferenceType }
-         *     
-         */
-        public DbReferenceType getDbReference() {
-            return dbReference;
-        }
-
-        /**
-         * Sets the value of the dbReference property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link DbReferenceType }
-         *     
-         */
-        public void setDbReference(DbReferenceType value) {
-            this.dbReference = value;
-        }
-
-        /**
-         * Gets the value of the id property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getId() {
-            return id;
-        }
-
-        /**
-         * Sets the value of the id property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
-
+    public List<EvidencedStringType> getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList<EvidencedStringType>();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Link
+  {
+
+    @XmlAttribute(name = "uri", required = true)
+    @XmlSchemaType(name = "anyURI")
+    protected String uri;
 
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * Gets the value of the uri property.
      * 
+     * @return possible object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "km",
-        "vmax",
-        "text"
-    })
-    public static class Kinetics {
-
-        @XmlElement(name = "KM")
-        protected List<EvidencedStringType> km;
-        @XmlElement(name = "Vmax")
-        protected List<EvidencedStringType> vmax;
-        protected List<EvidencedStringType> text;
-
-        /**
-         * Gets the value of the km property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the km property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getKM().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getKM() {
-            if (km == null) {
-                km = new ArrayList<EvidencedStringType>();
-            }
-            return this.km;
-        }
-
-        /**
-         * Gets the value of the vmax property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the vmax property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getVmax().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getVmax() {
-            if (vmax == null) {
-                vmax = new ArrayList<EvidencedStringType>();
-            }
-            return this.vmax;
-        }
-
-        /**
-         * Gets the value of the text property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the text property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getText().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getText() {
-            if (text == null) {
-                text = new ArrayList<EvidencedStringType>();
-            }
-            return this.text;
-        }
-
+    public String getUri()
+    {
+      return uri;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * Sets the value of the uri property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Link {
-
-        @XmlAttribute(name = "uri", required = true)
-        @XmlSchemaType(name = "anyURI")
-        protected String uri;
-
-        /**
-         * Gets the value of the uri property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getUri() {
-            return uri;
-        }
-
-        /**
-         * Sets the value of the uri property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setUri(String value) {
-            this.uri = value;
-        }
-
+    public void setUri(String value)
+    {
+      this.uri = value;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "text" })
+  public static class PhDependence
+  {
+
+    @XmlElement(required = true)
+    protected List<EvidencedStringType> text;
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the text property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the text property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getText().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "text"
-    })
-    public static class PhDependence {
-
-        @XmlElement(required = true)
-        protected List<EvidencedStringType> text;
-
-        /**
-         * Gets the value of the text property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the text property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getText().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getText() {
-            if (text == null) {
-                text = new ArrayList<EvidencedStringType>();
-            }
-            return this.text;
-        }
-
+    public List<EvidencedStringType> getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList<EvidencedStringType>();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "text" })
+  public static class RedoxPotential
+  {
+
+    @XmlElement(required = true)
+    protected List<EvidencedStringType> text;
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the text property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the text property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getText().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "text"
-    })
-    public static class RedoxPotential {
-
-        @XmlElement(required = true)
-        protected List<EvidencedStringType> text;
-
-        /**
-         * Gets the value of the text property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the text property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getText().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getText() {
-            if (text == null) {
-                text = new ArrayList<EvidencedStringType>();
-            }
-            return this.text;
-        }
-
+    public List<EvidencedStringType> getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList<EvidencedStringType>();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "text" })
+  public static class TemperatureDependence
+  {
+
+    @XmlElement(required = true)
+    protected List<EvidencedStringType> text;
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the text property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the text property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getText().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "text"
-    })
-    public static class TemperatureDependence {
-
-        @XmlElement(required = true)
-        protected List<EvidencedStringType> text;
-
-        /**
-         * Gets the value of the text property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the text property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getText().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getText() {
-            if (text == null) {
-                text = new ArrayList<EvidencedStringType>();
-            }
-            return this.text;
-        }
-
+    public List<EvidencedStringType> getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList<EvidencedStringType>();
+      }
+      return this.text;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java
index 71db504..5230b13 100644
--- a/src/jalview/xml/binding/uniprot/ConsortiumType.java
+++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,14 +12,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the authors of a citation when these are represented by a consortium.
- *             Equivalent to the flat file RG-line.
+ * Describes the authors of a citation when these are represented by a
+ * consortium. Equivalent to the flat file RG-line.
  * 
- * <p>Java class for consortiumType complex type.
+ * <p>
+ * Java class for consortiumType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="consortiumType">
@@ -36,33 +37,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "consortiumType")
-public class ConsortiumType {
+public class ConsortiumType
+{
 
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
+  @XmlAttribute(name = "name", required = true)
+  protected String name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java
index 73ccfa8..076a37c 100644
--- a/src/jalview/xml/binding/uniprot/DbReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes a database cross-reference.
- *             Equivalent to the flat file DR-line.
- *             
+ * Describes a database cross-reference. Equivalent to the flat file DR-line.
  * 
- * <p>Java class for dbReferenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * Java class for dbReferenceType complex type.
+ * 
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="dbReferenceType">
@@ -44,149 +44,153 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "dbReferenceType", propOrder = {
-    "molecule",
-    "property"
-})
-public class DbReferenceType {
-
-    protected MoleculeType molecule;
-    protected List<PropertyType> property;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-
-    /**
-     * Gets the value of the molecule property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public MoleculeType getMolecule() {
-        return molecule;
-    }
+@XmlType(name = "dbReferenceType", propOrder = { "molecule", "property" })
+public class DbReferenceType
+{
 
-    /**
-     * Sets the value of the molecule property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public void setMolecule(MoleculeType value) {
-        this.molecule = value;
-    }
+  protected MoleculeType molecule;
 
-    /**
-     * Gets the value of the property property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the property property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getProperty().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link PropertyType }
-     * 
-     * 
-     */
-    public List<PropertyType> getProperty() {
-        if (property == null) {
-            property = new ArrayList<PropertyType>();
-        }
-        return this.property;
-    }
+  protected List<PropertyType> property;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
+
+  /**
+   * Gets the value of the molecule property.
+   * 
+   * @return possible object is {@link MoleculeType }
+   * 
+   */
+  public MoleculeType getMolecule()
+  {
+    return molecule;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
+  /**
+   * Sets the value of the molecule property.
+   * 
+   * @param value
+   *          allowed object is {@link MoleculeType }
+   * 
+   */
+  public void setMolecule(MoleculeType value)
+  {
+    this.molecule = value;
+  }
+
+  /**
+   * Gets the value of the property property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the property property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getProperty().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link PropertyType }
+   * 
+   * 
+   */
+  public List<PropertyType> getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList<PropertyType>();
     }
+    return this.property;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java
index 21963a8..3cc0c73 100644
--- a/src/jalview/xml/binding/uniprot/Entry.java
+++ b/src/jalview/xml/binding/uniprot/Entry.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -19,11 +18,13 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.datatype.XMLGregorianCalendar;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -65,561 +66,594 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "accession",
-    "name",
-    "protein",
-    "gene",
-    "organism",
-    "organismHost",
-    "geneLocation",
-    "reference",
-    "comment",
-    "dbReference",
-    "proteinExistence",
-    "keyword",
-    "feature",
-    "evidence",
-    "sequence"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "accession", "name", "protein", "gene", "organism", "organismHost",
+      "geneLocation", "reference", "comment", "dbReference",
+      "proteinExistence", "keyword", "feature", "evidence", "sequence" })
 @XmlRootElement(name = "entry")
-public class Entry {
-
-    @XmlElement(required = true)
-    protected List<String> accession;
-    @XmlElement(required = true)
-    protected List<String> name;
-    @XmlElement(required = true)
-    protected ProteinType protein;
-    protected List<GeneType> gene;
-    @XmlElement(required = true)
-    protected OrganismType organism;
-    protected List<OrganismType> organismHost;
-    protected List<GeneLocationType> geneLocation;
-    @XmlElement(required = true)
-    protected List<ReferenceType> reference;
-    @XmlElement(nillable = true)
-    protected List<CommentType> comment;
-    protected List<DbReferenceType> dbReference;
-    @XmlElement(required = true)
-    protected ProteinExistenceType proteinExistence;
-    protected List<KeywordType> keyword;
-    protected List<FeatureType> feature;
-    protected List<EvidenceType> evidence;
-    @XmlElement(required = true)
-    protected SequenceType sequence;
-    @XmlAttribute(name = "dataset", required = true)
-    protected String dataset;
-    @XmlAttribute(name = "created", required = true)
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar created;
-    @XmlAttribute(name = "modified", required = true)
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar modified;
-    @XmlAttribute(name = "version", required = true)
-    protected int version;
-
-    /**
-     * Gets the value of the accession property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the accession property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getAccession().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getAccession() {
-        if (accession == null) {
-            accession = new ArrayList<String>();
-        }
-        return this.accession;
-    }
+public class Entry
+{
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the name property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getName().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getName() {
-        if (name == null) {
-            name = new ArrayList<String>();
-        }
-        return this.name;
-    }
+  @XmlElement(required = true)
+  protected List<String> accession;
 
-    /**
-     * Gets the value of the protein property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link ProteinType }
-     *     
-     */
-    public ProteinType getProtein() {
-        return protein;
-    }
+  @XmlElement(required = true)
+  protected List<String> name;
 
-    /**
-     * Sets the value of the protein property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link ProteinType }
-     *     
-     */
-    public void setProtein(ProteinType value) {
-        this.protein = value;
-    }
+  @XmlElement(required = true)
+  protected ProteinType protein;
 
-    /**
-     * Gets the value of the gene property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the gene property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getGene().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link GeneType }
-     * 
-     * 
-     */
-    public List<GeneType> getGene() {
-        if (gene == null) {
-            gene = new ArrayList<GeneType>();
-        }
-        return this.gene;
-    }
+  protected List<GeneType> gene;
 
-    /**
-     * Gets the value of the organism property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link OrganismType }
-     *     
-     */
-    public OrganismType getOrganism() {
-        return organism;
-    }
+  @XmlElement(required = true)
+  protected OrganismType organism;
 
-    /**
-     * Sets the value of the organism property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link OrganismType }
-     *     
-     */
-    public void setOrganism(OrganismType value) {
-        this.organism = value;
-    }
+  protected List<OrganismType> organismHost;
 
-    /**
-     * Gets the value of the organismHost property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the organismHost property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getOrganismHost().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link OrganismType }
-     * 
-     * 
-     */
-    public List<OrganismType> getOrganismHost() {
-        if (organismHost == null) {
-            organismHost = new ArrayList<OrganismType>();
-        }
-        return this.organismHost;
-    }
+  protected List<GeneLocationType> geneLocation;
 
-    /**
-     * Gets the value of the geneLocation property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the geneLocation property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getGeneLocation().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link GeneLocationType }
-     * 
-     * 
-     */
-    public List<GeneLocationType> getGeneLocation() {
-        if (geneLocation == null) {
-            geneLocation = new ArrayList<GeneLocationType>();
-        }
-        return this.geneLocation;
-    }
+  @XmlElement(required = true)
+  protected List<ReferenceType> reference;
 
-    /**
-     * Gets the value of the reference property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the reference property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getReference().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link ReferenceType }
-     * 
-     * 
-     */
-    public List<ReferenceType> getReference() {
-        if (reference == null) {
-            reference = new ArrayList<ReferenceType>();
-        }
-        return this.reference;
-    }
+  @XmlElement(nillable = true)
+  protected List<CommentType> comment;
 
-    /**
-     * Gets the value of the comment property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the comment property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getComment().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link CommentType }
-     * 
-     * 
-     */
-    public List<CommentType> getComment() {
-        if (comment == null) {
-            comment = new ArrayList<CommentType>();
-        }
-        return this.comment;
-    }
+  protected List<DbReferenceType> dbReference;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getDbReference().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link DbReferenceType }
-     * 
-     * 
-     */
-    public List<DbReferenceType> getDbReference() {
-        if (dbReference == null) {
-            dbReference = new ArrayList<DbReferenceType>();
-        }
-        return this.dbReference;
-    }
+  @XmlElement(required = true)
+  protected ProteinExistenceType proteinExistence;
 
-    /**
-     * Gets the value of the proteinExistence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link ProteinExistenceType }
-     *     
-     */
-    public ProteinExistenceType getProteinExistence() {
-        return proteinExistence;
-    }
+  protected List<KeywordType> keyword;
 
-    /**
-     * Sets the value of the proteinExistence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link ProteinExistenceType }
-     *     
-     */
-    public void setProteinExistence(ProteinExistenceType value) {
-        this.proteinExistence = value;
-    }
+  protected List<FeatureType> feature;
 
-    /**
-     * Gets the value of the keyword property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the keyword property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getKeyword().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link KeywordType }
-     * 
-     * 
-     */
-    public List<KeywordType> getKeyword() {
-        if (keyword == null) {
-            keyword = new ArrayList<KeywordType>();
-        }
-        return this.keyword;
-    }
+  protected List<EvidenceType> evidence;
 
-    /**
-     * Gets the value of the feature property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the feature property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getFeature().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link FeatureType }
-     * 
-     * 
-     */
-    public List<FeatureType> getFeature() {
-        if (feature == null) {
-            feature = new ArrayList<FeatureType>();
-        }
-        return this.feature;
-    }
+  @XmlElement(required = true)
+  protected SequenceType sequence;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidenceType }
-     * 
-     * 
-     */
-    public List<EvidenceType> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<EvidenceType>();
-        }
-        return this.evidence;
-    }
+  @XmlAttribute(name = "dataset", required = true)
+  protected String dataset;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link SequenceType }
-     *     
-     */
-    public SequenceType getSequence() {
-        return sequence;
-    }
+  @XmlAttribute(name = "created", required = true)
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar created;
 
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link SequenceType }
-     *     
-     */
-    public void setSequence(SequenceType value) {
-        this.sequence = value;
-    }
+  @XmlAttribute(name = "modified", required = true)
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar modified;
 
-    /**
-     * Gets the value of the dataset property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDataset() {
-        return dataset;
-    }
+  @XmlAttribute(name = "version", required = true)
+  protected int version;
 
