From 80b889f0cca49103e1b20ed806755a0719789906 Mon Sep 17 00:00:00 2001 From: James Procter Date: Fri, 19 May 2023 17:11:26 +0100 Subject: [PATCH] JAL-1551 spotlessApply --- src/jalview/analysis/AlignmentSorter.java | 4 +- src/jalview/analysis/AlignmentUtils.java | 94 +- src/jalview/analysis/AnnotationSorter.java | 19 +- src/jalview/analysis/AverageDistanceEngine.java | 2 +- src/jalview/analysis/TreeModel.java | 9 +- src/jalview/api/AlignViewportI.java | 10 +- src/jalview/appletgui/TreeCanvas.java | 13 +- src/jalview/bin/Cache.java | 9 +- src/jalview/datamodel/Alignment.java | 8 +- src/jalview/datamodel/AlignmentAnnotation.java | 12 +- src/jalview/datamodel/BinaryNode.java | 5 +- src/jalview/datamodel/ColumnSelection.java | 22 +- src/jalview/datamodel/ContactListI.java | 3 +- src/jalview/datamodel/ContactListImpl.java | 4 +- src/jalview/datamodel/ContactListProviderI.java | 14 +- src/jalview/datamodel/ContactMapHolder.java | 5 +- src/jalview/datamodel/ContactMatrix.java | 42 +- src/jalview/datamodel/ContactMatrixI.java | 57 +- src/jalview/datamodel/ContactRange.java | 5 +- src/jalview/datamodel/GroupSet.java | 20 +- .../datamodel/SeqDistanceContactMatrix.java | 11 +- src/jalview/datamodel/Sequence.java | 5 +- src/jalview/datamodel/SequenceNode.java | 12 +- .../annotations/AnnotationRowBuilder.java | 3 +- src/jalview/gui/AlignFrame.java | 68 +- src/jalview/gui/AlignViewport.java | 2 +- src/jalview/gui/AlignmentPanel.java | 5 +- src/jalview/gui/AnnotationLabels.java | 12 +- src/jalview/gui/AnnotationPanel.java | 78 +- src/jalview/gui/Desktop.java | 38 +- src/jalview/gui/OverviewCanvas.java | 5 +- src/jalview/gui/QuitHandler.java | 3 +- src/jalview/gui/StructureChooser.java | 13 +- src/jalview/gui/TreeCanvas.java | 118 +- src/jalview/gui/TreePanel.java | 14 +- src/jalview/gui/WebserviceInfo.java | 4 +- src/jalview/io/FileParse.java | 4 +- src/jalview/io/NewickFile.java | 19 +- src/jalview/io/PContactPredictionFile.java | 20 +- src/jalview/io/StockholmFile.java | 5 +- src/jalview/io/vamsas/Tree.java | 5 +- src/jalview/jbgui/GStructureChooser.java | 18 +- src/jalview/project/Jalview2XML.java | 99 +- src/jalview/renderer/AnnotationRenderer.java | 14 +- .../renderer/AnnotationRendererFactory.java | 8 +- src/jalview/renderer/ContactGeometry.java | 16 +- src/jalview/renderer/ContactMapRenderer.java | 39 +- src/jalview/renderer/OverviewResColourFinder.java | 1 + .../renderer/api/AnnotationRowRendererI.java | 7 +- .../renderer/seqfeatures/FeatureRenderer.java | 2 +- .../structures/models/AAStructureBindingModel.java | 2 +- src/jalview/viewmodel/AlignmentViewport.java | 1 - .../ws/datamodel/MappableContactMatrixI.java | 31 +- .../datamodel/alphafold/MappableContactMatrix.java | 118 +- .../ws/datamodel/alphafold/PAEContactMatrix.java | 103 +- src/jalview/ws/dbsources/EBIAlfaFold.java | 2 +- 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 | 585 +- 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 | 7 +- test/jalview/analysis/AlignmentUtilsTests.java | 75 +- .../analysis/AverageDistanceEngineTest.java | 116 +- test/jalview/datamodel/AlignmentTest.java | 5 +- test/jalview/datamodel/ContactRangeTest.java | 5 +- test/jalview/datamodel/PAEContactMatrixTest.java | 200 +- test/jalview/gui/AlignmentPanelTest.java | 16 +- test/jalview/gui/SeqPanelTest.java | 2 +- .../StructureChooserQuerySourceTest.java | 6 +- test/jalview/project/Jalview2xmlTests.java | 60 +- test/jalview/renderer/OverviewRendererTest.java | 4 +- .../renderer/OverviewResColourFinderTest.java | 9 +- .../seqfeatures/FeatureColourFinderTest.java | 3 +- 139 files changed, 21694 insertions(+), 20653 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 0fdabc8..1158c53 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 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) { @@ -1503,7 +1504,8 @@ public class AlignmentUtils /** * Adds annotations to the top of the alignment annotations, in the same order - * as their related sequences. If you already have an annotation and want to add it to a sequence in an alignment use {@code addReferenceAnnotationTo} + * as their related sequences. If you already have an annotation and want to + * add it to a sequence in an alignment use {@code addReferenceAnnotationTo} * * @param annotations * the annotations to add @@ -1520,52 +1522,60 @@ public class AlignmentUtils { for (AlignmentAnnotation ann : annotations.get(seq)) { - addReferenceAnnotationTo(alignment, seq,ann,selectionGroup); + addReferenceAnnotationTo(alignment, seq, ann, selectionGroup); } } } + /** - * Make a copy of a reference annotation {@code ann} and add it to an alignment sequence {@code seq} in {@code alignment}, optionally limited to the extent of {@code selectionGroup} + * Make a copy of a reference annotation {@code ann} and add it to an + * alignment sequence {@code seq} in {@code alignment}, optionally limited to + * the extent of {@code selectionGroup} + * * @param alignment * @param seq * @param ann - * @param selectionGroup - may be null + * @param selectionGroup + * - may be null * @return annotation added to {@code seq and {@code alignment} */ - public static AlignmentAnnotation addReferenceAnnotationTo(final AlignmentI alignment, final SequenceI seq,final AlignmentAnnotation ann,final SequenceGroup selectionGroup) + public static AlignmentAnnotation addReferenceAnnotationTo( + final AlignmentI alignment, final SequenceI seq, + final AlignmentAnnotation ann, final SequenceGroup selectionGroup) { - AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); - int startRes = 0; - int endRes = ann.annotations.length; - if (selectionGroup != null) - { - startRes = -1+Math.min(seq.getEnd(), Math.max(seq.getStart(),seq.findPosition(selectionGroup.getStartRes()))); - endRes = -1+Math.min(seq.getEnd(),seq.findPosition(selectionGroup.getEndRes())); - - } - copyAnn.restrict(startRes, endRes + 0); + AlignmentAnnotation copyAnn = new AlignmentAnnotation(ann); + int startRes = 0; + int endRes = ann.annotations.length; + if (selectionGroup != null) + { + startRes = -1 + Math.min(seq.getEnd(), Math.max(seq.getStart(), + seq.findPosition(selectionGroup.getStartRes()))); + endRes = -1 + Math.min(seq.getEnd(), + seq.findPosition(selectionGroup.getEndRes())); - /* - * Add to the sequence (sets copyAnn.datasetSequence), unless the - * original annotation is already on the sequence. - */ - if (!seq.hasAnnotation(ann)) - { - ContactMatrixI