-    /**
-     * Sets the value of the dataset property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDataset(String value) {
-        this.dataset = value;
+  /**
+   * Gets the value of the accession property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the accession property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAccession().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getAccession()
+  {
+    if (accession == null)
+    {
+      accession = new ArrayList<String>();
     }
-
-    /**
-     * Gets the value of the created property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public XMLGregorianCalendar getCreated() {
-        return created;
+    return this.accession;
+  }
+
+  /**
+   * Gets the value of the name property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the name property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList<String>();
     }
-
-    /**
-     * Sets the value of the created property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setCreated(XMLGregorianCalendar value) {
-        this.created = value;
+    return this.name;
+  }
+
+  /**
+   * Gets the value of the protein property.
+   * 
+   * @return possible object is {@link ProteinType }
+   * 
+   */
+  public ProteinType getProtein()
+  {
+    return protein;
+  }
+
+  /**
+   * Sets the value of the protein property.
+   * 
+   * @param value
+   *          allowed object is {@link ProteinType }
+   * 
+   */
+  public void setProtein(ProteinType value)
+  {
+    this.protein = value;
+  }
+
+  /**
+   * Gets the value of the gene property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the gene property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getGene().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link GeneType }
+   * 
+   * 
+   */
+  public List<GeneType> getGene()
+  {
+    if (gene == null)
+    {
+      gene = new ArrayList<GeneType>();
     }
-
-    /**
-     * Gets the value of the modified property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public XMLGregorianCalendar getModified() {
-        return modified;
+    return this.gene;
+  }
+
+  /**
+   * Gets the value of the organism property.
+   * 
+   * @return possible object is {@link OrganismType }
+   * 
+   */
+  public OrganismType getOrganism()
+  {
+    return organism;
+  }
+
+  /**
+   * Sets the value of the organism property.
+   * 
+   * @param value
+   *          allowed object is {@link OrganismType }
+   * 
+   */
+  public void setOrganism(OrganismType value)
+  {
+    this.organism = value;
+  }
+
+  /**
+   * Gets the value of the organismHost property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the organismHost property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getOrganismHost().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link OrganismType }
+   * 
+   * 
+   */
+  public List<OrganismType> getOrganismHost()
+  {
+    if (organismHost == null)
+    {
+      organismHost = new ArrayList<OrganismType>();
     }
-
-    /**
-     * Sets the value of the modified property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setModified(XMLGregorianCalendar value) {
-        this.modified = value;
+    return this.organismHost;
+  }
+
+  /**
+   * Gets the value of the geneLocation property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the geneLocation property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getGeneLocation().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link GeneLocationType }
+   * 
+   * 
+   */
+  public List<GeneLocationType> getGeneLocation()
+  {
+    if (geneLocation == null)
+    {
+      geneLocation = new ArrayList<GeneLocationType>();
     }
-
-    /**
-     * Gets the value of the version property.
-     * 
-     */
-    public int getVersion() {
-        return version;
+    return this.geneLocation;
+  }
+
+  /**
+   * Gets the value of the reference property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the reference property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getReference().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link ReferenceType }
+   * 
+   * 
+   */
+  public List<ReferenceType> getReference()
+  {
+    if (reference == null)
+    {
+      reference = new ArrayList<ReferenceType>();
     }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     */
-    public void setVersion(int value) {
-        this.version = value;
+    return this.reference;
+  }
+
+  /**
+   * Gets the value of the comment property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the comment property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getComment().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link CommentType
+   * }
+   * 
+   * 
+   */
+  public List<CommentType> getComment()
+  {
+    if (comment == null)
+    {
+      comment = new ArrayList<CommentType>();
+    }
+    return this.comment;
+  }
+
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the dbReference property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getDbReference().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List<DbReferenceType> getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList<DbReferenceType>();
+    }
+    return this.dbReference;
+  }
+
+  /**
+   * Gets the value of the proteinExistence property.
+   * 
+   * @return possible object is {@link ProteinExistenceType }
+   * 
+   */
+  public ProteinExistenceType getProteinExistence()
+  {
+    return proteinExistence;
+  }
+
+  /**
+   * Sets the value of the proteinExistence property.
+   * 
+   * @param value
+   *          allowed object is {@link ProteinExistenceType }
+   * 
+   */
+  public void setProteinExistence(ProteinExistenceType value)
+  {
+    this.proteinExistence = value;
+  }
+
+  /**
+   * Gets the value of the keyword property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the keyword property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getKeyword().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link KeywordType
+   * }
+   * 
+   * 
+   */
+  public List<KeywordType> getKeyword()
+  {
+    if (keyword == null)
+    {
+      keyword = new ArrayList<KeywordType>();
+    }
+    return this.keyword;
+  }
+
+  /**
+   * Gets the value of the feature property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the feature property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getFeature().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link FeatureType
+   * }
+   * 
+   * 
+   */
+  public List<FeatureType> getFeature()
+  {
+    if (feature == null)
+    {
+      feature = new ArrayList<FeatureType>();
+    }
+    return this.feature;
+  }
+
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidenceType }
+   * 
+   * 
+   */
+  public List<EvidenceType> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<EvidenceType>();
     }
+    return this.evidence;
+  }
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link SequenceType }
+   * 
+   */
+  public SequenceType getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link SequenceType }
+   * 
+   */
+  public void setSequence(SequenceType value)
+  {
+    this.sequence = value;
+  }
+
+  /**
+   * Gets the value of the dataset property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDataset()
+  {
+    return dataset;
+  }
+
+  /**
+   * Sets the value of the dataset property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDataset(String value)
+  {
+    this.dataset = value;
+  }
+
+  /**
+   * Gets the value of the created property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getCreated()
+  {
+    return created;
+  }
+
+  /**
+   * Sets the value of the created property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setCreated(XMLGregorianCalendar value)
+  {
+    this.created = value;
+  }
+
+  /**
+   * Gets the value of the modified property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getModified()
+  {
+    return modified;
+  }
+
+  /**
+   * Sets the value of the modified property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setModified(XMLGregorianCalendar value)
+  {
+    this.modified = value;
+  }
+
+  /**
+   * Gets the value of the version property.
+   * 
+   */
+  public int getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   */
+  public void setVersion(int value)
+  {
+    this.version = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java
index 0b4d4bd..49ab079 100644
--- a/src/jalview/xml/binding/uniprot/EventType.java
+++ b/src/jalview/xml/binding/uniprot/EventType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +12,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Describes the type of events that cause alternative products.
  * 
- * <p>Java class for eventType complex type.
+ * <p>
+ * Java class for eventType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="eventType">
@@ -44,33 +45,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "eventType")
-public class EventType {
+public class EventType
+{
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java
index 59c9857..1e6f734 100644
--- a/src/jalview/xml/binding/uniprot/EvidenceType.java
+++ b/src/jalview/xml/binding/uniprot/EvidenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -14,14 +13,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the evidence for an annotation.
- *             No flat file equivalent.
+ * Describes the evidence for an annotation. No flat file equivalent.
  * 
- * <p>Java class for evidenceType complex type.
+ * <p>
+ * Java class for evidenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="evidenceType">
@@ -41,113 +41,110 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidenceType", propOrder = {
-    "source",
-    "importedFrom"
-})
-public class EvidenceType {
-
-    protected SourceType source;
-    protected ImportedFromType importedFrom;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "key", required = true)
-    protected BigInteger key;
-
-    /**
-     * Gets the value of the source property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link SourceType }
-     *     
-     */
-    public SourceType getSource() {
-        return source;
-    }
-
-    /**
-     * Sets the value of the source property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link SourceType }
-     *     
-     */
-    public void setSource(SourceType value) {
-        this.source = value;
-    }
-
-    /**
-     * Gets the value of the importedFrom property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link ImportedFromType }
-     *     
-     */
-    public ImportedFromType getImportedFrom() {
-        return importedFrom;
-    }
-
-    /**
-     * Sets the value of the importedFrom property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link ImportedFromType }
-     *     
-     */
-    public void setImportedFrom(ImportedFromType value) {
-        this.importedFrom = value;
-    }
-
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
-
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
-
-    /**
-     * Gets the value of the key property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getKey() {
-        return key;
-    }
-
-    /**
-     * Sets the value of the key property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setKey(BigInteger value) {
-        this.key = value;
-    }
+@XmlType(name = "evidenceType", propOrder = { "source", "importedFrom" })
+public class EvidenceType
+{
+
+  protected SourceType source;
+
+  protected ImportedFromType importedFrom;
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
+
+  @XmlAttribute(name = "key", required = true)
+  protected BigInteger key;
+
+  /**
+   * Gets the value of the source property.
+   * 
+   * @return possible object is {@link SourceType }
+   * 
+   */
+  public SourceType getSource()
+  {
+    return source;
+  }
+
+  /**
+   * Sets the value of the source property.
+   * 
+   * @param value
+   *          allowed object is {@link SourceType }
+   * 
+   */
+  public void setSource(SourceType value)
+  {
+    this.source = value;
+  }
+
+  /**
+   * Gets the value of the importedFrom property.
+   * 
+   * @return possible object is {@link ImportedFromType }
+   * 
+   */
+  public ImportedFromType getImportedFrom()
+  {
+    return importedFrom;
+  }
+
+  /**
+   * Sets the value of the importedFrom property.
+   * 
+   * @param value
+   *          allowed object is {@link ImportedFromType }
+   * 
+   */
+  public void setImportedFrom(ImportedFromType value)
+  {
+    this.importedFrom = value;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the key property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getKey()
+  {
+    return key;
+  }
+
+  /**
+   * Sets the value of the key property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setKey(BigInteger value)
+  {
+    this.key = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
index 0fa25a6..0de4239 100644
--- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java
+++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
- * <p>Java class for evidencedStringType complex type.
+ * <p>
+ * Java class for evidencedStringType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="evidencedStringType">
@@ -44,93 +45,94 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidencedStringType", propOrder = {
-    "value"
-})
-public class EvidencedStringType {
+@XmlType(name = "evidencedStringType", propOrder = { "value" })
+public class EvidencedStringType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-    @XmlAttribute(name = "status")
-    protected String status;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  @XmlAttribute(name = "status")
+  protected String status;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Gets the value of the status property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getStatus() {
-        return status;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Sets the value of the status property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setStatus(String value) {
-        this.status = value;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
+
+  /**
+   * Gets the value of the status property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getStatus()
+  {
+    return status;
+  }
+
+  /**
+   * Sets the value of the status property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setStatus(String value)
+  {
+    this.status = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java
index f818e2e..e4bdc31 100644
--- a/src/jalview/xml/binding/uniprot/FeatureType.java
+++ b/src/jalview/xml/binding/uniprot/FeatureType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,14 +15,16 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes different types of sequence annotations.
- *             Equivalent to the flat file FT-line.
+ * Describes different types of sequence annotations. Equivalent to the flat
+ * file FT-line.
  * 
- * <p>Java class for featureType complex type.
+ * <p>
+ * Java class for featureType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="featureType">
@@ -100,254 +101,259 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "featureType", propOrder = {
-    "original",
-    "variation",
-    "location"
-})
-public class FeatureType {
+@XmlType(
+  name = "featureType",
+  propOrder =
+  { "original", "variation", "location" })
+public class FeatureType
+{
 
-    protected String original;
-    protected List<String> variation;
-    @XmlElement(required = true)
-    protected LocationType location;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "status")
-    protected String status;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "description")
-    protected String description;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-    @XmlAttribute(name = "ref")
-    protected String ref;
+  protected String original;
 
-    /**
-     * Gets the value of the original property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getOriginal() {
-        return original;
-    }
+  protected List<String> variation;
 
-    /**
-     * Sets the value of the original property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setOriginal(String value) {
-        this.original = value;
-    }
+  @XmlElement(required = true)
+  protected LocationType location;
 
-    /**
-     * Gets the value of the variation property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the variation property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getVariation().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getVariation() {
-        if (variation == null) {
-            variation = new ArrayList<String>();
-        }
-        return this.variation;
-    }
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the location property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link LocationType }
-     *     
-     */
-    public LocationType getLocation() {
-        return location;
-    }
+  @XmlAttribute(name = "status")
+  protected String status;
 
-    /**
-     * Sets the value of the location property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link LocationType }
-     *     
-     */
-    public void setLocation(LocationType value) {
-        this.location = value;
-    }
+  @XmlAttribute(name = "id")
+  protected String id;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  @XmlAttribute(name = "description")
+  protected String description;
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Gets the value of the status property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getStatus() {
-        return status;
-    }
+  @XmlAttribute(name = "ref")
+  protected String ref;
 
-    /**
-     * Sets the value of the status property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setStatus(String value) {
-        this.status = value;
-    }
+  /**
+   * Gets the value of the original property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getOriginal()
+  {
+    return original;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Sets the value of the original property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setOriginal(String value)
+  {
+    this.original = value;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
+  /**
+   * Gets the value of the variation property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the variation property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getVariation().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getVariation()
+  {
+    if (variation == null)
+    {
+      variation = new ArrayList<String>();
     }
+    return this.variation;
+  }
 
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
+  /**
+   * Gets the value of the location property.
+   * 
+   * @return possible object is {@link LocationType }
+   * 
+   */
+  public LocationType getLocation()
+  {
+    return location;
+  }
 
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
+  /**
+   * Sets the value of the location property.
+   * 
+   * @param value
+   *          allowed object is {@link LocationType }
+   * 
+   */
+  public void setLocation(LocationType value)
+  {
+    this.location = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Gets the value of the ref property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getRef() {
-        return ref;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the status property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getStatus()
+  {
+    return status;
+  }
+
+  /**
+   * Sets the value of the status property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setStatus(String value)
+  {
+    this.status = value;
+  }
 
-    /**
-     * Sets the value of the ref property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setRef(String value) {
-        this.ref = value;
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
+
+  /**
+   * Gets the value of the ref property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getRef()
+  {
+    return ref;
+  }
+
+  /**
+   * Sets the value of the ref property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setRef(String value)
+  {
+    this.ref = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java
index f2d5638..7ab7959 100644
--- a/src/jalview/xml/binding/uniprot/GeneLocationType.java
+++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,14 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes non-nuclear gene locations (organelles and plasmids).
- *             Equivalent to the flat file OG-line.
+ * Describes non-nuclear gene locations (organelles and plasmids). Equivalent to
+ * the flat file OG-line.
  * 
- * <p>Java class for geneLocationType complex type.
+ * <p>
+ * Java class for geneLocationType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="geneLocationType">
@@ -56,97 +57,102 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneLocationType", propOrder = {
-    "name"
-})
-public class GeneLocationType {
+@XmlType(name = "geneLocationType", propOrder = { "name" })
+public class GeneLocationType
+{
 
-    protected List<StatusType> name;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+  protected List<StatusType> name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the name property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getName().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link StatusType }
-     * 
-     * 
-     */
-    public List<StatusType> getName() {
-        if (name == null) {
-            name = new ArrayList<StatusType>();
-        }
-        return this.name;
-    }
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
+  /**
+   * Gets the value of the name property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the name property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link StatusType
+   * }
+   * 
+   * 
+   */
+  public List<StatusType> getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList<StatusType>();
     }
+    return this.name;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java
index 71af71f..bd21a83 100644
--- a/src/jalview/xml/binding/uniprot/GeneNameType.java
+++ b/src/jalview/xml/binding/uniprot/GeneNameType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,14 +15,16 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
- * Describes different types of gene designations.
- *             Equivalent to the flat file GN-line.
+ * Describes different types of gene designations. Equivalent to the flat file
+ * GN-line.
  * 
- * <p>Java class for geneNameType complex type.
+ * <p>
+ * Java class for geneNameType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="geneNameType">
@@ -48,93 +49,94 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneNameType", propOrder = {
-    "value"
-})
-public class GeneNameType {
+@XmlType(name = "geneNameType", propOrder = { "value" })
+public class GeneNameType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java
index 5fa628e..cbd47bf 100644
--- a/src/jalview/xml/binding/uniprot/GeneType.java
+++ b/src/jalview/xml/binding/uniprot/GeneType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,14 +14,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes a gene.
- *             Equivalent to the flat file GN-line.
+ * Describes a gene. Equivalent to the flat file GN-line.
  * 
- * <p>Java class for geneType complex type.
+ * <p>
+ * Java class for geneType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="geneType">
@@ -39,41 +39,43 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneType", propOrder = {
-    "name"
-})
-public class GeneType {
+@XmlType(name = "geneType", propOrder = { "name" })
+public class GeneType
+{
 
-    @XmlElement(required = true)
-    protected List<GeneNameType> name;
+  @XmlElement(required = true)
+  protected List<GeneNameType> name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the name property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getName().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link GeneNameType }
-     * 
-     * 
-     */
-    public List<GeneNameType> getName() {
-        if (name == null) {
-            name = new ArrayList<GeneNameType>();
-        }
-        return this.name;
+  /**
+   * Gets the value of the name property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the name property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link GeneNameType }
+   * 
+   * 
+   */
+  public List<GeneNameType> getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList<GeneNameType>();
     }
+    return this.name;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java
index 3d6c308..e003273 100644
--- a/src/jalview/xml/binding/uniprot/ImportedFromType.java
+++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +12,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
+ * Describes the source of the evidence, when it is not assigned by UniProt, but
+ * imported from an external database.
  * 
- * <p>Java class for importedFromType complex type.
+ * <p>
+ * Java class for importedFromType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="importedFromType">
@@ -36,36 +38,34 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "importedFromType", propOrder = {
-    "dbReference"
-})
-public class ImportedFromType {
+@XmlType(name = "importedFromType", propOrder = { "dbReference" })
+public class ImportedFromType
+{
 
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
+  @XmlElement(required = true)
+  protected DbReferenceType dbReference;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java
index c9cadc2..0ab941a 100644
--- a/src/jalview/xml/binding/uniprot/InteractantType.java
+++ b/src/jalview/xml/binding/uniprot/InteractantType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for interactantType complex type.
+ * <p>
+ * Java class for interactantType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="interactantType">
@@ -33,87 +34,84 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "interactantType", propOrder = {
-    "id",
-    "label"
-})
-public class InteractantType {
+@XmlType(name = "interactantType", propOrder = { "id", "label" })
+public class InteractantType
+{
+
+  protected String id;
+
+  protected String label;
 
-    protected String id;
-    protected String label;
-    @XmlAttribute(name = "intactId", required = true)
-    protected String intactId;
+  @XmlAttribute(name = "intactId", required = true)
+  protected String intactId;
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
-    /**
-     * Gets the value of the label property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getLabel() {
-        return label;
-    }
+  /**
+   * Gets the value of the label property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getLabel()
+  {
+    return label;
+  }
 
-    /**
-     * Sets the value of the label property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setLabel(String value) {
-        this.label = value;
-    }
+  /**
+   * Sets the value of the label property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setLabel(String value)
+  {
+    this.label = value;
+  }
 
-    /**
-     * Gets the value of the intactId property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getIntactId() {
-        return intactId;
-    }
+  /**
+   * Gets the value of the intactId property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getIntactId()
+  {
+    return intactId;
+  }
 
-    /**
-     * Sets the value of the intactId property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setIntactId(String value) {
-        this.intactId = value;
-    }
+  /**
+   * Sets the value of the intactId property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setIntactId(String value)
+  {
+    this.intactId = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java
index ea55664..20fbbb5 100644
--- a/src/jalview/xml/binding/uniprot/IsoformType.java
+++ b/src/jalview/xml/binding/uniprot/IsoformType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -17,13 +16,15 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
  * Describes isoforms in 'alternative products' annotations.
  * 
- * <p>Java class for isoformType complex type.
+ * <p>
+ * Java class for isoformType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="isoformType">
@@ -69,302 +70,316 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "isoformType", propOrder = {
-    "id",
-    "name",
-    "sequence",
-    "text"
-})
-public class IsoformType {
+@XmlType(
+  name = "isoformType",
+  propOrder =
+  { "id", "name", "sequence", "text" })
+public class IsoformType
+{
 
-    @XmlElement(required = true)
-    protected List<String> id;
-    @XmlElement(required = true)
-    protected List<IsoformType.Name> name;
-    @XmlElement(required = true)
-    protected IsoformType.Sequence sequence;
-    protected List<EvidencedStringType> text;
+  @XmlElement(required = true)
+  protected List<String> id;
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the id property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getId().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getId() {
-        if (id == null) {
-            id = new ArrayList<String>();
-        }
-        return this.id;
+  @XmlElement(required = true)
+  protected List<IsoformType.Name> name;
+
+  @XmlElement(required = true)
+  protected IsoformType.Sequence sequence;
+
+  protected List<EvidencedStringType> text;
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the id property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getId().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getId()
+  {
+    if (id == null)
+    {
+      id = new ArrayList<String>();
     }
+    return this.id;
+  }
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the name property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getName().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link IsoformType.Name }
-     * 
-     * 
-     */
-    public List<IsoformType.Name> getName() {
-        if (name == null) {
-            name = new ArrayList<IsoformType.Name>();
-        }
-        return this.name;
+  /**
+   * Gets the value of the name property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the name property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link IsoformType.Name }
+   * 
+   * 
+   */
+  public List<IsoformType.Name> getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList<IsoformType.Name>();
+    }
+    return this.name;
+  }
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link IsoformType.Sequence }
+   * 
+   */
+  public IsoformType.Sequence getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link IsoformType.Sequence }
+   * 
+   */
+  public void setSequence(IsoformType.Sequence value)
+  {
+    this.sequence = value;
+  }
+
+  /**
+   * Gets the value of the text property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the text property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getText().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List<EvidencedStringType> getText()
+  {
+    if (text == null)
+    {
+      text = new ArrayList<EvidencedStringType>();
     }
+    return this.text;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;simpleContent>
+   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     &lt;/extension>
+   *   &lt;/simpleContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Name
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
     /**
-     * Gets the value of the sequence property.
+     * Gets the value of the value property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link IsoformType.Sequence }
-     *     
      */
-    public IsoformType.Sequence getSequence() {
-        return sequence;
+    public String getValue()
+    {
+      return value;
     }
 
     /**
-     * Sets the value of the sequence property.
+     * Sets the value of the value property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link IsoformType.Sequence }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setSequence(IsoformType.Sequence value) {
-        this.sequence = value;
+    public void setValue(String value)
+    {
+      this.value = value;
     }
 
     /**
-     * Gets the value of the text property.
+     * Gets the value of the evidence property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the text 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
+     * <CODE>set</CODE> method for the evidence property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getText().add(newItem);
+     * getEvidence().add(newItem);
      * </pre>
      * 
      * 
      * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
+     * Objects of the following type(s) are allowed in the list {@link Integer }
      * 
      * 
      */
-    public List<EvidencedStringType> getText() {
-        if (text == null) {
-            text = new ArrayList<EvidencedStringType>();
-        }
-        return this.text;
+    public List<Integer> getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList<Integer>();
+      }
+      return this.evidence;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;attribute name="type" use="required">
+   *         &lt;simpleType>
+   *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             &lt;enumeration value="not described"/>
+   *             &lt;enumeration value="described"/>
+   *             &lt;enumeration value="displayed"/>
+   *             &lt;enumeration value="external"/>
+   *           &lt;/restriction>
+   *         &lt;/simpleType>
+   *       &lt;/attribute>
+   *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Sequence
+  {
+
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+
+    @XmlAttribute(name = "ref")
+    protected String ref;
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the type property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;simpleContent>
-     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     &lt;/extension>
-     *   &lt;/simpleContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public String getType()
+    {
+      return type;
+    }
+
+    /**
+     * Sets the value of the type property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "value"
-    })
-    public static class Name {
-
-        @XmlValue
-        protected String value;
-        @XmlAttribute(name = "evidence")
-        protected List<Integer> evidence;
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the evidence property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the evidence property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEvidence().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List<Integer> getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList<Integer>();
-            }
-            return this.evidence;
-        }
-
+    public void setType(String value)
+    {
+      this.type = value;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the ref property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="type" use="required">
-     *         &lt;simpleType>
-     *           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             &lt;enumeration value="not described"/>
-     *             &lt;enumeration value="described"/>
-     *             &lt;enumeration value="displayed"/>
-     *             &lt;enumeration value="external"/>
-     *           &lt;/restriction>
-     *         &lt;/simpleType>
-     *       &lt;/attribute>
-     *       &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public String getRef()
+    {
+      return ref;
+    }
+
+    /**
+     * Sets the value of the ref property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Sequence {
-
-        @XmlAttribute(name = "type", required = true)
-        protected String type;
-        @XmlAttribute(name = "ref")
-        protected String ref;
-
-        /**
-         * Gets the value of the type property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getType() {
-            return type;
-        }
-
-        /**
-         * Sets the value of the type property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setType(String value) {
-            this.type = value;
-        }
-
-        /**
-         * Gets the value of the ref property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getRef() {
-            return ref;
-        }
-
-        /**
-         * Sets the value of the ref property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setRef(String value) {
-            this.ref = value;
-        }
-
+    public void setRef(String value)
+    {
+      this.ref = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java
index f6409ee..a4e2b7c 100644
--- a/src/jalview/xml/binding/uniprot/KeywordType.java
+++ b/src/jalview/xml/binding/uniprot/KeywordType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
- * <p>Java class for keywordType complex type.
+ * <p>
+ * Java class for keywordType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="keywordType">
@@ -36,93 +37,94 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "keywordType", propOrder = {
-    "value"
-})
-public class KeywordType {
+@XmlType(name = "keywordType", propOrder = { "value" })
+public class KeywordType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
+
+  /**
+   * 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/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java
index 62e9999..ae3f321 100644
--- a/src/jalview/xml/binding/uniprot/LocationType.java
+++ b/src/jalview/xml/binding/uniprot/LocationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +12,17 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
+ * Describes a sequence location as either a range with a begin and end or as a
+ * position. The 'sequence' attribute is only used when the location is not on
+ * the canonical sequence displayed in the current entry.
  * 
- * <p>Java class for locationType complex type.
+ * <p>
+ * Java class for locationType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="locationType">
@@ -41,113 +44,109 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "locationType", propOrder = {
-    "begin",
-    "end",
-    "position"
-})
-public class LocationType {
-
-    protected PositionType begin;
-    protected PositionType end;
-    protected PositionType position;
-    @XmlAttribute(name = "sequence")
-    protected String sequence;
-
-    /**
-     * Gets the value of the begin property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link PositionType }
-     *     
-     */
-    public PositionType getBegin() {
-        return begin;
-    }
-
-    /**
-     * Sets the value of the begin property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link PositionType }
-     *     
-     */
-    public void setBegin(PositionType value) {
-        this.begin = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link PositionType }
-     *     
-     */
-    public PositionType getEnd() {
-        return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link PositionType }
-     *     
-     */
-    public void setEnd(PositionType value) {
-        this.end = value;
-    }
-
-    /**
-     * Gets the value of the position property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link PositionType }
-     *     
-     */
-    public PositionType getPosition() {
-        return position;
-    }
-
-    /**
-     * Sets the value of the position property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link PositionType }
-     *     
-     */
-    public void setPosition(PositionType value) {
-        this.position = value;
-    }
-
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSequence() {
-        return sequence;
-    }
-
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSequence(String value) {
-        this.sequence = value;
-    }
+@XmlType(name = "locationType", propOrder = { "begin", "end", "position" })
+public class LocationType
+{
+
+  protected PositionType begin;
+
+  protected PositionType end;
+
+  protected PositionType position;
+
+  @XmlAttribute(name = "sequence")
+  protected String sequence;
+
+  /**
+   * Gets the value of the begin property.
+   * 
+   * @return possible object is {@link PositionType }
+   * 
+   */
+  public PositionType getBegin()
+  {
+    return begin;
+  }
+
+  /**
+   * Sets the value of the begin property.
+   * 
+   * @param value
+   *          allowed object is {@link PositionType }
+   * 
+   */
+  public void setBegin(PositionType value)
+  {
+    this.begin = value;
+  }
+
+  /**
+   * Gets the value of the end property.
+   * 
+   * @return possible object is {@link PositionType }
+   * 
+   */
+  public PositionType getEnd()
+  {
+    return end;
+  }
+
+  /**
+   * Sets the value of the end property.
+   * 
+   * @param value
+   *          allowed object is {@link PositionType }
+   * 
+   */
+  public void setEnd(PositionType value)
+  {
+    this.end = value;
+  }
+
+  /**
+   * Gets the value of the position property.
+   * 
+   * @return possible object is {@link PositionType }
+   * 
+   */
+  public PositionType getPosition()
+  {
+    return position;
+  }
+
+  /**
+   * Sets the value of the position property.
+   * 
+   * @param value
+   *          allowed object is {@link PositionType }
+   * 
+   */
+  public void setPosition(PositionType value)
+  {
+    this.position = value;
+  }
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSequence(String value)
+  {
+    this.sequence = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java
index 8b52523..67e43d1 100644
--- a/src/jalview/xml/binding/uniprot/MoleculeType.java
+++ b/src/jalview/xml/binding/uniprot/MoleculeType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,13 +13,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
  * Describes a molecule by name or unique identifier.
  * 
- * <p>Java class for moleculeType complex type.
+ * <p>
+ * Java class for moleculeType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="moleculeType">
@@ -35,62 +36,60 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "moleculeType", propOrder = {
-    "value"
-})
-public class MoleculeType {
+@XmlType(name = "moleculeType", propOrder = { "value" })
+public class MoleculeType
+{
+
+  @XmlValue
+  protected String value;
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "id")
-    protected String id;
+  @XmlAttribute(name = "id")
+  protected String id;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java
index be68867..17918fb 100644
--- a/src/jalview/xml/binding/uniprot/NameListType.java
+++ b/src/jalview/xml/binding/uniprot/NameListType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for nameListType complex type.
+ * <p>
+ * Java class for nameListType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="nameListType">
@@ -38,45 +39,45 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "nameListType", propOrder = {
-    "consortiumOrPerson"
-})
-public class NameListType {
+@XmlType(name = "nameListType", propOrder = { "consortiumOrPerson" })
+public class NameListType
+{
 
-    @XmlElements({
-        @XmlElement(name = "consortium", type = ConsortiumType.class),
-        @XmlElement(name = "person", type = PersonType.class)
-    })
-    protected List<Object> consortiumOrPerson;
+  @XmlElements({
+      @XmlElement(name = "consortium", type = ConsortiumType.class),
+      @XmlElement(name = "person", type = PersonType.class) })
+  protected List<Object> consortiumOrPerson;
 
-    /**
-     * Gets the value of the consortiumOrPerson property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getConsortiumOrPerson().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link ConsortiumType }
-     * {@link PersonType }
-     * 
-     * 
-     */
-    public List<Object> getConsortiumOrPerson() {
-        if (consortiumOrPerson == null) {
-            consortiumOrPerson = new ArrayList<Object>();
-        }
-        return this.consortiumOrPerson;
+  /**
+   * Gets the value of the consortiumOrPerson property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the consortiumOrPerson property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getConsortiumOrPerson().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link ConsortiumType } {@link PersonType }
+   * 
+   * 
+   */
+  public List<Object> getConsortiumOrPerson()
+  {
+    if (consortiumOrPerson == null)
+    {
+      consortiumOrPerson = new ArrayList<Object>();
     }
+    return this.consortiumOrPerson;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java
index e2bb255..bf570f3 100644
--- a/src/jalview/xml/binding/uniprot/ObjectFactory.java
+++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.JAXBElement;
@@ -13,496 +12,558 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 import javax.xml.namespace.QName;
 