cm = seq.getDatasetSequence() - .getContactMatrixFor(ann); - if (cm != null) - { - seq.addContactListFor(copyAnn, cm); - } - seq.addAlignmentAnnotation(copyAnn); - } - // adjust for gaps - copyAnn.adjustForAlignment(); - // add to the alignment and set visible - alignment.addAnnotation(copyAnn); - copyAnn.visible = true; - - return copyAnn; + } + copyAnn.restrict(startRes, endRes + 0); + + /* + * Add to the sequence (sets copyAnn.datasetSequence), unless the + * original annotation is already on the sequence. + */ + if (!seq.hasAnnotation(ann)) + { + ContactMatrixI cm = seq.getDatasetSequence().getContactMatrixFor(ann); + if (cm != null) + { + seq.addContactListFor(copyAnn, cm); + } + seq.addAlignmentAnnotation(copyAnn); + } + // adjust for gaps + copyAnn.adjustForAlignment(); + // add to the alignment and set visible + alignment.addAnnotation(copyAnn); + copyAnn.visible = true; + + return copyAnn; } /** 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/AverageDistanceEngine.java b/src/jalview/analysis/AverageDistanceEngine.java index c52c7be..20b3e83 100644 --- a/src/jalview/analysis/AverageDistanceEngine.java +++ b/src/jalview/analysis/AverageDistanceEngine.java @@ -105,7 +105,7 @@ public class AverageDistanceEngine extends TreeEngine { distances.setValue(i, i, 0); ContactListI jth = cm.getContactList(j); - if (jth==null) + if (jth == null) { break; } diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java index ad3e88c..0e57a58 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 findLeaves(BinaryNode nd, - Vector leaves) + Vector findLeaves(BinaryNode nd, Vector leaves) { if (nd == null) { diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index e3478ea..0cfd03d 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -478,9 +478,13 @@ public interface AlignViewportI extends ViewStyleI SearchResultsI getSearchResults(); /** - * Retrieve a ContactListI corresponding to column in an annotation row in an alignment. - * @param _aa - annotation with associated matrix data - * @param column - column in alignment where _aa is associated + * Retrieve a ContactListI corresponding to column in an annotation row in an + * alignment. + * + * @param _aa + * - annotation with associated matrix data + * @param column + * - column in alignment where _aa is associated */ ContactListI getContactList(AlignmentAnnotation _aa, int column); 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 698cbb8..4891451 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1420,11 +1420,10 @@ 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 89ec5ad..514a326 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); @@ -2087,7 +2087,7 @@ public class Alignment implements AlignmentI, AutoCloseable && spos <= 1 + _aa.sequenceRef.getEnd()) { cl = _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, - spos-_aa.sequenceRef.getStart()); + 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/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java index 0ab69ea..624c2b9 100755 --- a/src/jalview/datamodel/BinaryNode.java +++ b/src/jalview/datamodel/BinaryNode.java @@ -58,7 +58,10 @@ public class BinaryNode /** DOCUMENT ME!! */ public Color color = Color.black; - /** if true, node is created to simulate polytomy between parent and its 3 or more children */ + /** + * if true, node is created to simulate polytomy between parent and its 3 or + * more children + */ public boolean dummy = false; /** diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 4882597..4a38ec0 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -278,22 +278,26 @@ public class ColumnSelection } /** - * add a series of start,end (inclusive) ranges to the column selection - * @param rng [start_0, end_0, start_1, end_1, ... ] - * @param baseOne - when true, ranges are base 1 and will be mapped to base 0 + * add a series of start,end (inclusive) ranges to the column selection + * + * @param rng + * [start_0, end_0, start_1, end_1, ... ] + * @param baseOne + * - when true, ranges are base 1 and will be mapped to base 0 */ - public void addRangeOfElements(int[] rng,boolean baseOne) + public void addRangeOfElements(int[] rng, boolean baseOne) { - int base=baseOne ? -1 : 0; + int base = baseOne ? -1 : 0; for (int c = 0; c < rng.length; c += 2) { for (int p = rng[c]; p <= rng[c + 1]; p++) { - selection.add(base+p); + selection.add(base + p); } } - + } + /** * clears column selection */ @@ -603,8 +607,8 @@ 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/ContactListI.java b/src/jalview/datamodel/ContactListI.java index d0544b8..da55403 100644 --- a/src/jalview/datamodel/ContactListI.java +++ b/src/jalview/datamodel/ContactListI.java @@ -16,7 +16,8 @@ public interface ContactListI extends ContactListProviderI */ ContactRange getRangeFor(int from_column, int to_column); - default Color getColourForGroup() { + default Color getColourForGroup() + { return null; } } diff --git a/src/jalview/datamodel/ContactListImpl.java b/src/jalview/datamodel/ContactListImpl.java index bde13ff..69dcf71 100644 --- a/src/jalview/datamodel/ContactListImpl.java +++ b/src/jalview/datamodel/ContactListImpl.java @@ -98,11 +98,13 @@ public class ContactListImpl implements ContactListI } return cr; } + @Override public int[] getMappedPositionsFor(int cStart, int cEnd) { - return clist.getMappedPositionsFor(cStart, cEnd); + return clist.getMappedPositionsFor(cStart, cEnd); } + @Override public Color getColourForGroup() { diff --git a/src/jalview/datamodel/ContactListProviderI.java b/src/jalview/datamodel/ContactListProviderI.java index 51f3126..d6e9ba9 100644 --- a/src/jalview/datamodel/ContactListProviderI.java +++ b/src/jalview/datamodel/ContactListProviderI.java @@ -28,18 +28,22 @@ public interface ContactListProviderI */ double getContactAt(int column); - /** - * Return positions in local reference corresponding to cStart and cEnd in matrix data. Positions are base 1 column indices for sequence associated matrices. + * Return positions in local reference corresponding to cStart and cEnd in + * matrix data. Positions are base 1 column indices for sequence associated + * matrices. + * * @param cStart * @param cEnd * @return int[] { start, end (inclusive) for each contiguous segment} */ - default int[] getMappedPositionsFor(int cStart, int cEnd) { - return new int[] { cStart, cEnd}; + default int[] getMappedPositionsFor(int cStart, int cEnd) + { + return new int[] { cStart, cEnd }; } - default Color getColourForGroup() { + default Color getColourForGroup() + { return null; } diff --git a/src/jalview/datamodel/ContactMapHolder.java b/src/jalview/datamodel/ContactMapHolder.java index d80a719..af083dd 100644 --- a/src/jalview/datamodel/ContactMapHolder.java +++ b/src/jalview/datamodel/ContactMapHolder.java @@ -32,9 +32,10 @@ public class ContactMapHolder implements ContactMapHolderI } if (cm instanceof MappableContactMatrixI) { - if (_aa.sequenceRef!=null) + if (_aa.sequenceRef != null) { - return ((MappableContactMatrixI)cm).getMappableContactList(_aa.sequenceRef, column); + return ((MappableContactMatrixI) cm) + .getMappableContactList(_aa.sequenceRef, column); } } // TODO: could resolve sequence position to column position here diff --git a/src/jalview/datamodel/ContactMatrix.java b/src/jalview/datamodel/ContactMatrix.java index 8f0afdf..bbc5100 100644 --- a/src/jalview/datamodel/ContactMatrix.java +++ b/src/jalview/datamodel/ContactMatrix.java @@ -160,12 +160,15 @@ public abstract class ContactMatrix implements ContactMatrixI { return "Contact Matrix"; } + GroupSet grps = new GroupSet(); + @Override public GroupSetI getGroupSet() { return grps; } + @Override public void setGroupSet(GroupSet makeGroups) { @@ -175,17 +178,19 @@ public abstract class ContactMatrix implements ContactMatrixI public static String contactToFloatString(ContactMatrixI cm) { StringBuilder sb = new StringBuilder(); - for (int c=0;c0) { - sb.append('\t'); + for (int h = 0; h <= cl.getContactHeight(); h++) + { + if (sb.length() > 0) + { + sb.append('\t'); + } + sb.append(cl.getContactAt(h)); } - sb.append(cl.getContactAt(h)); - } } } return sb.toString(); @@ -195,29 +200,30 @@ public abstract class ContactMatrix implements ContactMatrixI int rows) { float[][] vals = new float[cols][rows]; - StringTokenizer tabsep = new StringTokenizer(values,""+'\t'); - int c=0,r=0; - + StringTokenizer tabsep = new StringTokenizer(values, "" + '\t'); + int c = 0, r = 0; + while (tabsep.hasMoreTokens()) { double elem = Double.valueOf(tabsep.nextToken()); - vals[c][r++]=(float) elem; - if (r>=vals[c].length) + vals[c][r++] = (float) elem; + if (r >= vals[c].length) { - r=0; + r = 0; c++; } - if (c>=vals.length) + if (c >= vals.length) { - + break; } } if (tabsep.hasMoreElements()) { - Console.warn("Ignoring additional elements for Float string to contact matrix parsing."); + Console.warn( + "Ignoring additional elements for Float string to contact matrix parsing."); } - + return vals; } } diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java index 256d43d..546e979 100644 --- a/src/jalview/datamodel/ContactMatrixI.java +++ b/src/jalview/datamodel/ContactMatrixI.java @@ -19,69 +19,80 @@ public interface ContactMatrixI String getAnnotLabel(); /** - * string indicating how the contactMatrix should be rendered - stored in calcId - * @return + * string indicating how the contactMatrix should be rendered - stored in + * calcId + * + * @return */ String getType(); int getWidth(); + int getHeight(); - + public GroupSetI getGroupSet(); - + /// proxy methods to simplify use of the interface /// Mappable contact matrices can override these to perform mapping - + default public boolean hasGroupSet() { - return getGroupSet()!=null; + return getGroupSet() != null; } - default boolean hasGroups() { + default boolean hasGroups() + { return hasGroupSet() && getGroupSet().hasGroups(); } - - default BitSet getGroupsFor(int column) { + default BitSet getGroupsFor(int column) + { if (!hasGroupSet()) { - BitSet colbitset = new BitSet(); - colbitset.set(column); - return colbitset; + BitSet colbitset = new BitSet(); + colbitset.set(column); + return colbitset; } return getGroupSet().getGroupsFor(column); } - default List getGroups() { + default List getGroups() + { if (!hasGroupSet()) { - return Arrays.asList(); - } + return Arrays.asList(); + } return getGroupSet().getGroups(); } - default boolean hasTree() { + default boolean hasTree() + { return hasGroupSet() ? getGroupSet().hasTree() : false; } /** * Newick representation of clustered matrix + * * @return null unless hasTree is true */ - default String getNewick() { - return hasGroupSet() ? getGroupSet().getNewick(): null; + default String getNewick() + { + return hasGroupSet() ? getGroupSet().getNewick() : null; } - default String getTreeMethod() { - return hasGroupSet() ? getGroupSet().getTreeMethod() :null; + default String getTreeMethod() + { + return hasGroupSet() ? getGroupSet().getTreeMethod() : null; } - default boolean hasCutHeight() { + default boolean hasCutHeight() + { return hasGroupSet() ? getGroupSet().hasCutHeight() : false; } - default double getCutHeight() { - return hasGroupSet() ? getGroupSet().getCutHeight():0; + default double getCutHeight() + { + return hasGroupSet() ? getGroupSet().getCutHeight() : 0; } default void updateGroups(List colGroups) 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/GroupSet.java b/src/jalview/datamodel/GroupSet.java index b4d3e64..c7a73b7 100644 --- a/src/jalview/datamodel/GroupSet.java +++ b/src/jalview/datamodel/GroupSet.java @@ -16,12 +16,12 @@ public class GroupSet implements GroupSetI public GroupSet(GroupSet grps) { - abs=grps.abs; - colorMap=new HashMap(grps.colorMap); - groups=new ArrayList(grps.groups); - newick=grps.newick; - thresh=grps.thresh; - treeType=grps.treeType; + abs = grps.abs; + colorMap = new HashMap(grps.colorMap); + groups = new ArrayList(grps.groups); + newick = grps.newick; + thresh = grps.thresh; + treeType = grps.treeType; } public GroupSet() @@ -36,7 +36,7 @@ public class GroupSet implements GroupSetI thresh = thresh2; groups = groups2; treeType = treeType2; - newick=newick2; + newick = newick2; } @Override @@ -59,9 +59,9 @@ public class GroupSet implements GroupSetI return newick != null && newick.length() > 0; } - boolean abs=false; + boolean abs = false; - double thresh=0; + double thresh = 0; String treeType = null; @@ -179,7 +179,7 @@ public class GroupSet implements GroupSetI } groups.add(gpset); } - GroupSet grps = new GroupSet(abs,thresh,groups,treeType, newick); + GroupSet grps = new GroupSet(abs, thresh, groups, treeType, newick); return grps; } diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java index ec19b25..89daeb2 100644 --- a/src/jalview/datamodel/SeqDistanceContactMatrix.java +++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java @@ -14,9 +14,12 @@ import jalview.ws.datamodel.alphafold.MappableContactMatrix; * @author jprocter * */ -public class SeqDistanceContactMatrix extends MappableContactMatrix implements ContactMatrixI +public class SeqDistanceContactMatrix + extends MappableContactMatrix + implements ContactMatrixI { private static final String SEQUENCE_DISTANCE = "SEQUENCE_DISTANCE"; + private int width = 0; public SeqDistanceContactMatrix(int width) @@ -82,6 +85,7 @@ public class SeqDistanceContactMatrix extends MappableContactMatrix super(); } - public SequenceNode(SequenceI val, BinaryNode parent, String name, - double dist, int bootstrap, boolean dummy) + public SequenceNode(SequenceI val, BinaryNode parent, + String name, double dist, int bootstrap, boolean dummy) { super(val, parent, name, dist, bootstrap, dummy); } - public SequenceNode(SequenceI element, BinaryNode parent, String name, - double dist, int bootstrap) + public SequenceNode(SequenceI element, BinaryNode parent, + String name, double dist, int bootstrap) { super(element, parent, name, dist, bootstrap); } - public SequenceNode(SequenceI element, BinaryNode parent, String name, - double dist) + public SequenceNode(SequenceI element, BinaryNode parent, + String name, double dist) { super(element, parent, name, dist); } diff --git a/src/jalview/datamodel/annotations/AnnotationRowBuilder.java b/src/jalview/datamodel/annotations/AnnotationRowBuilder.java index b3d567a..c9b8f18 100644 --- a/src/jalview/datamodel/annotations/AnnotationRowBuilder.java +++ b/src/jalview/datamodel/annotations/AnnotationRowBuilder.java @@ -97,7 +97,8 @@ public class AnnotationRowBuilder name = string; } - public AnnotationRowBuilder(String name, float min, float max, StructureImportSettings.TFType tft) + public AnnotationRowBuilder(String name, float min, float max, + StructureImportSettings.TFType tft) { this(name, min, max); setTFType(tft); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 2d02e79..06298ba 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -3440,8 +3440,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, @Override public void overviewMenuItem_actionPerformed(ActionEvent e) { - boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, - false); + boolean showHiddenRegions = Cache + .getDefault(Preferences.SHOW_OV_HIDDEN_AT_START, false); openOverviewPanel(showHiddenRegions); } @@ -3452,14 +3452,15 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return alignPanel.overviewPanel; } JInternalFrame frame = new JInternalFrame(); - final OverviewPanel overview = new OverviewPanel(alignPanel, frame, showHidden); + final OverviewPanel overview = new OverviewPanel(alignPanel, frame, + showHidden); frame.setContentPane(overview); - Desktop.addInternalFrame(frame, "", true, frame.getWidth(), frame.getHeight(), - true, true); + Desktop.addInternalFrame(frame, "", true, frame.getWidth(), + frame.getHeight(), true, true); frame.setFrameIcon(null); frame.pack(); frame.setLayer(JLayeredPane.PALETTE_LAYER); - final AlignmentPanel thePanel = this.alignPanel; + final AlignmentPanel thePanel = this.alignPanel; frame.addInternalFrameListener( new javax.swing.event.InternalFrameAdapter() { @@ -3478,7 +3479,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, alignPanel.setOverviewPanel(overview); alignPanel.setOverviewTitle(this); - + return overview; } @@ -4133,7 +4134,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return showNewickTree(nf, treeTitle, null, w, h, x, y); } - /** * Add a treeviewer for the tree extracted from a Newick file object to the * current alignment view @@ -4184,13 +4184,12 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - public void showContactMapTree(AlignmentAnnotation aa, PAEContactMatrix cm) { int x = 4, y = 5; int w = 400, h = 500; - + try { NewickFile fin = new NewickFile( @@ -4198,42 +4197,43 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, String title = "PAE Matrix Tree for " + cm.getReferenceSeq().getDisplayId(false); - showColumnWiseTree(fin, aa, title, w,h, x,y); + showColumnWiseTree(fin, aa, title, w, h, x, y); } catch (Throwable xx) { Console.error("Unexpected exception showing tree for contact matrix", xx); } } - public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, String treeTitle, - int w, int h, int x, int y) + + public TreePanel showColumnWiseTree(NewickFile nf, AlignmentAnnotation aa, + String treeTitle, int w, int h, int x, int y) { - try + try + { + nf.parse(); + if (nf.getTree() == null) { - nf.parse(); - if (nf.getTree() == null) - { - return null; - } - TreePanel tp = new TreePanel(alignPanel, nf, aa, title); - - tp.setSize(w, h); + return null; + } + TreePanel tp = new TreePanel(alignPanel, nf, aa, title); - if (x > 0 && y > 0) - { - tp.setLocation(x, y); - } + tp.setSize(w, h); - Desktop.addInternalFrame(tp, title, w, h); - return tp; - } catch (Throwable xx) + if (x > 0 && y > 0) { - Console.error("Unexpected exception showing tree for contact matrix", - xx); + tp.setLocation(x, y); } - return null; + + Desktop.addInternalFrame(tp, title, w, h); + return tp; + } catch (Throwable xx) + { + Console.error("Unexpected exception showing tree for contact matrix", + xx); + } + return null; } - + private boolean buildingMenu = false; /** @@ -5027,7 +5027,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, * to add view name "Original" if necessary */ alignPanel.setOverviewTitle(this); - + /* * switch panels and set Overview title (if there is one * because it was opened automatically) diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 90f627e..fea74db 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -340,7 +340,7 @@ public class AlignViewport extends AlignmentViewport viewStyle.setFontName(font.getName()); viewStyle.setFontStyle(font.getStyle()); viewStyle.setFontSize(font.getSize()); - + validCharWidth = true; } diff --git a/src/jalview/gui/AlignmentPanel.java b/src/jalview/gui/AlignmentPanel.java index 2d057bb..8aa9997 100644 --- a/src/jalview/gui/AlignmentPanel.java +++ b/src/jalview/gui/AlignmentPanel.java @@ -229,8 +229,9 @@ public class AlignmentPanel extends GAlignmentPanel implements // set idCanvas bufferedImage to null // to prevent drawing old image FontMetrics fm = getFontMetrics(av.getFont()); - - // update the flag controlling whether the grid is too small to render the font + + // update the flag controlling whether the grid