-
 /**
- * This object contains factory methods for each 
- * Java content interface and Java element interface 
- * generated in the jalview.xml.binding.uniprot package. 
- * <p>An ObjectFactory allows you to programatically 
- * construct new instances of the Java representation 
- * for XML content. The Java representation of XML 
- * content can consist of schema derived interfaces 
- * and classes representing the binding of schema 
- * type definitions, element declarations and model 
- * groups.  Factory methods for each of these are 
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.uniprot package.
+ * <p>
+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory {
-
-    private final static QName _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright");
-
-    /**
-     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot
-     * 
-     */
-    public ObjectFactory() {
-    }
-
-    /**
-     * Create an instance of {@link SourceDataType }
-     * 
-     */
-    public SourceDataType createSourceDataType() {
-        return new SourceDataType();
-    }
-
-    /**
-     * Create an instance of {@link IsoformType }
-     * 
-     */
-    public IsoformType createIsoformType() {
-        return new IsoformType();
-    }
-
-    /**
-     * Create an instance of {@link CommentType }
-     * 
-     */
-    public CommentType createCommentType() {
-        return new CommentType();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.Conflict }
-     * 
-     */
-    public CommentType.Conflict createCommentTypeConflict() {
-        return new CommentType.Conflict();
-    }
-
-    /**
-     * Create an instance of {@link OrganismType }
-     * 
-     */
-    public OrganismType createOrganismType() {
-        return new OrganismType();
-    }
-
-    /**
-     * Create an instance of {@link ProteinType }
-     * 
-     */
-    public ProteinType createProteinType() {
-        return new ProteinType();
-    }
-
-    /**
-     * Create an instance of {@link Entry }
-     * 
-     */
-    public Entry createEntry() {
-        return new Entry();
-    }
-
-    /**
-     * Create an instance of {@link GeneType }
-     * 
-     */
-    public GeneType createGeneType() {
-        return new GeneType();
-    }
-
-    /**
-     * Create an instance of {@link GeneLocationType }
-     * 
-     */
-    public GeneLocationType createGeneLocationType() {
-        return new GeneLocationType();
-    }
-
-    /**
-     * Create an instance of {@link ReferenceType }
-     * 
-     */
-    public ReferenceType createReferenceType() {
-        return new ReferenceType();
-    }
-
-    /**
-     * Create an instance of {@link DbReferenceType }
-     * 
-     */
-    public DbReferenceType createDbReferenceType() {
-        return new DbReferenceType();
-    }
-
-    /**
-     * Create an instance of {@link ProteinExistenceType }
-     * 
-     */
-    public ProteinExistenceType createProteinExistenceType() {
-        return new ProteinExistenceType();
-    }
-
-    /**
-     * Create an instance of {@link KeywordType }
-     * 
-     */
-    public KeywordType createKeywordType() {
-        return new KeywordType();
-    }
-
-    /**
-     * Create an instance of {@link FeatureType }
-     * 
-     */
-    public FeatureType createFeatureType() {
-        return new FeatureType();
-    }
-
-    /**
-     * Create an instance of {@link EvidenceType }
-     * 
-     */
-    public EvidenceType createEvidenceType() {
-        return new EvidenceType();
-    }
-
-    /**
-     * Create an instance of {@link SequenceType }
-     * 
-     */
-    public SequenceType createSequenceType() {
-        return new SequenceType();
-    }
-
-    /**
-     * Create an instance of {@link Uniprot }
-     * 
-     */
-    public Uniprot createUniprot() {
-        return new Uniprot();
-    }
-
-    /**
-     * Create an instance of {@link StatusType }
-     * 
-     */
-    public StatusType createStatusType() {
-        return new StatusType();
-    }
-
-    /**
-     * Create an instance of {@link PositionType }
-     * 
-     */
-    public PositionType createPositionType() {
-        return new PositionType();
-    }
-
-    /**
-     * Create an instance of {@link ConsortiumType }
-     * 
-     */
-    public ConsortiumType createConsortiumType() {
-        return new ConsortiumType();
-    }
-
-    /**
-     * Create an instance of {@link GeneNameType }
-     * 
-     */
-    public GeneNameType createGeneNameType() {
-        return new GeneNameType();
-    }
-
-    /**
-     * Create an instance of {@link LocationType }
-     * 
-     */
-    public LocationType createLocationType() {
-        return new LocationType();
-    }
-
-    /**
-     * Create an instance of {@link CitationType }
-     * 
-     */
-    public CitationType createCitationType() {
-        return new CitationType();
-    }
-
-    /**
-     * Create an instance of {@link PropertyType }
-     * 
-     */
-    public PropertyType createPropertyType() {
-        return new PropertyType();
-    }
-
-    /**
-     * Create an instance of {@link PhysiologicalReactionType }
-     * 
-     */
-    public PhysiologicalReactionType createPhysiologicalReactionType() {
-        return new PhysiologicalReactionType();
-    }
-
-    /**
-     * Create an instance of {@link CofactorType }
-     * 
-     */
-    public CofactorType createCofactorType() {
-        return new CofactorType();
-    }
-
-    /**
-     * Create an instance of {@link EvidencedStringType }
-     * 
-     */
-    public EvidencedStringType createEvidencedStringType() {
-        return new EvidencedStringType();
-    }
-
-    /**
-     * Create an instance of {@link PersonType }
-     * 
-     */
-    public PersonType createPersonType() {
-        return new PersonType();
-    }
-
-    /**
-     * Create an instance of {@link ImportedFromType }
-     * 
-     */
-    public ImportedFromType createImportedFromType() {
-        return new ImportedFromType();
-    }
-
-    /**
-     * Create an instance of {@link EventType }
-     * 
-     */
-    public EventType createEventType() {
-        return new EventType();
-    }
-
-    /**
-     * Create an instance of {@link InteractantType }
-     * 
-     */
-    public InteractantType createInteractantType() {
-        return new InteractantType();
-    }
-
-    /**
-     * Create an instance of {@link NameListType }
-     * 
-     */
-    public NameListType createNameListType() {
-        return new NameListType();
-    }
-
-    /**
-     * Create an instance of {@link ReactionType }
-     * 
-     */
-    public ReactionType createReactionType() {
-        return new ReactionType();
-    }
-
-    /**
-     * Create an instance of {@link SourceType }
-     * 
-     */
-    public SourceType createSourceType() {
-        return new SourceType();
-    }
-
-    /**
-     * Create an instance of {@link MoleculeType }
-     * 
-     */
-    public MoleculeType createMoleculeType() {
-        return new MoleculeType();
-    }
-
-    /**
-     * Create an instance of {@link OrganismNameType }
-     * 
-     */
-    public OrganismNameType createOrganismNameType() {
-        return new OrganismNameType();
-    }
-
-    /**
-     * Create an instance of {@link SubcellularLocationType }
-     * 
-     */
-    public SubcellularLocationType createSubcellularLocationType() {
-        return new SubcellularLocationType();
-    }
-
-    /**
-     * Create an instance of {@link SourceDataType.Strain }
-     * 
-     */
-    public SourceDataType.Strain createSourceDataTypeStrain() {
-        return new SourceDataType.Strain();
-    }
-
-    /**
-     * Create an instance of {@link SourceDataType.Plasmid }
-     * 
-     */
-    public SourceDataType.Plasmid createSourceDataTypePlasmid() {
-        return new SourceDataType.Plasmid();
-    }
-
-    /**
-     * Create an instance of {@link SourceDataType.Transposon }
-     * 
-     */
-    public SourceDataType.Transposon createSourceDataTypeTransposon() {
-        return new SourceDataType.Transposon();
-    }
-
-    /**
-     * Create an instance of {@link SourceDataType.Tissue }
-     * 
-     */
-    public SourceDataType.Tissue createSourceDataTypeTissue() {
-        return new SourceDataType.Tissue();
-    }
-
-    /**
-     * Create an instance of {@link IsoformType.Name }
-     * 
-     */
-    public IsoformType.Name createIsoformTypeName() {
-        return new IsoformType.Name();
-    }
-
-    /**
-     * Create an instance of {@link IsoformType.Sequence }
-     * 
-     */
-    public IsoformType.Sequence createIsoformTypeSequence() {
-        return new IsoformType.Sequence();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.Absorption }
-     * 
-     */
-    public CommentType.Absorption createCommentTypeAbsorption() {
-        return new CommentType.Absorption();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.Kinetics }
-     * 
-     */
-    public CommentType.Kinetics createCommentTypeKinetics() {
-        return new CommentType.Kinetics();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.PhDependence }
-     * 
-     */
-    public CommentType.PhDependence createCommentTypePhDependence() {
-        return new CommentType.PhDependence();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.RedoxPotential }
-     * 
-     */
-    public CommentType.RedoxPotential createCommentTypeRedoxPotential() {
-        return new CommentType.RedoxPotential();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.TemperatureDependence }
-     * 
-     */
-    public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() {
-        return new CommentType.TemperatureDependence();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.Link }
-     * 
-     */
-    public CommentType.Link createCommentTypeLink() {
-        return new CommentType.Link();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.Disease }
-     * 
-     */
-    public CommentType.Disease createCommentTypeDisease() {
-        return new CommentType.Disease();
-    }
-
-    /**
-     * Create an instance of {@link CommentType.Conflict.Sequence }
-     * 
-     */
-    public CommentType.Conflict.Sequence createCommentTypeConflictSequence() {
-        return new CommentType.Conflict.Sequence();
-    }
-
-    /**
-     * Create an instance of {@link OrganismType.Lineage }
-     * 
-     */
-    public OrganismType.Lineage createOrganismTypeLineage() {
-        return new OrganismType.Lineage();
-    }
-
-    /**
-     * Create an instance of {@link ProteinType.RecommendedName }
-     * 
-     */
-    public ProteinType.RecommendedName createProteinTypeRecommendedName() {
-        return new ProteinType.RecommendedName();
-    }
-
-    /**
-     * Create an instance of {@link ProteinType.AlternativeName }
-     * 
-     */
-    public ProteinType.AlternativeName createProteinTypeAlternativeName() {
-        return new ProteinType.AlternativeName();
-    }
-
-    /**
-     * Create an instance of {@link ProteinType.SubmittedName }
-     * 
-     */
-    public ProteinType.SubmittedName createProteinTypeSubmittedName() {
-        return new ProteinType.SubmittedName();
-    }
-
-    /**
-     * Create an instance of {@link ProteinType.Domain }
-     * 
-     */
-    public ProteinType.Domain createProteinTypeDomain() {
-        return new ProteinType.Domain();
-    }
-
-    /**
-     * Create an instance of {@link ProteinType.Component }
-     * 
-     */
-    public ProteinType.Component createProteinTypeComponent() {
-        return new ProteinType.Component();
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
-     * 
-     */
-    @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
-    public JAXBElement<String> createCopyright(String value) {
-        return new JAXBElement<String>(_Copyright_QNAME, String.class, null, value);
-    }
+public class ObjectFactory
+{
+
+  private final static QName _Copyright_QNAME = new QName(
+          "http://uniprot.org/uniprot", "copyright");
+
+  /**
+   * Create a new ObjectFactory that can be used to create new instances of
+   * schema derived classes for package: jalview.xml.binding.uniprot
+   * 
+   */
+  public ObjectFactory()
+  {
+  }
+
+  /**
+   * Create an instance of {@link SourceDataType }
+   * 
+   */
+  public SourceDataType createSourceDataType()
+  {
+    return new SourceDataType();
+  }
+
+  /**
+   * Create an instance of {@link IsoformType }
+   * 
+   */
+  public IsoformType createIsoformType()
+  {
+    return new IsoformType();
+  }
+
+  /**
+   * Create an instance of {@link CommentType }
+   * 
+   */
+  public CommentType createCommentType()
+  {
+    return new CommentType();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.Conflict }
+   * 
+   */
+  public CommentType.Conflict createCommentTypeConflict()
+  {
+    return new CommentType.Conflict();
+  }
+
+  /**
+   * Create an instance of {@link OrganismType }
+   * 
+   */
+  public OrganismType createOrganismType()
+  {
+    return new OrganismType();
+  }
+
+  /**
+   * Create an instance of {@link ProteinType }
+   * 
+   */
+  public ProteinType createProteinType()
+  {
+    return new ProteinType();
+  }
+
+  /**
+   * Create an instance of {@link Entry }
+   * 
+   */
+  public Entry createEntry()
+  {
+    return new Entry();
+  }
+
+  /**
+   * Create an instance of {@link GeneType }
+   * 
+   */
+  public GeneType createGeneType()
+  {
+    return new GeneType();
+  }
+
+  /**
+   * Create an instance of {@link GeneLocationType }
+   * 
+   */
+  public GeneLocationType createGeneLocationType()
+  {
+    return new GeneLocationType();
+  }
+
+  /**
+   * Create an instance of {@link ReferenceType }
+   * 
+   */
+  public ReferenceType createReferenceType()
+  {
+    return new ReferenceType();
+  }
+
+  /**
+   * Create an instance of {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType createDbReferenceType()
+  {
+    return new DbReferenceType();
+  }
+
+  /**
+   * Create an instance of {@link ProteinExistenceType }
+   * 
+   */
+  public ProteinExistenceType createProteinExistenceType()
+  {
+    return new ProteinExistenceType();
+  }
+
+  /**
+   * Create an instance of {@link KeywordType }
+   * 
+   */
+  public KeywordType createKeywordType()
+  {
+    return new KeywordType();
+  }
+
+  /**
+   * Create an instance of {@link FeatureType }
+   * 
+   */
+  public FeatureType createFeatureType()
+  {
+    return new FeatureType();
+  }
+
+  /**
+   * Create an instance of {@link EvidenceType }
+   * 
+   */
+  public EvidenceType createEvidenceType()
+  {
+    return new EvidenceType();
+  }
+
+  /**
+   * Create an instance of {@link SequenceType }
+   * 
+   */
+  public SequenceType createSequenceType()
+  {
+    return new SequenceType();
+  }
+
+  /**
+   * Create an instance of {@link Uniprot }
+   * 
+   */
+  public Uniprot createUniprot()
+  {
+    return new Uniprot();
+  }
+
+  /**
+   * Create an instance of {@link StatusType }
+   * 
+   */
+  public StatusType createStatusType()
+  {
+    return new StatusType();
+  }
+
+  /**
+   * Create an instance of {@link PositionType }
+   * 
+   */
+  public PositionType createPositionType()
+  {
+    return new PositionType();
+  }
+
+  /**
+   * Create an instance of {@link ConsortiumType }
+   * 
+   */
+  public ConsortiumType createConsortiumType()
+  {
+    return new ConsortiumType();
+  }
+
+  /**
+   * Create an instance of {@link GeneNameType }
+   * 
+   */
+  public GeneNameType createGeneNameType()
+  {
+    return new GeneNameType();
+  }
+
+  /**
+   * Create an instance of {@link LocationType }
+   * 
+   */
+  public LocationType createLocationType()
+  {
+    return new LocationType();
+  }
+
+  /**
+   * Create an instance of {@link CitationType }
+   * 
+   */
+  public CitationType createCitationType()
+  {
+    return new CitationType();
+  }
+
+  /**
+   * Create an instance of {@link PropertyType }
+   * 
+   */
+  public PropertyType createPropertyType()
+  {
+    return new PropertyType();
+  }
+
+  /**
+   * Create an instance of {@link PhysiologicalReactionType }
+   * 
+   */
+  public PhysiologicalReactionType createPhysiologicalReactionType()
+  {
+    return new PhysiologicalReactionType();
+  }
+
+  /**
+   * Create an instance of {@link CofactorType }
+   * 
+   */
+  public CofactorType createCofactorType()
+  {
+    return new CofactorType();
+  }
+
+  /**
+   * Create an instance of {@link EvidencedStringType }
+   * 
+   */
+  public EvidencedStringType createEvidencedStringType()
+  {
+    return new EvidencedStringType();
+  }
+
+  /**
+   * Create an instance of {@link PersonType }
+   * 
+   */
+  public PersonType createPersonType()
+  {
+    return new PersonType();
+  }
+
+  /**
+   * Create an instance of {@link ImportedFromType }
+   * 
+   */
+  public ImportedFromType createImportedFromType()
+  {
+    return new ImportedFromType();
+  }
+
+  /**
+   * Create an instance of {@link EventType }
+   * 
+   */
+  public EventType createEventType()
+  {
+    return new EventType();
+  }
+
+  /**
+   * Create an instance of {@link InteractantType }
+   * 
+   */
+  public InteractantType createInteractantType()
+  {
+    return new InteractantType();
+  }
+
+  /**
+   * Create an instance of {@link NameListType }
+   * 
+   */
+  public NameListType createNameListType()
+  {
+    return new NameListType();
+  }
+
+  /**
+   * Create an instance of {@link ReactionType }
+   * 
+   */
+  public ReactionType createReactionType()
+  {
+    return new ReactionType();
+  }
+
+  /**
+   * Create an instance of {@link SourceType }
+   * 
+   */
+  public SourceType createSourceType()
+  {
+    return new SourceType();
+  }
+
+  /**
+   * Create an instance of {@link MoleculeType }
+   * 
+   */
+  public MoleculeType createMoleculeType()
+  {
+    return new MoleculeType();
+  }
+
+  /**
+   * Create an instance of {@link OrganismNameType }
+   * 
+   */
+  public OrganismNameType createOrganismNameType()
+  {
+    return new OrganismNameType();
+  }
+
+  /**
+   * Create an instance of {@link SubcellularLocationType }
+   * 
+   */
+  public SubcellularLocationType createSubcellularLocationType()
+  {
+    return new SubcellularLocationType();
+  }
+
+  /**
+   * Create an instance of {@link SourceDataType.Strain }
+   * 
+   */
+  public SourceDataType.Strain createSourceDataTypeStrain()
+  {
+    return new SourceDataType.Strain();
+  }
+
+  /**
+   * Create an instance of {@link SourceDataType.Plasmid }
+   * 
+   */
+  public SourceDataType.Plasmid createSourceDataTypePlasmid()
+  {
+    return new SourceDataType.Plasmid();
+  }
+
+  /**
+   * Create an instance of {@link SourceDataType.Transposon }
+   * 
+   */
+  public SourceDataType.Transposon createSourceDataTypeTransposon()
+  {
+    return new SourceDataType.Transposon();
+  }
+
+  /**
+   * Create an instance of {@link SourceDataType.Tissue }
+   * 
+   */
+  public SourceDataType.Tissue createSourceDataTypeTissue()
+  {
+    return new SourceDataType.Tissue();
+  }
+
+  /**
+   * Create an instance of {@link IsoformType.Name }
+   * 
+   */
+  public IsoformType.Name createIsoformTypeName()
+  {
+    return new IsoformType.Name();
+  }
+
+  /**
+   * Create an instance of {@link IsoformType.Sequence }
+   * 
+   */
+  public IsoformType.Sequence createIsoformTypeSequence()
+  {
+    return new IsoformType.Sequence();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.Absorption }
+   * 
+   */
+  public CommentType.Absorption createCommentTypeAbsorption()
+  {
+    return new CommentType.Absorption();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.Kinetics }
+   * 
+   */
+  public CommentType.Kinetics createCommentTypeKinetics()
+  {
+    return new CommentType.Kinetics();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.PhDependence }
+   * 
+   */
+  public CommentType.PhDependence createCommentTypePhDependence()
+  {
+    return new CommentType.PhDependence();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.RedoxPotential }
+   * 
+   */
+  public CommentType.RedoxPotential createCommentTypeRedoxPotential()
+  {
+    return new CommentType.RedoxPotential();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.TemperatureDependence }
+   * 
+   */
+  public CommentType.TemperatureDependence createCommentTypeTemperatureDependence()
+  {
+    return new CommentType.TemperatureDependence();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.Link }
+   * 
+   */
+  public CommentType.Link createCommentTypeLink()
+  {
+    return new CommentType.Link();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.Disease }
+   * 
+   */
+  public CommentType.Disease createCommentTypeDisease()
+  {
+    return new CommentType.Disease();
+  }
+
+  /**
+   * Create an instance of {@link CommentType.Conflict.Sequence }
+   * 
+   */
+  public CommentType.Conflict.Sequence createCommentTypeConflictSequence()
+  {
+    return new CommentType.Conflict.Sequence();
+  }
+
+  /**
+   * Create an instance of {@link OrganismType.Lineage }
+   * 
+   */
+  public OrganismType.Lineage createOrganismTypeLineage()
+  {
+    return new OrganismType.Lineage();
+  }
+
+  /**
+   * Create an instance of {@link ProteinType.RecommendedName }
+   * 
+   */
+  public ProteinType.RecommendedName createProteinTypeRecommendedName()
+  {
+    return new ProteinType.RecommendedName();
+  }
+
+  /**
+   * Create an instance of {@link ProteinType.AlternativeName }
+   * 
+   */
+  public ProteinType.AlternativeName createProteinTypeAlternativeName()
+  {
+    return new ProteinType.AlternativeName();
+  }
+
+  /**
+   * Create an instance of {@link ProteinType.SubmittedName }
+   * 
+   */
+  public ProteinType.SubmittedName createProteinTypeSubmittedName()
+  {
+    return new ProteinType.SubmittedName();
+  }
+
+  /**
+   * Create an instance of {@link ProteinType.Domain }
+   * 
+   */
+  public ProteinType.Domain createProteinTypeDomain()
+  {
+    return new ProteinType.Domain();
+  }
+
+  /**
+   * Create an instance of {@link ProteinType.Component }
+   * 
+   */
+  public ProteinType.Component createProteinTypeComponent()
+  {
+    return new ProteinType.Component();
+  }
+
+  /**
+   * Create an instance of {@link JAXBElement }{@code <}{@link String
+   * }{@code >}}
+   * 
+   */
+  @XmlElementDecl(
+    namespace = "http://uniprot.org/uniprot",
+    name = "copyright")
+  public JAXBElement<String> createCopyright(String value)
+  {
+    return new JAXBElement<String>(_Copyright_QNAME, String.class, null,
+            value);
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java
index bc5c8c5..f2964dc 100644
--- a/src/jalview/xml/binding/uniprot/OrganismNameType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,13 +13,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
  * Describes different types of source organism names.
  * 
- * <p>Java class for organismNameType complex type.
+ * <p>
+ * Java class for organismNameType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="organismNameType">
@@ -45,62 +46,60 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismNameType", propOrder = {
-    "value"
-})
-public class OrganismNameType {
+@XmlType(name = "organismNameType", propOrder = { "value" })
+public class OrganismNameType
+{
+
+  @XmlValue
+  protected String value;
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java
index bb76add..033e498 100644
--- a/src/jalview/xml/binding/uniprot/OrganismType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Describes the source organism.
  * 
- * <p>Java class for organismType complex type.
+ * <p>
+ * Java class for organismType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="organismType">
@@ -52,190 +53,203 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismType", propOrder = {
-    "name",
-    "dbReference",
-    "lineage"
-})
-public class OrganismType {
-
-    @XmlElement(required = true)
-    protected List<OrganismNameType> name;
-    @XmlElement(required = true)
-    protected List<DbReferenceType> dbReference;
-    protected OrganismType.Lineage lineage;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the name property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getName().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link OrganismNameType }
-     * 
-     * 
-     */
-    public List<OrganismNameType> getName() {
-        if (name == null) {
-            name = new ArrayList<OrganismNameType>();
-        }
-        return this.name;
+@XmlType(
+  name = "organismType",
+  propOrder =
+  { "name", "dbReference", "lineage" })
+public class OrganismType
+{
+
+  @XmlElement(required = true)
+  protected List<OrganismNameType> name;
+
+  @XmlElement(required = true)
+  protected List<DbReferenceType> dbReference;
+
+  protected OrganismType.Lineage lineage;
+
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
+
+  /**
+   * Gets the value of the name property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the name property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link OrganismNameType }
+   * 
+   * 
+   */
+  public List<OrganismNameType> getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList<OrganismNameType>();
     }
-
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getDbReference().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link DbReferenceType }
-     * 
-     * 
-     */
-    public List<DbReferenceType> getDbReference() {
-        if (dbReference == null) {
-            dbReference = new ArrayList<DbReferenceType>();
-        }
-        return this.dbReference;
+    return this.name;
+  }
+
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the dbReference property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getDbReference().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List<DbReferenceType> getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList<DbReferenceType>();
     }
-
-    /**
-     * Gets the value of the lineage property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link OrganismType.Lineage }
-     *     
-     */
-    public OrganismType.Lineage getLineage() {
-        return lineage;
+    return this.dbReference;
+  }
+
+  /**
+   * Gets the value of the lineage property.
+   * 
+   * @return possible object is {@link OrganismType.Lineage }
+   * 
+   */
+  public OrganismType.Lineage getLineage()
+  {
+    return lineage;
+  }
+
+  /**
+   * Sets the value of the lineage property.
+   * 
+   * @param value
+   *          allowed object is {@link OrganismType.Lineage }
+   * 
+   */
+  public void setLineage(OrganismType.Lineage value)
+  {
+    this.lineage = value;
+  }
+
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "taxon" })
+  public static class Lineage
+  {
 
-    /**
-     * Sets the value of the lineage property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link OrganismType.Lineage }
-     *     
-     */
-    public void setLineage(OrganismType.Lineage value) {
-        this.lineage = value;
-    }
+    @XmlElement(required = true)
+    protected List<String> taxon;
 
     /**
-     * Gets the value of the evidence property.
+     * Gets the value of the taxon property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence 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
+     * <CODE>set</CODE> method for the taxon property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getEvidence().add(newItem);
+     * getTaxon().add(newItem);
      * </pre>
      * 
      * 
      * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
+     * Objects of the following type(s) are allowed in the list {@link String }
      * 
      * 
      */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+    public List<String> getTaxon()
+    {
+      if (taxon == null)
+      {
+        taxon = new ArrayList<String>();
+      }
+      return this.taxon;
     }
 