is too small to render the + // font av.validCharWidth = fm.charWidth('M') <= av.getCharWidth(); scalePanelHolder.setPreferredSize( diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index d781ebb..0a9d35f 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -422,13 +422,13 @@ 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.hasTree()) + if (cm != null && cm.hasTree()) { item = new JMenuItem("Show Tree for Matrix"); item.addActionListener(new ActionListener() @@ -438,7 +438,7 @@ public class AnnotationLabels extends JPanel public void actionPerformed(ActionEvent e) { - ap.alignFrame.showContactMapTree(aa[selectedRow],cm); + ap.alignFrame.showContactMapTree(aa[selectedRow], cm); } }); @@ -1123,7 +1123,8 @@ public class AnnotationLabels extends JPanel } olY = y; // look ahead to next annotation - for (nexAA=i+1; nexAAMean:" + cr.getMean(); - + int col = ann.sequenceRef.findPosition(column); int[][] highlightPos; int[] mappedPos = clist.getMappedPositionsFor(ci.cStart, ci.cEnd); diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index 1521d0a..d5584b6 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -808,7 +808,7 @@ public class Desktop extends jalview.jbgui.GDesktop // TODO - write tests and fix AlignFrame.paste() which doesn't track if // clipboard has come from a different alignment window than the one where // paste has been called! JAL-4151 - + if (Desktop.jalviewClipboard != null) { // The clipboard was filled from within Jalview, we must use the @@ -835,30 +835,32 @@ public class Desktop extends jalview.jbgui.GDesktop } Desktop.addInternalFrame(af, newtitle, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + AlignFrame.DEFAULT_HEIGHT); - } else { - try + } + else { - Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); - Transferable contents = c.getContents(this); - - if (contents != null) + try { - String file = (String) contents - .getTransferData(DataFlavor.stringFlavor); + Clipboard c = Toolkit.getDefaultToolkit().getSystemClipboard(); + Transferable contents = c.getContents(this); - FileFormatI format = new IdentifyFile().identify(file, - DataSourceType.PASTE); + if (contents != null) + { + String file = (String) contents + .getTransferData(DataFlavor.stringFlavor); - new FileLoader().LoadFile(file, DataSourceType.PASTE, format); + FileFormatI format = new IdentifyFile().identify(file, + DataSourceType.PASTE); + new FileLoader().LoadFile(file, DataSourceType.PASTE, format); + + } + } catch (Exception ex) + { + System.out.println( + "Unable to paste alignment from system clipboard:\n" + ex); } - } catch (Exception ex) - { - System.out.println( - "Unable to paste alignment from system clipboard:\n" + ex); - } } } 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/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 5cd339b..4ecde85 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -736,16 +736,18 @@ public class StructureChooser extends GStructureChooser if (value == JalviewFileChooser.APPROVE_OPTION) { String fileName = chooser.getSelectedFile().getPath(); - try { + try + { PAEContactMatrix.validateContactMatrixFile(fileName); } catch (Exception thr) { JvOptionPane.showInternalMessageDialog(this, MessageManager .formatMessage("label.couldnt_load_file", new Object[] - { fileName})+"
"+thr.getLocalizedMessage(), + { fileName }) + "
" + thr.getLocalizedMessage(), MessageManager.getString("label.error_loading_file"), JvOptionPane.WARNING_MESSAGE); - Console.error("Couldn't import "+fileName+" as a PAE matrix",thr); + Console.error("Couldn't import " + fileName + " as a PAE matrix", + thr); return; } localPdbPaeMatrixFileName = fileName; @@ -1205,8 +1207,9 @@ public class StructureChooser extends GStructureChooser btn_newView.setEnabled(false); btn_cancel.setEnabled(false); actionsPanel.setEnabled(false); - - final String progress=MessageManager.getString("label.working_ellipsis"); + + final String progress = MessageManager + .getString("label.working_ellipsis"); setProgressBar(progress, progress.hashCode()); Runnable viewStruc = new Runnable() { diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 9463634..b331e60 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -191,7 +191,7 @@ 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; } @@ -287,9 +287,10 @@ 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(); @@ -356,8 +357,7 @@ 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); @@ -828,14 +828,17 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, else { Vector 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(); } @@ -1000,7 +1003,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { AlignmentPanel[] aps = getAssociatedPanels(); List colGroups = new ArrayList<>(); - Map colors=new HashMap(); + Map colors = new HashMap(); for (int i = 0; i < groups.size(); i++) { Color col = new Color((int) (Math.random() * 255), @@ -1008,10 +1011,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector 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); @@ -1020,40 +1026,45 @@ 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)); } } // stash colors in linked annotation row. // doesn't work yet. TESTS! - int sstart=aa.sequenceRef!=null ? aa.sequenceRef.getStart()-1 : 0; + int sstart = aa.sequenceRef != null ? aa.sequenceRef.getStart() - 1 + : 0; Annotation ae; Color gpcol = null; - int[] seqpos=null; + int[] seqpos = null; for (BitSet gp : colors.keySet()) { gpcol = colors.get(gp); - for (int p = gp.nextSetBit(0); p >= 0 && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1)) + for (int p = gp.nextSetBit(0); p >= 0 + && p < Integer.MAX_VALUE; p = gp.nextSetBit(p + 1)) { if (cm instanceof MappableContactMatrixI) { MappableContactMatrixI mcm = (MappableContactMatrixI) cm; - seqpos = mcm.getMappedPositionsFor(aa.sequenceRef,p); - if (seqpos==null) + seqpos = mcm.getMappedPositionsFor(aa.sequenceRef, p); + if (seqpos == null) { // no mapping for this column. continue; } // TODO: handle ranges... ae = aa.getAnnotationForPosition(seqpos[0]); - } else { - ae = aa.getAnnotationForPosition(p+sstart); + } + else + { + ae = aa.getAnnotationForPosition(p + sstart); } if (ae != null) { @@ -1091,46 +1102,50 @@ 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 l, - Color col) + + private BitSet createColumnGroupFor(Vector 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); } @@ -1141,7 +1156,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Color