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "taxon"
-    })
-    public static class Lineage {
-
-        @XmlElement(required = true)
-        protected List<String> taxon;
-
-        /**
-         * Gets the value of the taxon property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the taxon property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getTaxon().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List<String> getTaxon() {
-            if (taxon == null) {
-                taxon = new ArrayList<String>();
-            }
-            return this.taxon;
-        }
-
-    }
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java
index 1354092..66a5161 100644
--- a/src/jalview/xml/binding/uniprot/PersonType.java
+++ b/src/jalview/xml/binding/uniprot/PersonType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for personType complex type.
+ * <p>
+ * Java class for personType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="personType">
@@ -33,33 +34,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "personType")
-public class PersonType {
+public class PersonType
+{
 
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
+  @XmlAttribute(name = "name", required = true)
+  protected String name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
index e674452..9e805f0 100644
--- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
+++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Describes a physiological reaction.
  * 
- * <p>Java class for physiologicalReactionType complex type.
+ * <p>
+ * Java class for physiologicalReactionType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="physiologicalReactionType">
@@ -48,93 +49,94 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "physiologicalReactionType", propOrder = {
-    "dbReference"
-})
-public class PhysiologicalReactionType {
+@XmlType(name = "physiologicalReactionType", propOrder = { "dbReference" })
+public class PhysiologicalReactionType
+{
 
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
-    @XmlAttribute(name = "direction", required = true)
-    protected String direction;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+  @XmlElement(required = true)
+  protected DbReferenceType dbReference;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  @XmlAttribute(name = "direction", required = true)
+  protected String direction;
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Gets the value of the direction property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDirection() {
-        return direction;
-    }
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
 
-    /**
-     * Sets the value of the direction property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDirection(String value) {
-        this.direction = value;
-    }
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
+
+  /**
+   * Gets the value of the direction property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDirection()
+  {
+    return direction;
+  }
+
+  /**
+   * Sets the value of the direction property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDirection(String value)
+  {
+    this.direction = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java
index a00d698..8eebd3d 100644
--- a/src/jalview/xml/binding/uniprot/PositionType.java
+++ b/src/jalview/xml/binding/uniprot/PositionType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for positionType complex type.
+ * <p>
+ * Java class for positionType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="positionType">
@@ -49,95 +50,101 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "positionType")
-public class PositionType {
+public class PositionType
+{
 
-    @XmlAttribute(name = "position")
-    @XmlSchemaType(name = "unsignedLong")
-    protected BigInteger position;
-    @XmlAttribute(name = "status")
-    protected String status;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+  @XmlAttribute(name = "position")
+  @XmlSchemaType(name = "unsignedLong")
+  protected BigInteger position;
 
-    /**
-     * Gets the value of the position property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getPosition() {
-        return position;
-    }
+  @XmlAttribute(name = "status")
+  protected String status;
 
-    /**
-     * Sets the value of the position property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setPosition(BigInteger value) {
-        this.position = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Gets the value of the status property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getStatus() {
-        if (status == null) {
-            return "certain";
-        } else {
-            return status;
-        }
-    }
+  /**
+   * Gets the value of the position property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getPosition()
+  {
+    return position;
+  }
+
+  /**
+   * Sets the value of the position property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setPosition(BigInteger value)
+  {
+    this.position = value;
+  }
 
-    /**
-     * Sets the value of the status property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setStatus(String value) {
-        this.status = value;
+  /**
+   * Gets the value of the status property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getStatus()
+  {
+    if (status == null)
+    {
+      return "certain";
     }
+    else
+    {
+      return status;
+    }
+  }
+
+  /**
+   * Sets the value of the status property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setStatus(String value)
+  {
+    this.status = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java
index c9f169c..a701b99 100644
--- a/src/jalview/xml/binding/uniprot/PropertyType.java
+++ b/src/jalview/xml/binding/uniprot/PropertyType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for propertyType complex type.
+ * <p>
+ * Java class for propertyType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="propertyType">
@@ -34,59 +35,59 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "propertyType")
-public class PropertyType {
+public class PropertyType
+{
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
+  @XmlAttribute(name = "value", required = true)
+  protected String value;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
index c34a0f5..5b914d0 100644
--- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,14 +12,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the evidence for the protein's existence.
- *             Equivalent to the flat file PE-line.
+ * Describes the evidence for the protein's existence. Equivalent to the flat
+ * file PE-line.
  * 
- * <p>Java class for proteinExistenceType complex type.
+ * <p>
+ * Java class for proteinExistenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="proteinExistenceType">
@@ -46,33 +47,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "proteinExistenceType")
-public class ProteinExistenceType {
+public class ProteinExistenceType
+{
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java
index 7b106fb..d35b45f 100644
--- a/src/jalview/xml/binding/uniprot/ProteinType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,14 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the names for the protein and parts thereof.
- *             Equivalent to the flat file DE-line.
+ * Describes the names for the protein and parts thereof. Equivalent to the flat
+ * file DE-line.
  * 
- * <p>Java class for proteinType complex type.
+ * <p>
+ * Java class for proteinType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="proteinType">
@@ -57,66 +58,497 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "proteinType", propOrder = {
-    "recommendedName",
-    "alternativeName",
-    "submittedName",
-    "allergenName",
-    "biotechName",
-    "cdAntigenName",
-    "innName",
-    "domain",
-    "component"
-})
-public class ProteinType {
+@XmlType(
+  name = "proteinType",
+  propOrder =
+  { "recommendedName", "alternativeName", "submittedName", "allergenName",
+      "biotechName", "cdAntigenName", "innName", "domain", "component" })
+public class ProteinType
+{
+
+  protected ProteinType.RecommendedName recommendedName;
+
+  protected List<ProteinType.AlternativeName> alternativeName;
+
+  protected List<ProteinType.SubmittedName> submittedName;
+
+  protected EvidencedStringType allergenName;
+
+  protected EvidencedStringType biotechName;
+
+  protected List<EvidencedStringType> cdAntigenName;
+
+  protected List<EvidencedStringType> innName;
+
+  protected List<ProteinType.Domain> domain;
+
+  protected List<ProteinType.Component> component;
+
+  /**
+   * Gets the value of the recommendedName property.
+   * 
+   * @return possible object is {@link ProteinType.RecommendedName }
+   * 
+   */
+  public ProteinType.RecommendedName getRecommendedName()
+  {
+    return recommendedName;
+  }
+
+  /**
+   * Sets the value of the recommendedName property.
+   * 
+   * @param value
+   *          allowed object is {@link ProteinType.RecommendedName }
+   * 
+   */
+  public void setRecommendedName(ProteinType.RecommendedName value)
+  {
+    this.recommendedName = value;
+  }
+
+  /**
+   * Gets the value of the alternativeName property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the alternativeName property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getAlternativeName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.AlternativeName }
+   * 
+   * 
+   */
+  public List<ProteinType.AlternativeName> getAlternativeName()
+  {
+    if (alternativeName == null)
+    {
+      alternativeName = new ArrayList<ProteinType.AlternativeName>();
+    }
+    return this.alternativeName;
+  }
+
+  /**
+   * Gets the value of the submittedName property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the submittedName property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getSubmittedName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.SubmittedName }
+   * 
+   * 
+   */
+  public List<ProteinType.SubmittedName> getSubmittedName()
+  {
+    if (submittedName == null)
+    {
+      submittedName = new ArrayList<ProteinType.SubmittedName>();
+    }
+    return this.submittedName;
+  }
+
+  /**
+   * Gets the value of the allergenName property.
+   * 
+   * @return possible object is {@link EvidencedStringType }
+   * 
+   */
+  public EvidencedStringType getAllergenName()
+  {
+    return allergenName;
+  }
+
+  /**
+   * Sets the value of the allergenName property.
+   * 
+   * @param value
+   *          allowed object is {@link EvidencedStringType }
+   * 
+   */
+  public void setAllergenName(EvidencedStringType value)
+  {
+    this.allergenName = value;
+  }
+
+  /**
+   * Gets the value of the biotechName property.
+   * 
+   * @return possible object is {@link EvidencedStringType }
+   * 
+   */
+  public EvidencedStringType getBiotechName()
+  {
+    return biotechName;
+  }
+
+  /**
+   * Sets the value of the biotechName property.
+   * 
+   * @param value
+   *          allowed object is {@link EvidencedStringType }
+   * 
+   */
+  public void setBiotechName(EvidencedStringType value)
+  {
+    this.biotechName = value;
+  }
+
+  /**
+   * Gets the value of the cdAntigenName property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the cdAntigenName property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getCdAntigenName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List<EvidencedStringType> getCdAntigenName()
+  {
+    if (cdAntigenName == null)
+    {
+      cdAntigenName = new ArrayList<EvidencedStringType>();
+    }
+    return this.cdAntigenName;
+  }
+
+  /**
+   * Gets the value of the innName property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the innName property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getInnName().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List<EvidencedStringType> getInnName()
+  {
+    if (innName == null)
+    {
+      innName = new ArrayList<EvidencedStringType>();
+    }
+    return this.innName;
+  }
+
+  /**
+   * Gets the value of the domain property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the domain property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getDomain().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.Domain }
+   * 
+   * 
+   */
+  public List<ProteinType.Domain> getDomain()
+  {
+    if (domain == null)
+    {
+      domain = new ArrayList<ProteinType.Domain>();
+    }
+    return this.domain;
+  }
+
+  /**
+   * Gets the value of the component property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the component property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getComponent().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.Component }
+   * 
+   * 
+   */
+  public List<ProteinType.Component> getComponent()
+  {
+    if (component == null)
+    {
+      component = new ArrayList<ProteinType.Component>();
+    }
+    return this.component;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+   *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+  public static class AlternativeName
+  {
+
+    protected EvidencedStringType fullName;
+
+    protected List<EvidencedStringType> shortName;
+
+    protected List<EvidencedStringType> ecNumber;
+
+    /**
+     * Gets the value of the fullName property.
+     * 
+     * @return possible object is {@link EvidencedStringType }
+     * 
+     */
+    public EvidencedStringType getFullName()
+    {
+      return fullName;
+    }
+
+    /**
+     * Sets the value of the fullName property.
+     * 
+     * @param value
+     *          allowed object is {@link EvidencedStringType }
+     * 
+     */
+    public void setFullName(EvidencedStringType value)
+    {
+      this.fullName = value;
+    }
+
+    /**
+     * Gets the value of the shortName property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the shortName property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getShortName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List<EvidencedStringType> getShortName()
+    {
+      if (shortName == null)
+      {
+        shortName = new ArrayList<EvidencedStringType>();
+      }
+      return this.shortName;
+    }
+
+    /**
+     * Gets the value of the ecNumber property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the ecNumber property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getEcNumber().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List<EvidencedStringType> getEcNumber()
+    {
+      if (ecNumber == null)
+      {
+        ecNumber = new ArrayList<EvidencedStringType>();
+      }
+      return this.ecNumber;
+    }
+
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "recommendedName", "alternativeName", "submittedName", "allergenName",
+        "biotechName", "cdAntigenName", "innName" })
+  public static class Component
+  {
 
     protected ProteinType.RecommendedName recommendedName;
+
     protected List<ProteinType.AlternativeName> alternativeName;
+
     protected List<ProteinType.SubmittedName> submittedName;
+
     protected EvidencedStringType allergenName;
+
     protected EvidencedStringType biotechName;
+
     protected List<EvidencedStringType> cdAntigenName;
+
     protected List<EvidencedStringType> innName;
-    protected List<ProteinType.Domain> domain;
-    protected List<ProteinType.Component> component;
 
     /**
      * Gets the value of the recommendedName property.
      * 
-     * @return
-     *     possible object is
-     *     {@link ProteinType.RecommendedName }
-     *     
+     * @return possible object is {@link ProteinType.RecommendedName }
+     * 
      */
-    public ProteinType.RecommendedName getRecommendedName() {
-        return recommendedName;
+    public ProteinType.RecommendedName getRecommendedName()
+    {
+      return recommendedName;
     }
 
     /**
      * Sets the value of the recommendedName property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link ProteinType.RecommendedName }
-     *     
+     *          allowed object is {@link ProteinType.RecommendedName }
+     * 
      */
-    public void setRecommendedName(ProteinType.RecommendedName value) {
-        this.recommendedName = value;
+    public void setRecommendedName(ProteinType.RecommendedName value)
+    {
+      this.recommendedName = value;
     }
 
     /**
      * Gets the value of the alternativeName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the alternativeName 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
+     * <CODE>set</CODE> method for the alternativeName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getAlternativeName().add(newItem);
+     * getAlternativeName().add(newItem);
      * </pre>
      * 
      * 
@@ -126,26 +558,29 @@ public class ProteinType {
      * 
      * 
      */
-    public List<ProteinType.AlternativeName> getAlternativeName() {
-        if (alternativeName == null) {
-            alternativeName = new ArrayList<ProteinType.AlternativeName>();
-        }
-        return this.alternativeName;
+    public List<ProteinType.AlternativeName> getAlternativeName()
+    {
+      if (alternativeName == null)
+      {
+        alternativeName = new ArrayList<ProteinType.AlternativeName>();
+      }
+      return this.alternativeName;
     }
 
     /**
      * Gets the value of the submittedName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the submittedName 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
+     * <CODE>set</CODE> method for the submittedName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getSubmittedName().add(newItem);
+     * getSubmittedName().add(newItem);
      * </pre>
      * 
      * 
@@ -155,74 +590,75 @@ public class ProteinType {
      * 
      * 
      */
-    public List<ProteinType.SubmittedName> getSubmittedName() {
-        if (submittedName == null) {
-            submittedName = new ArrayList<ProteinType.SubmittedName>();
-        }
-        return this.submittedName;
+    public List<ProteinType.SubmittedName> getSubmittedName()
+    {
+      if (submittedName == null)
+      {
+        submittedName = new ArrayList<ProteinType.SubmittedName>();
+      }
+      return this.submittedName;
     }
 
     /**
      * Gets the value of the allergenName property.
      * 
-     * @return
-     *     possible object is
-     *     {@link EvidencedStringType }
-     *     
+     * @return possible object is {@link EvidencedStringType }
+     * 
      */
-    public EvidencedStringType getAllergenName() {
-        return allergenName;
+    public EvidencedStringType getAllergenName()
+    {
+      return allergenName;
     }
 
     /**
      * Sets the value of the allergenName property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link EvidencedStringType }
-     *     
+     *          allowed object is {@link EvidencedStringType }
+     * 
      */
-    public void setAllergenName(EvidencedStringType value) {
-        this.allergenName = value;
+    public void setAllergenName(EvidencedStringType value)
+    {
+      this.allergenName = value;
     }
 
     /**
      * Gets the value of the biotechName property.
      * 
-     * @return
-     *     possible object is
-     *     {@link EvidencedStringType }
-     *     
+     * @return possible object is {@link EvidencedStringType }
+     * 
      */
-    public EvidencedStringType getBiotechName() {
-        return biotechName;
+    public EvidencedStringType getBiotechName()
+    {
+      return biotechName;
     }
 
     /**
      * Sets the value of the biotechName property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link EvidencedStringType }
-     *     
+     *          allowed object is {@link EvidencedStringType }
+     * 
      */
-    public void setBiotechName(EvidencedStringType value) {
-        this.biotechName = value;
+    public void setBiotechName(EvidencedStringType value)
+    {
+      this.biotechName = value;
     }
 
     /**
      * Gets the value of the cdAntigenName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the cdAntigenName 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
+     * <CODE>set</CODE> method for the cdAntigenName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getCdAntigenName().add(newItem);
+     * getCdAntigenName().add(newItem);
      * </pre>
      * 
      * 
@@ -232,26 +668,29 @@ public class ProteinType {
      * 
      * 
      */
-    public List<EvidencedStringType> getCdAntigenName() {
-        if (cdAntigenName == null) {
-            cdAntigenName = new ArrayList<EvidencedStringType>();
-        }
-        return this.cdAntigenName;
+    public List<EvidencedStringType> getCdAntigenName()
+    {
+      if (cdAntigenName == null)
+      {
+        cdAntigenName = new ArrayList<EvidencedStringType>();
+      }
+      return this.cdAntigenName;
     }
 
     /**
      * Gets the value of the innName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the innName 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
+     * <CODE>set</CODE> method for the innName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getInnName().add(newItem);
+     * getInnName().add(newItem);
      * </pre>
      * 
      * 
@@ -261,849 +700,472 @@ public class ProteinType {
      * 
      * 
      */
-    public List<EvidencedStringType> getInnName() {
-        if (innName == null) {
-            innName = new ArrayList<EvidencedStringType>();
-        }
-        return this.innName;
+    public List<EvidencedStringType> getInnName()
+    {
+      if (innName == null)
+      {
+        innName = new ArrayList<EvidencedStringType>();
+      }
+      return this.innName;
+    }
+
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "recommendedName", "alternativeName", "submittedName", "allergenName",
+        "biotechName", "cdAntigenName", "innName" })
+  public static class Domain
+  {
+
+    protected ProteinType.RecommendedName recommendedName;
+
+    protected List<ProteinType.AlternativeName> alternativeName;
+
+    protected List<ProteinType.SubmittedName> submittedName;
+
+    protected EvidencedStringType allergenName;
+
+    protected EvidencedStringType biotechName;
+
+    protected List<EvidencedStringType> cdAntigenName;
+
+    protected List<EvidencedStringType> innName;
+
+    /**
+     * Gets the value of the recommendedName property.
+     * 
+     * @return possible object is {@link ProteinType.RecommendedName }
+     * 
+     */
+    public ProteinType.RecommendedName getRecommendedName()
+    {
+      return recommendedName;
     }
 