col) { SequenceI rseq = tp.assocAnnotation.sequenceRef; - + if (av == null || av.getAlignment() == null) { // alignment is closed @@ -1160,7 +1175,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, continue; } // TODO - sort indices for faster lookup - + ColumnSelection cs = av.getColumnSelection(); HiddenColumns hc = av.getAlignment().getHiddenColumns(); ContactMatrixI cm = av.getContactMatrix(tp.assocAnnotation); @@ -1169,14 +1184,15 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (cm instanceof MappableContactMatrixI) { mcm = (MappableContactMatrixI) cm; - int[] seqpos = mcm.getMappedPositionsFor(tp.assocAnnotation.sequenceRef,colm); - if (seqpos==null) + int[] seqpos = mcm.getMappedPositionsFor( + tp.assocAnnotation.sequenceRef, colm); + if (seqpos == null) { // no mapping for this column. continue; } // TODO: handle ranges... - offp=seqpos[0]; + offp = seqpos[0]; } else { 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/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/NewickFile.java b/src/jalview/io/NewickFile.java index 269ffb3..67923db 100755 --- a/src/jalview/io/NewickFile.java +++ b/src/jalview/io/NewickFile.java @@ -488,7 +488,8 @@ public class NewickFile extends FileParse { try { - distance = (Double.valueOf(ndist.stringMatched(1))).floatValue(); + distance = (Double.valueOf(ndist.stringMatched(1))) + .floatValue(); HasDistances = true; nodehasdistance = true; } catch (Exception e) @@ -877,20 +878,20 @@ public class NewickFile extends FileParse { if (root.isDummy()) { - _print(tf, root.right()); - _print(tf, root.left()); + _print(tf, root.right()); + _print(tf, root.left()); } else { tf.append("("); - _print(tf, root.right()); + _print(tf, root.right()); if (root.left() != null) { tf.append(","); } - _print(tf, root.left()); + _print(tf, root.left()); tf.append(")" + printRootField(root)); } } @@ -910,24 +911,24 @@ public class NewickFile extends FileParse { if (c.isDummy()) { - _print(tf, c.left()); + _print(tf, c.left()); if (c.left() != null) { tf.append(","); } - _print(tf, c.right()); + _print(tf, c.right()); } else { tf.append("("); - _print(tf, c.right()); + _print(tf, c.right()); if (c.left() != null) { tf.append(","); } - _print(tf, c.left()); + _print(tf, c.left()); tf.append(")" + printNodeField(c)); } } 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 a3f7531..dbdaf2a 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 { diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java index 2ad3573..f6d17d4 100644 --- a/src/jalview/io/vamsas/Tree.java +++ b/src/jalview/io/vamsas/Tree.java @@ -358,7 +358,7 @@ public class Tree extends DatastoreItem } if (jvseq instanceof SequenceI) { - leaf.setElement((SequenceI)jvseq); + leaf.setElement((SequenceI) jvseq); leaf.setPlaceholder(false); } else @@ -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/jbgui/GStructureChooser.java b/src/jalview/jbgui/GStructureChooser.java index d5e36c1..8cb5b3c 100644 --- a/src/jalview/jbgui/GStructureChooser.java +++ b/src/jalview/jbgui/GStructureChooser.java @@ -123,7 +123,8 @@ public abstract class GStructureChooser extends JPanel protected StringBuilder errorWarning = new StringBuilder(); - protected JButton btn_cancel; + protected JButton btn_cancel; + protected JButton btn_add; protected JButton btn_newView; @@ -417,8 +418,7 @@ public abstract class GStructureChooser extends JPanel } }); - btn_cancel = new JButton( - MessageManager.getString("action.cancel")); + btn_cancel = new JButton(MessageManager.getString("action.cancel")); btn_cancel.setFont(VERDANA_12); btn_cancel.addActionListener(new ActionListener() { @@ -572,7 +572,8 @@ public abstract class GStructureChooser extends JPanel lbl_pdbFile.setFont(VERDANA_10); lbl_chooseTempFacType.setFont(VERDANA_12); - lbl_chooseTempFacType.setText(MessageManager.getString("label.interpret_tempfac_as")); + lbl_chooseTempFacType.setText( + MessageManager.getString("label.interpret_tempfac_as")); combo_tempFacAs.setFont(VERDANA_12); for (TFType t : TFType.values()) @@ -590,7 +591,8 @@ public abstract class GStructureChooser extends JPanel }); btn_paeMatrixFile.setFont(VERDANA_12); - btn_paeMatrixFile.setText(MessageManager.getString("label.add_pae_matrix_file")); + btn_paeMatrixFile + .setText(MessageManager.getString("label.add_pae_matrix_file")); btn_paeMatrixFile.addActionListener(new ActionListener() { @Override @@ -726,9 +728,11 @@ public abstract class GStructureChooser extends JPanel gbc.gridy++; gbc.insets = new Insets(0, 0, 2, 0); - pnl_fileOptions.add(new JLabel(MessageManager.getString("label.structure_import_options")), gbc); + pnl_fileOptions.add(new JLabel( + MessageManager.getString("label.structure_import_options")), + gbc); gbc.gridy++; - + gbc.insets = new Insets(0, 0, 6, 0); pnl_fileOptions.add(lbl_chooseTempFacType, gbc); gbc.gridy++; diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index a2ded9f..4a2c96e 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -1526,7 +1526,7 @@ 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(), @@ -2307,22 +2307,24 @@ 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()) { xmlmat.getGroups().add(stringifyBitset(gp)); } @@ -2337,7 +2339,7 @@ public class Jalview2XML { xmlmat.setCutHeight(cm.getCutHeight()); } - + // set/get properties if (cm instanceof MappableContactMatrixI) { @@ -2478,38 +2480,44 @@ public class Jalview2XML } - private String stringifyBitset(BitSet gp) { + private String stringifyBitset(BitSet gp) + { StringBuilder sb = new StringBuilder(); - for (long val:gp.toLongArray()) + for (long val : gp.toLongArray()) { - if (sb.length()>0) { + if (sb.length() > 0) + { sb.append(","); } sb.append(val); } return sb.toString(); } - private BitSet deStringifyBitset(String stringified) { - if ("".equals(stringified) || stringified==null) + + private BitSet deStringifyBitset(String stringified) + { + if ("".equals(stringified) || stringified == null) { return new BitSet(); } String[] longvals = stringified.split(","); long[] newlongvals = new long[longvals.length]; - for (int lv=0;lv 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()); } @@ -4039,12 +4048,13 @@ public class Jalview2XML xmlmat.getCols().intValue(), xmlmat.getRows().intValue()); jalview.util.MapList mapping = null; - if (xmlmat.getMapping()!