     /**
-     * Gets the value of the domain property.
+     * Sets the value of the recommendedName property.
+     * 
+     * @param value
+     *          allowed object is {@link ProteinType.RecommendedName }
+     * 
+     */
+    public void setRecommendedName(ProteinType.RecommendedName value)
+    {
+      this.recommendedName = value;
+    }
+
+    /**
+     * Gets the value of the alternativeName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the domain 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
+     * <CODE>set</CODE> method for the alternativeName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getDomain().add(newItem);
+     * getAlternativeName().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.Domain }
+     * {@link ProteinType.AlternativeName }
      * 
      * 
      */
-    public List<ProteinType.Domain> getDomain() {
-        if (domain == null) {
-            domain = new ArrayList<ProteinType.Domain>();
-        }
-        return this.domain;
+    public List<ProteinType.AlternativeName> getAlternativeName()
+    {
+      if (alternativeName == null)
+      {
+        alternativeName = new ArrayList<ProteinType.AlternativeName>();
+      }
+      return this.alternativeName;
     }
 
     /**
-     * Gets the value of the component property.
+     * Gets the value of the submittedName property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the component 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
+     * <CODE>set</CODE> method for the submittedName property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getComponent().add(newItem);
+     * getSubmittedName().add(newItem);
      * </pre>
      * 
      * 
      * <p>
      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.Component }
+     * {@link ProteinType.SubmittedName }
      * 
      * 
      */
-    public List<ProteinType.Component> getComponent() {
-        if (component == null) {
-            component = new ArrayList<ProteinType.Component>();
-        }
-        return this.component;
+    public List<ProteinType.SubmittedName> getSubmittedName()
+    {
+      if (submittedName == null)
+      {
+        submittedName = new ArrayList<ProteinType.SubmittedName>();
+      }
+      return this.submittedName;
     }
 
+    /**
+     * Gets the value of the allergenName property.
+     * 
+     * @return possible object is {@link EvidencedStringType }
+     * 
+     */
+    public EvidencedStringType getAllergenName()
+    {
+      return allergenName;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Sets the value of the allergenName property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link EvidencedStringType }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-     *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public void setAllergenName(EvidencedStringType value)
+    {
+      this.allergenName = value;
+    }
+
+    /**
+     * Gets the value of the biotechName property.
      * 
+     * @return possible object is {@link EvidencedStringType }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "fullName",
-        "shortName",
-        "ecNumber"
-    })
-    public static class AlternativeName {
-
-        protected EvidencedStringType fullName;
-        protected List<EvidencedStringType> shortName;
-        protected List<EvidencedStringType> ecNumber;
-
-        /**
-         * Gets the value of the fullName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getFullName() {
-            return fullName;
-        }
-
-        /**
-         * Sets the value of the fullName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setFullName(EvidencedStringType value) {
-            this.fullName = value;
-        }
-
-        /**
-         * Gets the value of the shortName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the shortName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getShortName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getShortName() {
-            if (shortName == null) {
-                shortName = new ArrayList<EvidencedStringType>();
-            }
-            return this.shortName;
-        }
-
-        /**
-         * Gets the value of the ecNumber property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEcNumber().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getEcNumber() {
-            if (ecNumber == null) {
-                ecNumber = new ArrayList<EvidencedStringType>();
-            }
-            return this.ecNumber;
-        }
+    public EvidencedStringType getBiotechName()
+    {
+      return biotechName;
+    }
 
+    /**
+     * Sets the value of the biotechName property.
+     * 
+     * @param value
+     *          allowed object is {@link EvidencedStringType }
+     * 
+     */
+    public void setBiotechName(EvidencedStringType value)
+    {
+      this.biotechName = value;
     }
 
+    /**
+     * Gets the value of the cdAntigenName property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the cdAntigenName property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * 
+     * <pre>
+     * getCdAntigenName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List<EvidencedStringType> getCdAntigenName()
+    {
+      if (cdAntigenName == null)
+      {
+        cdAntigenName = new ArrayList<EvidencedStringType>();
+      }
+      return this.cdAntigenName;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the innName property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the innName property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getInnName().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "recommendedName",
-        "alternativeName",
-        "submittedName",
-        "allergenName",
-        "biotechName",
-        "cdAntigenName",
-        "innName"
-    })
-    public static class Component {
-
-        protected ProteinType.RecommendedName recommendedName;
-        protected List<ProteinType.AlternativeName> alternativeName;
-        protected List<ProteinType.SubmittedName> submittedName;
-        protected EvidencedStringType allergenName;
-        protected EvidencedStringType biotechName;
-        protected List<EvidencedStringType> cdAntigenName;
-        protected List<EvidencedStringType> innName;
-
-        /**
-         * Gets the value of the recommendedName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link ProteinType.RecommendedName }
-         *     
-         */
-        public ProteinType.RecommendedName getRecommendedName() {
-            return recommendedName;
-        }
-
-        /**
-         * Sets the value of the recommendedName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link ProteinType.RecommendedName }
-         *     
-         */
-        public void setRecommendedName(ProteinType.RecommendedName value) {
-            this.recommendedName = value;
-        }
-
-        /**
-         * Gets the value of the alternativeName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getAlternativeName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.AlternativeName }
-         * 
-         * 
-         */
-        public List<ProteinType.AlternativeName> getAlternativeName() {
-            if (alternativeName == null) {
-                alternativeName = new ArrayList<ProteinType.AlternativeName>();
-            }
-            return this.alternativeName;
-        }
-
-        /**
-         * Gets the value of the submittedName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the submittedName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getSubmittedName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.SubmittedName }
-         * 
-         * 
-         */
-        public List<ProteinType.SubmittedName> getSubmittedName() {
-            if (submittedName == null) {
-                submittedName = new ArrayList<ProteinType.SubmittedName>();
-            }
-            return this.submittedName;
-        }
-
-        /**
-         * Gets the value of the allergenName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getAllergenName() {
-            return allergenName;
-        }
-
-        /**
-         * Sets the value of the allergenName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setAllergenName(EvidencedStringType value) {
-            this.allergenName = value;
-        }
-
-        /**
-         * Gets the value of the biotechName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getBiotechName() {
-            return biotechName;
-        }
-
-        /**
-         * Sets the value of the biotechName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setBiotechName(EvidencedStringType value) {
-            this.biotechName = value;
-        }
-
-        /**
-         * Gets the value of the cdAntigenName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getCdAntigenName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getCdAntigenName() {
-            if (cdAntigenName == null) {
-                cdAntigenName = new ArrayList<EvidencedStringType>();
-            }
-            return this.cdAntigenName;
-        }
-
-        /**
-         * Gets the value of the innName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the innName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getInnName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getInnName() {
-            if (innName == null) {
-                innName = new ArrayList<EvidencedStringType>();
-            }
-            return this.innName;
-        }
+    public List<EvidencedStringType> getInnName()
+    {
+      if (innName == null)
+      {
+        innName = new ArrayList<EvidencedStringType>();
+      }
+      return this.innName;
+    }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+   *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+  public static class RecommendedName
+  {
+
+    @XmlElement(required = true)
+    protected EvidencedStringType fullName;
+
+    protected List<EvidencedStringType> shortName;
+
+    protected List<EvidencedStringType> ecNumber;
+
+    /**
+     * Gets the value of the fullName property.
+     * 
+     * @return possible object is {@link EvidencedStringType }
+     * 
+     */
+    public EvidencedStringType getFullName()
+    {
+      return fullName;
     }
 
+    /**
+     * Sets the value of the fullName property.
+     * 
+     * @param value
+     *          allowed object is {@link EvidencedStringType }
+     * 
+     */
+    public void setFullName(EvidencedStringType value)
+    {
+      this.fullName = value;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the shortName property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the shortName property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getShortName().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "recommendedName",
-        "alternativeName",
-        "submittedName",
-        "allergenName",
-        "biotechName",
-        "cdAntigenName",
-        "innName"
-    })
-    public static class Domain {
-
-        protected ProteinType.RecommendedName recommendedName;
-        protected List<ProteinType.AlternativeName> alternativeName;
-        protected List<ProteinType.SubmittedName> submittedName;
-        protected EvidencedStringType allergenName;
-        protected EvidencedStringType biotechName;
-        protected List<EvidencedStringType> cdAntigenName;
-        protected List<EvidencedStringType> innName;
-
-        /**
-         * Gets the value of the recommendedName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link ProteinType.RecommendedName }
-         *     
-         */
-        public ProteinType.RecommendedName getRecommendedName() {
-            return recommendedName;
-        }
-
-        /**
-         * Sets the value of the recommendedName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link ProteinType.RecommendedName }
-         *     
-         */
-        public void setRecommendedName(ProteinType.RecommendedName value) {
-            this.recommendedName = value;
-        }
-
-        /**
-         * Gets the value of the alternativeName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getAlternativeName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.AlternativeName }
-         * 
-         * 
-         */
-        public List<ProteinType.AlternativeName> getAlternativeName() {
-            if (alternativeName == null) {
-                alternativeName = new ArrayList<ProteinType.AlternativeName>();
-            }
-            return this.alternativeName;
-        }
-
-        /**
-         * Gets the value of the submittedName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the submittedName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getSubmittedName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.SubmittedName }
-         * 
-         * 
-         */
-        public List<ProteinType.SubmittedName> getSubmittedName() {
-            if (submittedName == null) {
-                submittedName = new ArrayList<ProteinType.SubmittedName>();
-            }
-            return this.submittedName;
-        }
-
-        /**
-         * Gets the value of the allergenName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getAllergenName() {
-            return allergenName;
-        }
-
-        /**
-         * Sets the value of the allergenName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setAllergenName(EvidencedStringType value) {
-            this.allergenName = value;
-        }
-
-        /**
-         * Gets the value of the biotechName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getBiotechName() {
-            return biotechName;
-        }
-
-        /**
-         * Sets the value of the biotechName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setBiotechName(EvidencedStringType value) {
-            this.biotechName = value;
-        }
-
-        /**
-         * Gets the value of the cdAntigenName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getCdAntigenName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getCdAntigenName() {
-            if (cdAntigenName == null) {
-                cdAntigenName = new ArrayList<EvidencedStringType>();
-            }
-            return this.cdAntigenName;
-        }
-
-        /**
-         * Gets the value of the innName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the innName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getInnName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getInnName() {
-            if (innName == null) {
-                innName = new ArrayList<EvidencedStringType>();
-            }
-            return this.innName;
-        }
-
+    public List<EvidencedStringType> getShortName()
+    {
+      if (shortName == null)
+      {
+        shortName = new ArrayList<EvidencedStringType>();
+      }
+      return this.shortName;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the ecNumber property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the ecNumber property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-     *         &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getEcNumber().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "fullName",
-        "shortName",
-        "ecNumber"
-    })
-    public static class RecommendedName {
-
-        @XmlElement(required = true)
-        protected EvidencedStringType fullName;
-        protected List<EvidencedStringType> shortName;
-        protected List<EvidencedStringType> ecNumber;
-
-        /**
-         * Gets the value of the fullName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getFullName() {
-            return fullName;
-        }
-
-        /**
-         * Sets the value of the fullName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setFullName(EvidencedStringType value) {
-            this.fullName = value;
-        }
-
-        /**
-         * Gets the value of the shortName property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the shortName property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getShortName().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getShortName() {
-            if (shortName == null) {
-                shortName = new ArrayList<EvidencedStringType>();
-            }
-            return this.shortName;
-        }
-
-        /**
-         * Gets the value of the ecNumber property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEcNumber().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getEcNumber() {
-            if (ecNumber == null) {
-                ecNumber = new ArrayList<EvidencedStringType>();
-            }
-            return this.ecNumber;
-        }
+    public List<EvidencedStringType> getEcNumber()
+    {
+      if (ecNumber == null)
+      {
+        ecNumber = new ArrayList<EvidencedStringType>();
+      }
+      return this.ecNumber;
+    }
+
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;complexContent>
+   *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       &lt;sequence>
+   *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+   *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       &lt;/sequence>
+   *     &lt;/restriction>
+   *   &lt;/complexContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "fullName", "ecNumber" })
+  public static class SubmittedName
+  {
+
+    @XmlElement(required = true)
+    protected EvidencedStringType fullName;
+
+    protected List<EvidencedStringType> ecNumber;
 
+    /**
+     * Gets the value of the fullName property.
+     * 
+     * @return possible object is {@link EvidencedStringType }
+     * 
+     */
+    public EvidencedStringType getFullName()
+    {
+      return fullName;
     }
 
+    /**
+     * Sets the value of the fullName property.
+     * 
+     * @param value
+     *          allowed object is {@link EvidencedStringType }
+     * 
+     */
+    public void setFullName(EvidencedStringType value)
+    {
+      this.fullName = value;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the ecNumber property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the ecNumber property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-     *         &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
+     * getEcNumber().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "fullName",
-        "ecNumber"
-    })
-    public static class SubmittedName {
-
-        @XmlElement(required = true)
-        protected EvidencedStringType fullName;
-        protected List<EvidencedStringType> ecNumber;
-
-        /**
-         * Gets the value of the fullName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public EvidencedStringType getFullName() {
-            return fullName;
-        }
-
-        /**
-         * Sets the value of the fullName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EvidencedStringType }
-         *     
-         */
-        public void setFullName(EvidencedStringType value) {
-            this.fullName = value;
-        }
-
-        /**
-         * Gets the value of the ecNumber property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEcNumber().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List<EvidencedStringType> getEcNumber() {
-            if (ecNumber == null) {
-                ecNumber = new ArrayList<EvidencedStringType>();
-            }
-            return this.ecNumber;
-        }
-
+    public List<EvidencedStringType> getEcNumber()
+    {
+      if (ecNumber == null)
+      {
+        ecNumber = new ArrayList<EvidencedStringType>();
+      }
+      return this.ecNumber;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java
index 8d9d51d..2260842 100644
--- a/src/jalview/xml/binding/uniprot/ReactionType.java
+++ b/src/jalview/xml/binding/uniprot/ReactionType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Describes a chemical reaction.
  * 
- * <p>Java class for reactionType complex type.
+ * <p>
+ * Java class for reactionType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="reactionType">
@@ -41,99 +42,103 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "reactionType", propOrder = {
-    "text",
-    "dbReference"
-})
-public class ReactionType {
+@XmlType(name = "reactionType", propOrder = { "text", "dbReference" })
+public class ReactionType
+{
 
-    @XmlElement(required = true)
-    protected String text;
-    @XmlElement(required = true)
-    protected List<DbReferenceType> dbReference;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
+  @XmlElement(required = true)
+  protected String text;
 
-    /**
-     * Gets the value of the text property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getText() {
-        return text;
-    }
+  @XmlElement(required = true)
+  protected List<DbReferenceType> dbReference;
 
-    /**
-     * Sets the value of the text property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setText(String value) {
-        this.text = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
+
+  /**
+   * Gets the value of the text property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getText()
+  {
+    return text;
+  }
+
+  /**
+   * Sets the value of the text property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setText(String value)
+  {
+    this.text = value;
+  }
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the dbReference property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getDbReference().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link DbReferenceType }
-     * 
-     * 
-     */
-    public List<DbReferenceType> getDbReference() {
-        if (dbReference == null) {
-            dbReference = new ArrayList<DbReferenceType>();
-        }
-        return this.dbReference;
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the dbReference property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getDbReference().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List<DbReferenceType> getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList<DbReferenceType>();
     }
+    return this.dbReference;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java
index e5f9fde..2f7daa3 100644
--- a/src/jalview/xml/binding/uniprot/ReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/ReferenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,14 +15,16 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes a citation and a summary of its content.
- *             Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
+ * Describes a citation and a summary of its content. Equivalent to the flat
+ * file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
  * 
- * <p>Java class for referenceType complex type.
+ * <p>
+ * Java class for referenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="referenceType">
@@ -43,151 +44,156 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "referenceType", propOrder = {
-    "citation",
-    "scope",
-    "source"
-})
-public class ReferenceType {
-
-    @XmlElement(required = true)
-    protected CitationType citation;
-    @XmlElement(required = true)
-    protected List<String> scope;
-    protected SourceDataType source;
-    @XmlAttribute(name = "evidence")
-    protected List<Integer> evidence;
-    @XmlAttribute(name = "key", required = true)
-    protected String key;
-
-    /**
-     * Gets the value of the citation property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CitationType }
-     *     
-     */
-    public CitationType getCitation() {
-        return citation;
-    }
+@XmlType(
+  name = "referenceType",
+  propOrder =
+  { "citation", "scope", "source" })
+public class ReferenceType
+{
 
-    /**
-     * Sets the value of the citation property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CitationType }
-     *     
-     */
-    public void setCitation(CitationType value) {
-        this.citation = value;
-    }
+  @XmlElement(required = true)
+  protected CitationType citation;
 
-    /**
-     * Gets the value of the scope property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the scope property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getScope().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List<String> getScope() {
-        if (scope == null) {
-            scope = new ArrayList<String>();
-        }
-        return this.scope;
-    }
+  @XmlElement(required = true)
+  protected List<String> scope;
 
-    /**
-     * Gets the value of the source property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link SourceDataType }
-     *     
-     */
-    public SourceDataType getSource() {
-        return source;
-    }
+  protected SourceDataType source;
 
-    /**
-     * Sets the value of the source property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link SourceDataType }
-     *     
-     */
-    public void setSource(SourceDataType value) {
-        this.source = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List<Integer> evidence;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the evidence property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEvidence().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List<Integer> getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList<Integer>();
-        }
-        return this.evidence;
-    }
+  @XmlAttribute(name = "key", required = true)
+  protected String key;
+
+  /**
+   * Gets the value of the citation property.
+   * 
+   * @return possible object is {@link CitationType }
+   * 
+   */
+  public CitationType getCitation()
+  {
+    return citation;
+  }
 
-    /**
-     * Gets the value of the key property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getKey() {
-        return key;
+  /**
+   * Sets the value of the citation property.
+   * 
+   * @param value
+   *          allowed object is {@link CitationType }
+   * 
+   */
+  public void setCitation(CitationType value)
+  {
+    this.citation = value;
+  }
+
+  /**
+   * Gets the value of the scope property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the scope property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getScope().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List<String> getScope()
+  {
+    if (scope == null)
+    {
+      scope = new ArrayList<String>();
     }
+    return this.scope;
+  }
+
+  /**
+   * Gets the value of the source property.
+   * 
+   * @return possible object is {@link SourceDataType }
+   * 
+   */
+  public SourceDataType getSource()
+  {
+    return source;
+  }
 