=null) + if (xmlmat.getMapping() != null) { MapListType m = xmlmat.getMapping(); // Mapping m = dr.getMapping(); int fr[] = new int[m.getMapListFrom().size() * 2]; - Iterator from = m.getMapListFrom().iterator();// enumerateMapListFrom(); + Iterator from = m.getMapListFrom() + .iterator();// enumerateMapListFrom(); for (int _i = 0; from.hasNext(); _i += 2) { MapListFrom mf = from.next(); @@ -4060,29 +4070,35 @@ public class Jalview2XML fto[_i + 1] = mf.getEnd(); } - mapping = new jalview.util.MapList(fr, fto, m.getMapFromUnit().intValue(),m.getMapToUnit().intValue()); + mapping = new jalview.util.MapList(fr, fto, + m.getMapFromUnit().intValue(), + m.getMapToUnit().intValue()); } - List newgroups=new ArrayList(); - if (xmlmat.getGroups().size()>0) + List newgroups = new ArrayList(); + if (xmlmat.getGroups().size() > 0) { - for (String sgroup:xmlmat.getGroups()) + for (String sgroup : xmlmat.getGroups()) { newgroups.add(deStringifyBitset(sgroup)); } } - 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; GroupSet grpset = new GroupSet(); grpset.restoreGroups(newgroups, treeMethod, nwk, thresh); PAEContactMatrix newpae = new PAEContactMatrix( - jaa.sequenceRef, mapping, elements,grpset); + jaa.sequenceRef, mapping, elements, grpset); jaa.sequenceRef.addContactListFor(jaa, newpae); } } @@ -4330,8 +4346,8 @@ 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; } @@ -4478,8 +4494,8 @@ 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( @@ -5037,10 +5053,11 @@ 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()); @@ -5367,7 +5384,7 @@ 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/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index eb83f31..7d6b7b8 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -1077,22 +1077,22 @@ public class AnnotationRenderer .getRendererFor(row); if (renderer != null) { - renderer.renderRow(g, charWidth, charHeight, - hasHiddenColumns, av, hiddenColumns, columnSelection, - row, row_annotations, startRes, endRes, row.graphMin, + renderer.renderRow(g, charWidth, charHeight, hasHiddenColumns, + av, hiddenColumns, columnSelection, row, + row_annotations, startRes, endRes, row.graphMin, row.graphMax, y); } if (debugRedraw) { if (renderer == null) { - System.err.println("No renderer found for " - + row.toString()); + System.err + .println("No renderer found for " + row.toString()); } else { - System.err.println("rendered with " - + renderer.getClass().toString()); + System.err.println( + "rendered with " + renderer.getClass().toString()); } } 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/ContactGeometry.java b/src/jalview/renderer/ContactGeometry.java index ad741ff..9fd4de6 100644 --- a/src/jalview/renderer/ContactGeometry.java +++ b/src/jalview/renderer/ContactGeometry.java @@ -16,9 +16,9 @@ import jalview.renderer.ContactGeometry.contactInterval; */ public class ContactGeometry { - + final ContactListI contacts; - + final int pixels_step; final double contacts_per_pixel; @@ -29,7 +29,7 @@ public class ContactGeometry public ContactGeometry(final ContactListI contacts, int graphHeight) { - this.contacts=contacts; + this.contacts = contacts; this.graphHeight = graphHeight; contact_height = contacts.getContactHeight(); // fractional number of contacts covering each pixel @@ -70,14 +70,18 @@ public class ContactGeometry public final int pEnd; } + /** * * @param columnSelection * @param ci - * @param visibleOnly - when true, only test intersection of visible columns given matrix range - * @return true if the range on the matrix specified by ci intersects with selected columns in the ContactListI's reference frame. + * @param visibleOnly + * - when true, only test intersection of visible columns given + * matrix range + * @return true if the range on the matrix specified by ci intersects with + * selected columns in the ContactListI's reference frame. */ - + boolean intersects(contactInterval ci, ColumnSelection columnSelection, HiddenColumns hiddenColumns, boolean visibleOnly) { diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java index 00a6169..ef95360 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() @@ -147,16 +151,19 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI continue; } // ContactListI from viewport can map column -> group - Color gpcol = (cm==null) ? Color.white: contacts.getColourForGroup(); // cm.getColourForGroup(cm.getGroupsFor(column)); - + Color gpcol = (cm == null) ? Color.white + : contacts.getColourForGroup(); // 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; - // TODO: optionally pass visible column mask to the ContactGeometry object so it maps + // TODO: optionally pass visible column mask to the ContactGeometry object + // so it maps // only visible contacts to geometry // Bean holding mapping from contact list to pixels - // TODO: allow bracketing/limiting of range on contacts to render (like visible column mask but more flexible?) - + // TODO: allow bracketing/limiting of range on contacts to render (like + // visible column mask but more flexible?) + // COntactListI provides mapping for column -> cm-groupmapping final ContactGeometry cgeom = new ContactGeometry(contacts, _aa.graphHeight); @@ -164,7 +171,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI for (int ht = y2, eht = y2 - _aa.graphHeight; ht >= eht; ht -= cgeom.pixels_step) { - + ContactGeometry.contactInterval ci = cgeom.mapFor(y2 - ht, y2 - ht + cgeom.pixels_step); // cstart = (int) Math.floor(((double) y2 - ht) * contacts_per_pixel); @@ -175,7 +182,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI boolean rowsel = false, containsHidden = false; if (columnSelection != null) { - rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, maskHiddenCols); + rowsel = cgeom.intersects(ci, columnSelection, hiddenColumns, + maskHiddenCols); } // TODO: show selected region if (colsel || rowsel) @@ -200,14 +208,17 @@ 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); @@ -224,8 +235,8 @@ 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 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/structures/models/AAStructureBindingModel.java b/src/jalview/structures/models/AAStructureBindingModel.java index 9e8f286..7d9674e 100644 --- a/src/jalview/structures/models/AAStructureBindingModel.java +++ b/src/jalview/structures/models/AAStructureBindingModel.java @@ -973,7 +973,7 @@ public abstract class AAStructureBindingModel } List finalView = commandGenerator .centerViewOn(models); - if (finalView!