-    /**
-     * Sets the value of the key property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setKey(String value) {
-        this.key = value;
+  /**
+   * Sets the value of the source property.
+   * 
+   * @param value
+   *          allowed object is {@link SourceDataType }
+   * 
+   */
+  public void setSource(SourceDataType value)
+  {
+    this.source = value;
+  }
+
+  /**
+   * Gets the value of the evidence property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the evidence property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEvidence().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List<Integer> getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList<Integer>();
     }
+    return this.evidence;
+  }
+
+  /**
+   * Gets the value of the key property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getKey()
+  {
+    return key;
+  }
+
+  /**
+   * Sets the value of the key property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setKey(String value)
+  {
+    this.key = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java
index 49cd130..42d8c58 100644
--- a/src/jalview/xml/binding/uniprot/SequenceType.java
+++ b/src/jalview/xml/binding/uniprot/SequenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 import javax.xml.datatype.XMLGregorianCalendar;
 
-
 /**
- * <p>Java class for sequenceType complex type.
+ * <p>
+ * Java class for sequenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="sequenceType">
@@ -48,195 +49,202 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sequenceType", propOrder = {
-    "value"
-})
-public class SequenceType {
-
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "length", required = true)
-    protected int length;
-    @XmlAttribute(name = "mass", required = true)
-    protected int mass;
-    @XmlAttribute(name = "checksum", required = true)
-    protected String checksum;
-    @XmlAttribute(name = "modified", required = true)
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar modified;
-    @XmlAttribute(name = "version", required = true)
-    protected int version;
-    @XmlAttribute(name = "precursor")
-    protected Boolean precursor;
-    @XmlAttribute(name = "fragment")
-    protected String fragment;
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
-
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
-
-    /**
-     * Gets the value of the length property.
-     * 
-     */
-    public int getLength() {
-        return length;
-    }
-
-    /**
-     * Sets the value of the length property.
-     * 
-     */
-    public void setLength(int value) {
-        this.length = value;
-    }
-
-    /**
-     * Gets the value of the mass property.
-     * 
-     */
-    public int getMass() {
-        return mass;
-    }
-
-    /**
-     * Sets the value of the mass property.
-     * 
-     */
-    public void setMass(int value) {
-        this.mass = value;
-    }
-
-    /**
-     * Gets the value of the checksum property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getChecksum() {
-        return checksum;
-    }
-
-    /**
-     * Sets the value of the checksum property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setChecksum(String value) {
-        this.checksum = value;
-    }
-
-    /**
-     * Gets the value of the modified property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public XMLGregorianCalendar getModified() {
-        return modified;
-    }
-
-    /**
-     * Sets the value of the modified property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setModified(XMLGregorianCalendar value) {
-        this.modified = value;
-    }
-
-    /**
-     * Gets the value of the version property.
-     * 
-     */
-    public int getVersion() {
-        return version;
-    }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     */
-    public void setVersion(int value) {
-        this.version = value;
-    }
-
-    /**
-     * Gets the value of the precursor property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isPrecursor() {
-        return precursor;
-    }
-
-    /**
-     * Sets the value of the precursor property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setPrecursor(Boolean value) {
-        this.precursor = value;
-    }
-
-    /**
-     * Gets the value of the fragment property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getFragment() {
-        return fragment;
-    }
-
-    /**
-     * Sets the value of the fragment property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setFragment(String value) {
-        this.fragment = value;
-    }
+@XmlType(name = "sequenceType", propOrder = { "value" })
+public class SequenceType
+{
+
+  @XmlValue
+  protected String value;
+
+  @XmlAttribute(name = "length", required = true)
+  protected int length;
+
+  @XmlAttribute(name = "mass", required = true)
+  protected int mass;
+
+  @XmlAttribute(name = "checksum", required = true)
+  protected String checksum;
+
+  @XmlAttribute(name = "modified", required = true)
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar modified;
+
+  @XmlAttribute(name = "version", required = true)
+  protected int version;
+
+  @XmlAttribute(name = "precursor")
+  protected Boolean precursor;
+
+  @XmlAttribute(name = "fragment")
+  protected String fragment;
+
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
+
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
+
+  /**
+   * Gets the value of the length property.
+   * 
+   */
+  public int getLength()
+  {
+    return length;
+  }
+
+  /**
+   * Sets the value of the length property.
+   * 
+   */
+  public void setLength(int value)
+  {
+    this.length = value;
+  }
+
+  /**
+   * Gets the value of the mass property.
+   * 
+   */
+  public int getMass()
+  {
+    return mass;
+  }
+
+  /**
+   * Sets the value of the mass property.
+   * 
+   */
+  public void setMass(int value)
+  {
+    this.mass = value;
+  }
+
+  /**
+   * Gets the value of the checksum property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getChecksum()
+  {
+    return checksum;
+  }
+
+  /**
+   * Sets the value of the checksum property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setChecksum(String value)
+  {
+    this.checksum = value;
+  }
+
+  /**
+   * Gets the value of the modified property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getModified()
+  {
+    return modified;
+  }
+
+  /**
+   * Sets the value of the modified property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setModified(XMLGregorianCalendar value)
+  {
+    this.modified = value;
+  }
+
+  /**
+   * Gets the value of the version property.
+   * 
+   */
+  public int getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   */
+  public void setVersion(int value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the precursor property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isPrecursor()
+  {
+    return precursor;
+  }
+
+  /**
+   * Sets the value of the precursor property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setPrecursor(Boolean value)
+  {
+    this.precursor = value;
+  }
+
+  /**
+   * Gets the value of the fragment property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getFragment()
+  {
+    return fragment;
+  }
+
+  /**
+   * Sets the value of the fragment property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setFragment(String value)
+  {
+    this.fragment = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java
index 9796260..5fa8cd6 100644
--- a/src/jalview/xml/binding/uniprot/SourceDataType.java
+++ b/src/jalview/xml/binding/uniprot/SourceDataType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -18,14 +17,16 @@ import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
- * Describes the source of the sequence according to the citation.
- *             Equivalent to the flat file RC-line.
+ * Describes the source of the sequence according to the citation. Equivalent to
+ * the flat file RC-line.
  * 
- * <p>Java class for sourceDataType complex type.
+ * <p>
+ * Java class for sourceDataType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="sourceDataType">
@@ -77,385 +78,401 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceDataType", propOrder = {
-    "strainOrPlasmidOrTransposon"
-})
-public class SourceDataType {
-
-    @XmlElements({
-        @XmlElement(name = "strain", type = SourceDataType.Strain.class),
-        @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
-        @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
-        @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
-    })
-    protected List<Object> strainOrPlasmidOrTransposon;
+@XmlType(
+  name = "sourceDataType",
+  propOrder =
+  { "strainOrPlasmidOrTransposon" })
+public class SourceDataType
+{
+
+  @XmlElements({
+      @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+      @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+      @XmlElement(
+        name = "transposon",
+        type = SourceDataType.Transposon.class),
+      @XmlElement(name = "tissue", type = SourceDataType.Tissue.class) })
+  protected List<Object> strainOrPlasmidOrTransposon;
+
+  /**
+   * Gets the value of the strainOrPlasmidOrTransposon property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the strainOrPlasmidOrTransposon property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getStrainOrPlasmidOrTransposon().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link SourceDataType.Strain } {@link SourceDataType.Plasmid }
+   * {@link SourceDataType.Transposon } {@link SourceDataType.Tissue }
+   * 
+   * 
+   */
+  public List<Object> getStrainOrPlasmidOrTransposon()
+  {
+    if (strainOrPlasmidOrTransposon == null)
+    {
+      strainOrPlasmidOrTransposon = new ArrayList<Object>();
+    }
+    return this.strainOrPlasmidOrTransposon;
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;simpleContent>
+   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     &lt;/extension>
+   *   &lt;/simpleContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Plasmid
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getValue()
+    {
+      return value;
+    }
 
     /**
-     * Gets the value of the strainOrPlasmidOrTransposon property.
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setValue(String value)
+    {
+      this.value = value;
+    }
+
+    /**
+     * Gets the value of the evidence property.
      * 
      * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon 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
+     * <CODE>set</CODE> method for the evidence property.
      * 
      * <p>
      * For example, to add a new item, do as follows:
+     * 
      * <pre>
-     *    getStrainOrPlasmidOrTransposon().add(newItem);
+     * getEvidence().add(newItem);
      * </pre>
      * 
      * 
      * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link SourceDataType.Strain }
-     * {@link SourceDataType.Plasmid }
-     * {@link SourceDataType.Transposon }
-     * {@link SourceDataType.Tissue }
+     * Objects of the following type(s) are allowed in the list {@link Integer }
      * 
      * 
      */
-    public List<Object> getStrainOrPlasmidOrTransposon() {
-        if (strainOrPlasmidOrTransposon == null) {
-            strainOrPlasmidOrTransposon = new ArrayList<Object>();
-        }
-        return this.strainOrPlasmidOrTransposon;
+    public List<Integer> getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList<Integer>();
+      }
+      return this.evidence;
     }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;simpleContent>
+   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     &lt;/extension>
+   *   &lt;/simpleContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Strain
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the value property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;simpleContent>
-     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     &lt;/extension>
-     *   &lt;/simpleContent>
-     * &lt;/complexType>
-     * </pre>
+     */
+    public String getValue()
+    {
+      return value;
+    }
+
+    /**
+     * Sets the value of the value property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "value"
-    })
-    public static class Plasmid {
-
-        @XmlValue
-        protected String value;
-        @XmlAttribute(name = "evidence")
-        protected List<Integer> evidence;
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the evidence property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the evidence property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEvidence().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List<Integer> getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList<Integer>();
-            }
-            return this.evidence;
-        }
-
+    public void setValue(String value)
+    {
+      this.value = value;
     }
 
-
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the evidence property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;simpleContent>
-     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     &lt;/extension>
-     *   &lt;/simpleContent>
-     * &lt;/complexType>
+     * getEvidence().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "value"
-    })
-    public static class Strain {
-
-        @XmlValue
-        protected String value;
-        @XmlAttribute(name = "evidence")
-        protected List<Integer> evidence;
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the evidence property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the evidence property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEvidence().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List<Integer> getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList<Integer>();
-            }
-            return this.evidence;
-        }
+    public List<Integer> getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList<Integer>();
+      }
+      return this.evidence;
+    }
+
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;simpleContent>
+   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     &lt;/extension>
+   *   &lt;/simpleContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Tissue
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
 
+    /**
+     * 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;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the evidence property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;simpleContent>
-     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     &lt;/extension>
-     *   &lt;/simpleContent>
-     * &lt;/complexType>
+     * getEvidence().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "value"
-    })
-    public static class Tissue {
-
-        @XmlValue
-        protected String value;
-        @XmlAttribute(name = "evidence")
-        protected List<Integer> evidence;
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the evidence property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the evidence property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEvidence().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List<Integer> getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList<Integer>();
-            }
-            return this.evidence;
-        }
+    public List<Integer> getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList<Integer>();
+      }
+      return this.evidence;
+    }
 
+  }
+
+  /**
+   * <p>
+   * Java class for anonymous complex type.
+   * 
+   * <p>
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * <pre>
+   * &lt;complexType>
+   *   &lt;simpleContent>
+   *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+   *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     &lt;/extension>
+   *   &lt;/simpleContent>
+   * &lt;/complexType>
+   * </pre>
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Transposon
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List<Integer> evidence;
+
+    /**
+     * 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;
+    }
 
     /**
-     * <p>Java class for anonymous complex type.
+     * Gets the value of the evidence property.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * <p>
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * <CODE>set</CODE> method for the evidence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
      * 
      * <pre>
-     * &lt;complexType>
-     *   &lt;simpleContent>
-     *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *       &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     &lt;/extension>
-     *   &lt;/simpleContent>
-     * &lt;/complexType>
+     * getEvidence().add(newItem);
      * </pre>
      * 
      * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * 
+     * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "value"
-    })
-    public static class Transposon {
-
-        @XmlValue
-        protected String value;
-        @XmlAttribute(name = "evidence")
-        protected List<Integer> evidence;
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the evidence property.
-         * 
-         * <p>
-         * This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the evidence property.
-         * 
-         * <p>
-         * For example, to add a new item, do as follows:
-         * <pre>
-         *    getEvidence().add(newItem);
-         * </pre>
-         * 
-         * 
-         * <p>
-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List<Integer> getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList<Integer>();
-            }
-            return this.evidence;
-        }
-
+    public List<Integer> getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList<Integer>();
+      }
+      return this.evidence;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java
index 9293a64..4500112 100644
--- a/src/jalview/xml/binding/uniprot/SourceType.java
+++ b/src/jalview/xml/binding/uniprot/SourceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -14,13 +13,17 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
+ * Describes the source of the data using a database cross-reference (or a 'ref'
+ * attribute when the source cannot be found in a public data source, such as
+ * PubMed, and is cited only within the UniProtKB entry).
  * 
- * <p>Java class for sourceType complex type.
+ * <p>
+ * Java class for sourceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="sourceType">
@@ -38,61 +41,59 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceType", propOrder = {
-    "dbReference"
-})
-public class SourceType {
+@XmlType(name = "sourceType", propOrder = { "dbReference" })
+public class SourceType
+{
+
+  protected DbReferenceType dbReference;
 
-    protected DbReferenceType dbReference;
-    @XmlAttribute(name = "ref")
-    protected BigInteger ref;
+  @XmlAttribute(name = "ref")
+  protected BigInteger ref;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
 
-    /**
-     * Gets the value of the ref property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getRef() {
-        return ref;
-    }
+  /**
+   * Gets the value of the ref property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getRef()
+  {
+    return ref;
+  }
 
-    /**
-     * Sets the value of the ref property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setRef(BigInteger value) {
-        this.ref = value;
-    }
+  /**
+   * Sets the value of the ref property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setRef(BigInteger value)
+  {
+    this.ref = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java
index dd3308b..551c67a 100644
--- a/src/jalview/xml/binding/uniprot/StatusType.java
+++ b/src/jalview/xml/binding/uniprot/StatusType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,13 +13,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
  * Indicates whether the name of a plasmid is known or unknown.
  * 
- * <p>Java class for statusType complex type.
+ * <p>
+ * Java class for statusType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="statusType">
@@ -42,66 +43,67 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "statusType", propOrder = {
-    "value"
-})
-public class StatusType {
+@XmlType(name = "statusType", propOrder = { "value" })
+public class StatusType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "status")
-    protected String status;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "status")
+  protected String status;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Gets the value of the status property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getStatus() {
-        if (status == null) {
-            return "known";
-        } else {
-            return status;
-        }
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Sets the value of the status property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setStatus(String value) {
-        this.status = value;
+  /**
+   * Gets the value of the status property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getStatus()
+  {
+    if (status == null)
+    {
+      return "known";
+    }
+    else
+    {
+      return status;
     }
+  }
+
+  /**
+   * Sets the value of the status property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setStatus(String value)
+  {
+    this.status = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
index 97522e2..c9dbdf8 100644
--- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
+++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the subcellular location and optionally the topology and orientation of a molecule.
+ * Describes the subcellular location and optionally the topology and
+ * orientation of a molecule.
  * 
- * <p>Java class for subcellularLocationType complex type.
+ * <p>
+ * Java class for subcellularLocationType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType name="subcellularLocationType">
@@ -40,103 +42,114 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "subcellularLocationType", propOrder = {
-    "location",
-    "topology",
-    "orientation"
-})
-public class SubcellularLocationType {
+@XmlType(
+  name = "subcellularLocationType",
+  propOrder =
+  { "location", "topology", "orientation" })
+public class SubcellularLocationType
+{
+
+  @XmlElement(required = true)
+  protected List<EvidencedStringType> location;
+
+  protected List<EvidencedStringType> topology;
 
-    @XmlElement(required = true)
-    protected List<EvidencedStringType> location;
-    protected List<EvidencedStringType> topology;
-    protected List<EvidencedStringType> orientation;
+  protected List<EvidencedStringType> orientation;
 
-    /**
-     * Gets the value of the location property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the location property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getLocation().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
-     */
-    public List<EvidencedStringType> getLocation() {
-        if (location == null) {
-            location = new ArrayList<EvidencedStringType>();
-        }
-        return this.location;
+  /**
+   * Gets the value of the location property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the location property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getLocation().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List<EvidencedStringType> getLocation()
+  {
+    if (location == null)
+    {
+      location = new ArrayList<EvidencedStringType>();
     }
+    return this.location;
+  }
 
-    /**
-     * Gets the value of the topology property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the topology property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getTopology().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
-     */
-    public List<EvidencedStringType> getTopology() {
-        if (topology == null) {
-            topology = new ArrayList<EvidencedStringType>();
-        }
-        return this.topology;
+  /**
+   * Gets the value of the topology property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the topology property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getTopology().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List<EvidencedStringType> getTopology()
+  {
+    if (topology == null)
+    {
+      topology = new ArrayList<EvidencedStringType>();
     }
+    return this.topology;
+  }
 
-    /**
-     * Gets the value of the orientation property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the orientation property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getOrientation().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidencedStringType }
-     * 
-     * 
-     */
-    public List<EvidencedStringType> getOrientation() {
-        if (orientation == null) {
-            orientation = new ArrayList<EvidencedStringType>();
-        }
-        return this.orientation;
+  /**
+   * Gets the value of the orientation property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the orientation property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getOrientation().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List<EvidencedStringType> getOrientation()
+  {
+    if (orientation == null)
+    {
+      orientation = new ArrayList<EvidencedStringType>();
     }
+    return this.orientation;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java
index 14f96df..a2f8c6b 100644
--- a/src/jalview/xml/binding/uniprot/Uniprot.java
+++ b/src/jalview/xml/binding/uniprot/Uniprot.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * <pre>
  * &lt;complexType>
@@ -38,68 +39,68 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "entry",
-    "copyright"
-})
+@XmlType(name = "", propOrder = { "entry", "copyright" })
 @XmlRootElement(name = "uniprot")
-public class Uniprot {
+public class Uniprot
+{
 
-    @XmlElement(required = true)
-    protected List<Entry> entry;
-    protected String copyright;
+  @XmlElement(required = true)
+  protected List<Entry> entry;
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * <p>
-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the entry property.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
-     * <pre>
-     *    getEntry().add(newItem);
-     * </pre>
-     * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
-     * {@link Entry }
-     * 
-     * 
-     */
-    public List<Entry> getEntry() {
-        if (entry == null) {
-            entry = new ArrayList<Entry>();
-        }
-        return this.entry;
-    }
+  protected String copyright;
 
-    /**
-     * Gets the value of the copyright property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getCopyright() {
-        return copyright;
+  /**
+   * Gets the value of the entry property.
+   * 
+   * <p>
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+   * for the entry property.
+   * 
+   * <p>
+   * For example, to add a new item, do as follows:
+   * 
+   * <pre>
+   * getEntry().add(newItem);
+   * </pre>
+   * 
+   * 
+   * <p>
+   * Objects of the following type(s) are allowed in the list {@link Entry }
+   * 
+   * 
+   */
+  public List<Entry> getEntry()
+  {
+    if (entry == null)
+    {
+      entry = new ArrayList<Entry>();
     }
+    return this.entry;
+  }
 
-    /**
-     * Sets the value of the copyright property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setCopyright(String value) {
-        this.copyright = value;
-    }
+  /**
+   * Gets the value of the copyright property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getCopyright()
+  {
+    return copyright;
+  }
+
+  /**
+   * Sets the value of the copyright property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setCopyright(String value)
+  {
+    this.copyright = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java
index a7bc67c..0b60eaa 100644
--- a/src/jalview/xml/binding/uniprot/package-info.java
+++ b/src/jalview/xml/binding/uniprot/package-info.java
@@ -5,5 +5,7 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+  namespace = "http://uniprot.org/uniprot",
+  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.uniprot;
diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java
index 6d02630..5b209d0 100755
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -717,8 +717,8 @@ public class PDBChain
         // Useful for debugging mappings - adds annotation for mapped position
         float min = -1, max = 0;
         Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1];
-        for (int i = sq.getStart(), j = sq.getEnd(),
-                k = 0; i <= j; i++, k++)
+        for (int i = sq.getStart(), j = sq
+                .getEnd(), k = 0; i <= j; i++, k++)
         {
           int prn = mapping.getPDBResNum(k + 1);
 
diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 4baa384..c526fa1 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2630,7 +2630,8 @@ public class AlignmentUtilsTests
     assertNotNull(
             "No contact matrix recovered after reference annotation transfer",
             cl);
-    // semantics of sequence associated contact list is slightly tricky - column 3 in alignment should have data
+    // semantics of sequence associated contact list is slightly tricky - column
+    // 3 in alignment should have data
     cl = al.getContactListFor(alan, 3);
     assertNotNull(
             "Contact matrix should have data for last position in sequence",
diff --git a/test/jalview/analysis/AverageDistanceEngineTest.java b/test/jalview/analysis/AverageDistanceEngineTest.java
index 6d9ab50..f7688b5 100644
--- a/test/jalview/analysis/AverageDistanceEngineTest.java
+++ b/test/jalview/analysis/AverageDistanceEngineTest.java
@@ -32,66 +32,78 @@ import jalview.ws.datamodel.alphafold.PAEContactMatrix;
 public class AverageDistanceEngineTest
 {
 
-    @BeforeClass(alwaysRun = true)
-    public void setUpJvOptionPane()
+  @BeforeClass(alwaysRun = true)
+  public void setUpJvOptionPane()
+  {
+    JvOptionPane.setInteractiveMode(false);
+    JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+  }
+
+  @BeforeMethod(alwaysRun = true)
+  public void loadProperties()
+  {
+    Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
+  }
+
+  @Test
+  public void testUPGMAEngine() throws Exception
+  {
+    AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded(
+            "examples/test_fab41.result/sample.a3m", DataSourceType.FILE);
+    AlignmentI seqs = af.getViewport().getAlignment();
+    SequenceI target = seqs.getSequenceAt(0);
+    File testPAE = new File(
+            "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
+    List<Object> pae_obj = (List<Object>) Platform
+            .parseJSON(new FileInputStream(testPAE));
+    if (pae_obj == null)
     {
-      JvOptionPane.setInteractiveMode(false);
-      JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+      Assert.fail("JSON PAE file did not parse properly.");
     }
+    ContactMatrixI matrix = new PAEContactMatrix(target,
+            (Map<String, Object>) pae_obj.get(0));
+    AlignmentAnnotation aa = target.addContactList(matrix);
+    System.out.println("Matrix has max=" + matrix.getMax() + " and min="
+            + matrix.getMin());
+    long start = System.currentTimeMillis();
+    AverageDistanceEngine clusterer = new AverageDistanceEngine(
+            af.getViewport(), null, matrix);
+    System.out.println("built a tree in "
+            + (System.currentTimeMillis() - start) * 0.001 + " seconds.");
+    StringBuffer sb = new StringBuffer();
+    System.out.println("Newick string\n"
+            + new jalview.io.NewickFile(clusterer.getTopNode(), true, true)
+                    .print());
 
-    @BeforeMethod(alwaysRun = true)
-    public void loadProperties()
+    double height = clusterer.findHeight(clusterer.getTopNode());
+    // compute height fraction to cut
+    // PAE matrixes are absolute measure in angstrom, so
+    // cluster all regions within threshold (e.g. 2A) - if height above
+    // threshold. Otherwise all nodes are in one cluster
+    double thr = .2;
+    List<BinaryNode> groups;
+    if (height > thr)
     {
-      Cache.loadProperties("test/jalview/bin/TestProps.jvprops");
+      float cut = (float) (thr / height);
+      System.out.println("Threshold " + cut + " for height=" + height);
+      groups = clusterer.groupNodes(cut);
     }
-    @Test
-    public void testUPGMAEngine() throws Exception
+    else
     {
-      AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded("examples/test_fab41.result/sample.a3m",DataSourceType.FILE);
-      AlignmentI seqs = af.getViewport().getAlignment();
-      SequenceI target = seqs.getSequenceAt(0);
-      File testPAE = new File("examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json");
-      List<Object> pae_obj = (List<Object>) Platform.parseJSON(new FileInputStream(testPAE));
-      if (pae_obj == null)
-      {
-        Assert.fail("JSON PAE file did not parse properly.");
-      }
-      ContactMatrixI matrix = new PAEContactMatrix(target,
-              (Map<String, Object>) pae_obj.get(0));
-      AlignmentAnnotation aa = target.addContactList(matrix);
-      System.out.println("Matrix has max="+matrix.getMax()+" and min="+matrix.getMin());
-      long start = System.currentTimeMillis();
-      AverageDistanceEngine clusterer = new AverageDistanceEngine(af.getViewport(), null, matrix);
-      System.out.println("built a tree in "+(System.currentTimeMillis()-start)*0.001+" seconds.");
-      StringBuffer sb = new StringBuffer(); 
-      System.out.println("Newick string\n"+      new jalview.io.NewickFile(clusterer.getTopNode(),true,true).print());
-      
-      double height = clusterer.findHeight(clusterer.getTopNode());
-      // compute height fraction to cut 
-      // PAE matrixes are absolute measure in angstrom, so 
-      // cluster all regions within threshold (e.g. 2A) - if height above threshold. Otherwise all nodes are in one cluster
-      double thr=.2;
-      List<BinaryNode> groups;
-      if (height>thr)
-      {
-        float cut = (float) (thr/height);
-        System.out.println("Threshold "+cut+" for height="+height);
-        groups = clusterer.groupNodes(cut);
-      } else{
-        groups=new ArrayList<BinaryNode>();
-        groups.add(clusterer.getTopNode());
-      }
-      int n=1;
-      for (BinaryNode root:groups)
+      groups = new ArrayList<BinaryNode>();
+      groups.add(clusterer.getTopNode());
+    }
+    int n = 1;
+    for (BinaryNode root : groups)
+    {
+      System.out.println("Cluster " + n++);
+      for (BinaryNode leaf : clusterer.findLeaves(root))
       {
-        System.out.println("Cluster "+n++);
-        for (BinaryNode leaf:clusterer.findLeaves(root))
-        {
-          System.out.print(" "+leaf.getName());
-        }
-        System.out.println("\\");
+        System.out.print(" " + leaf.getName());
       }
-      
+      System.out.println("\\");
     }
 
+  }
+
 }
diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java
index 92db223..1c27420 100644
--- a/test/jalview/datamodel/AlignmentTest.java
+++ b/test/jalview/datamodel/AlignmentTest.java
@@ -1591,7 +1591,8 @@ public class AlignmentTest
     // ?
 
   }
-  @Test(groups = {"Functional"})
+
+  @Test(groups = { "Functional" })
   public void testEquals()
   {
     SequenceI seq1 = new Sequence("seq1", "ABCDEF--");
@@ -1599,6 +1600,6 @@ public class AlignmentTest
     SequenceI seq3 = new Sequence("seq2", "-PQR");
     AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 });
     a.setDataset(null);
-    assertEquals(a.getDataset(),a.getDataset());
+    assertEquals(a.getDataset(), a.getDataset());
   }
 }
diff --git a/test/jalview/datamodel/ContactRangeTest.java b/test/jalview/datamodel/ContactRangeTest.java
index 431834c..8bde11e 100644
--- a/test/jalview/datamodel/ContactRangeTest.java
+++ b/test/jalview/datamodel/ContactRangeTest.java
@@ -3,13 +3,14 @@ package jalview.datamodel;
 import org.testng.Assert;
 import org.testng.annotations.Test;
 
-public class ContactRangeTest {
+public class ContactRangeTest
+{
 
   @Test
   public void testContactRangeBean()
   {
     ContactRange cr = new ContactRange();
-    cr.update(5, 15, 6, 0.2, 12, 1.5,3.7);
+    cr.update(5, 15, 6, 0.2, 12, 1.5, 3.7);
     Assert.assertEquals(5, cr.getFrom_column());
     Assert.assertEquals(15, cr.getTo_column());
     Assert.assertEquals(6, cr.getMinPos());
diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java
index 2d7e3dc..c1896bc 100644
--- a/test/jalview/gui/AlignmentPanelTest.java
+++ b/test/jalview/gui/AlignmentPanelTest.java
@@ -291,41 +291,43 @@ public class AlignmentPanelTest
     Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
     assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
   }
- 
+
   @Test(groups = "Functional")
   public void testSetOverviewTitle()
   {
     OverviewPanel ov1 = this.af.openOverviewPanel(true);
     String alignFrameTitle = af.getTitle();
     assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
-    
+
     /*
      * on New View, existing overview should get " Original" added to title
      * and new view's overview should get " View 1" added
      */
     af.newView_actionPerformed(null);
-    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+    assertEquals(ov1.getTitle(),
+            "Overview " + alignFrameTitle + " Original");
     OverviewPanel ov2 = this.af.openOverviewPanel(true);
     assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
   }
-  
+
   @Test(groups = "Functional")
   public void testSetOverviewTitle_automaticOverview()
   {
-    Cache.setProperty("SHOW_OVERVIEW",  "true");
+    Cache.setProperty("SHOW_OVERVIEW", "true");
     AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded(
             "examples/uniref50.fa", DataSourceType.FILE);
     OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel();
     assertNotNull(ov1);
     String alignFrameTitle = alignFrame.getTitle();
     assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle);
-    
+
     /*
      * on New View, existing overview should get " Original" added to title
      * and new view's automatic overview should have " View 1" added
      */
     alignFrame.newView_actionPerformed(null);
-    assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original");
+    assertEquals(ov1.getTitle(),
+            "Overview " + alignFrameTitle + " Original");
     OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel();
     assertNotNull(ov2);
     assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1");
diff --git a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
index 16f4b7e..c21add1 100644
--- a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
+++ b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java
@@ -250,8 +250,7 @@ public class StructureChooserQuerySourceTest
   }
 
   @SuppressWarnings("deprecation")
-  @Test(groups =
-  { "Functional" })
+  @Test(groups = { "Functional" })
   public void buildPDBQueryTest()
   {
     System.out.println("seq >>>> " + seq);
@@ -299,8 +298,7 @@ public class StructureChooserQuerySourceTest
   }
 
   @SuppressWarnings("deprecation")
-  @Test(groups =
-  { "Functional" })
+  @Test(groups = { "Functional" })
   public void buildThreeDBQueryTest()
   {
     System.out.println("seq >>>> " + upSeq);
diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java
index 0189ef2..c46477a 100644
--- a/test/jalview/io/CrossRef2xmlTests.java
+++ b/test/jalview/io/CrossRef2xmlTests.java
@@ -418,7 +418,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     cra_views2.add(af2.getViewport().getAlignPanel());
                     cra_views2.add(((jalview.gui.AlignViewport) af2
                             .getViewport().getCodingComplement())
-                            .getAlignPanel());
+                                    .getAlignPanel());
 
                   }
                   else
@@ -426,7 +426,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase
                     // bottom view, then top
                     cra_views2.add(((jalview.gui.AlignViewport) af2
                             .getViewport().getCodingComplement())
-                            .getAlignPanel());
+                                    .getAlignPanel());
                     cra_views2.add(af2.getViewport().getAlignPanel());
                   }
                   Assert.assertEquals(cra_views2.size(), 2);
diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index 6b2982d..10f368a 100644
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -136,27 +136,30 @@ public class StockholmFileTest
             "Couldn't find Uniprot DBRef on re-imported sequence.");
 
   }
+
   @Test(groups = { "Functional" })
   public void descriptionLineOutput() throws Exception
   {
     // quick test that sequence description is exported & reimported
 
     SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF");
-    String expected_descr="This is a description !@&^%@£@";
+    String expected_descr = "This is a description !@&^%@£@";
     sq.setDescription(expected_descr);
     AppletFormatAdapter af = new AppletFormatAdapter();
     String toStockholm = af.formatSequences(FileFormat.Stockholm,
             new Alignment(new SequenceI[]
             { sq }), false);
     System.out.println(toStockholm);
-    
+
     // bleh - java.util.Regex sucks
-    assertTrue(toStockholm.contains(expected_descr),"Couldn't locate expected description srting in generated Stockholm file.");
-    
+    assertTrue(toStockholm.contains(expected_descr),
+            "Couldn't locate expected description srting in generated Stockholm file.");
+
     AlignmentI fromStockholm = af.readFile(toStockholm,
             DataSourceType.PASTE, FileFormat.Stockholm);
     SequenceI importedSeq = fromStockholm.getSequenceAt(0);
-    assertEquals( "Description did not get reimported.",expected_descr,importedSeq.getDescription());
+    assertEquals("Description did not get reimported.", expected_descr,
+            importedSeq.getDescription());
   }
 
   /**
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index af52eda..d74cd31 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -245,9 +245,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
 
     boolean diffseqcols = false, diffgseqcols = false;
     SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray();
-    for (int p = 0,
-            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
-                    && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0, pSize = af.getViewport().getAlignment()
+            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs
               .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f))
@@ -266,9 +265,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(__rcs.isSeqAssociated(),
             "Group Annotation colourscheme wasn't sequence associated");
 
-    for (int p = 0,
-            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
-                    && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0, pSize = af.getViewport().getAlignment()
+            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java
index cdb69e3..829eec5 100644
--- a/test/jalview/renderer/OverviewRendererTest.java
+++ b/test/jalview/renderer/OverviewRendererTest.java
@@ -47,8 +47,8 @@ public class OverviewRendererTest
   public void testGetColumnColourFromSequence()
   {
     // gapColour, residueColour, hiddenColour
-    OverviewResColourFinder cf = new OverviewResColourFinder(
-            Color.PINK, Color.white, Color.green); 
+    OverviewResColourFinder cf = new OverviewResColourFinder(Color.PINK,
+            Color.white, Color.green);
     Sequence seq1 = new Sequence("seq1", "PQ-RL-");
     Sequence seq2 = new Sequence("seq2", "FVE");
     AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 });
diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java
index 028777e..1c9daea 100644
--- a/test/jalview/renderer/OverviewResColourFinderTest.java
+++ b/test/jalview/renderer/OverviewResColourFinderTest.java
@@ -186,7 +186,8 @@ public class OverviewResColourFinderTest
             av.getResidueShading(), groups, seq, 2, null));
 
     // use legacy colouring
-    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+            Color.red);
 
     // G in group specified as magenta in Zappo
     assertEquals(Color.magenta, rcf.getResidueColour(false,
@@ -237,7 +238,8 @@ public class OverviewResColourFinderTest
     assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c);
 
     // legacy colouring set explicitly via constructor
-    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+            Color.red);
     shader = new ResidueShader();
 
     // residues light gray
@@ -273,7 +275,8 @@ public class OverviewResColourFinderTest
     assertEquals(Color.blue, c);
 
     // legacy colouring with colour scheme
-    rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red);
+    rcf = new OverviewResColourFinder(Color.white, Color.lightGray,
+            Color.red);
 
     // M residue pink
     c = rcf.getBoxColour(shader, seq, 0);
diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
index 637bbf4..3d8313d 100644
--- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
+++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java
@@ -169,7 +169,8 @@ public class FeatureColourFinderTest
   @Test(groups = "Functional")
   public void testFindFeatureColour_nestedFeatures()
   {
-    SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120, 0f, null);
+    SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120,
+            0f, null);
     seq.addSequenceFeature(sf1);
     SequenceFeature sf2 = new SequenceFeature("domain", "binding", 10, 20,
             0f, null);
-- 
1.7.10.2