=null && finalView.size()>0) + if (finalView != null && finalView.size() > 0) { executeCommands(finalView, false, "Centered on Superposition"); } 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/ws/datamodel/MappableContactMatrixI.java b/src/jalview/ws/datamodel/MappableContactMatrixI.java index d1a5ff7..b8a9779 100644 --- a/src/jalview/ws/datamodel/MappableContactMatrixI.java +++ b/src/jalview/ws/datamodel/MappableContactMatrixI.java @@ -12,33 +12,44 @@ public interface MappableContactMatrixI extends ContactMatrixI boolean hasReferenceSeq(); SequenceI getReferenceSeq(); + /** * remaps the matrix to a new reference sequence - * @param dsq - * @param sqmpping - mapping from current reference to new reference - 1:1 only + * + * @param dsq + * @param sqmpping + * - mapping from current reference to new reference - 1:1 only * @return new ContactMatrixI instance with updated mapping */ MappableContactMatrixI liftOver(SequenceI dsq, Mapping sqmpping); - + /** * like ContactMatrixI.getContactList(int column) but - * @param localFrame - sequence or other object that this contact matrix is associated with - * @param column - position in localFrame + * + * @param localFrame + * - sequence or other object that this contact matrix is associated + * with + * @param column + * - position in localFrame * @return ContactListI that returns contacts w.r.t. localFrame */ - + ContactListI getMappableContactList(SequenceI localFrame, int column); /** * - * Similar to AlignedCodonFrame.getMappingBetween + * Similar to AlignedCodonFrame.getMappingBetween * - * @param sequenceRef - a reference sequence mappable to this contactMatrix - may be null - * @return null or the MapList mapping to the coordinates of the reference sequence (or if hasReferenceSeq() is false, and sequenceRef is null, any mapping present) + * @param sequenceRef + * - a reference sequence mappable to this contactMatrix - may be + * null + * @return null or the MapList mapping to the coordinates of the reference + * sequence (or if hasReferenceSeq() is false, and sequenceRef is + * null, any mapping present) * */ MapList getMapFor(SequenceI sequenceRef); - + /** * Locate a position in the mapped sequence for a column in the matrix - use * this to resolve positions corresponding to column clusters diff --git a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java index dc8e0d3..9a01738 100644 --- a/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/MappableContactMatrix.java @@ -14,9 +14,11 @@ import jalview.datamodel.SequenceI; import jalview.util.MapList; import jalview.ws.datamodel.MappableContactMatrixI; -public abstract class MappableContactMatrix> implements MappableContactMatrixI +public abstract class MappableContactMatrix> + implements MappableContactMatrixI { SequenceI refSeq = null; + MapList toSeq = null; /** @@ -24,7 +26,6 @@ public abstract class MappableContactMatrix> */ int length; - @Override public boolean hasReferenceSeq() { @@ -36,15 +37,18 @@ public abstract class MappableContactMatrix> { return refSeq; } + /** * container for groups - defined on matrix columns */ - GroupSet grps=new GroupSet(); + GroupSet grps = new GroupSet(); + @Override public GroupSetI getGroupSet() { return grps; }; + @Override public void setGroupSet(GroupSet makeGroups) { @@ -54,28 +58,33 @@ public abstract class MappableContactMatrix> @Override public MapList getMapFor(SequenceI mapSeq) { - if (refSeq!=null) + if (refSeq != null) { - while (mapSeq!=refSeq && mapSeq.getDatasetSequence()!=null) + while (mapSeq != refSeq && mapSeq.getDatasetSequence() != null) { mapSeq = mapSeq.getDatasetSequence(); } - if (mapSeq!=refSeq) + if (mapSeq != refSeq) { return null; } - } else { - if (mapSeq!=null) { + } + else + { + if (mapSeq != null) + { // our MapList does not concern this seq return null; } } - + return toSeq; } /** - * set the reference sequence and construct the mapping between the start-end positions of given sequence and row/columns of contact matrix + * set the reference sequence and construct the mapping between the start-end + * positions of given sequence and row/columns of contact matrix + * * @param _refSeq */ public void setRefSeq(SequenceI _refSeq) @@ -86,9 +95,13 @@ public abstract class MappableContactMatrix> refSeq = refSeq.getDatasetSequence(); } length = _refSeq.getEnd() - _refSeq.getStart() + 1; -// if (length!=refSeq.getLength() || _refSeq.getStart()!=1) + // if (length!=refSeq.getLength() || _refSeq.getStart()!=1) { - toSeq = new MapList(new int[] { _refSeq.getStart(), _refSeq.getEnd()}, new int[] { 0,length-1}, 1,1); + toSeq = new MapList( + new int[] + { _refSeq.getStart(), _refSeq.getEnd() }, + new int[] + { 0, length - 1 }, 1, 1); } } @@ -163,31 +176,34 @@ public abstract class MappableContactMatrix> return newCM; } - protected abstract T newMappableContactMatrix(SequenceI newRefSeq, + protected abstract T newMappableContactMatrix(SequenceI newRefSeq, MapList newFromMapList); + @Override public int[] getMappedPositionsFor(final SequenceI localFrame, final int column) { - return getMappedPositionsFor(localFrame,column,column); + return getMappedPositionsFor(localFrame, column, column); } - public int[] getMappedPositionsFor(final SequenceI localFrame, - int from,int to) + + public int[] getMappedPositionsFor(final SequenceI localFrame, int from, + int to) { - if (localFrame==null) + if (localFrame == null) { throw new Error("Unimplemented when no local sequence given."); } // return a ContactListI for column // column is index into localFrame // 1. map column to corresponding column in matrix - - final int _lcolumn=localFrame.findPosition(from); - final int _rcolumn=(from==to) ? _lcolumn:localFrame.findPosition(to); + + final int _lcolumn = localFrame.findPosition(from); + final int _rcolumn = (from == to) ? _lcolumn + : localFrame.findPosition(to); if (toSeq == null) { // no mapping - return new int[] { _lcolumn,_rcolumn}; + return new int[] { _lcolumn, _rcolumn }; } SequenceI lf = localFrame, uf = refSeq; @@ -213,26 +229,26 @@ public abstract class MappableContactMatrix> + "' is not mappable for the given localFrame sequence. (" + localFrame.getName() + ")"); } - - int[] mappedPositions = toSeq.locateInFrom(_lcolumn,_rcolumn); + + int[] mappedPositions = toSeq.locateInFrom(_lcolumn, _rcolumn); // TODO - trim to localFrame ? -// if (mappedPositions!=null) { -// int s=-1,e=-1; -// for (int p=0;p=localFrame.getStart()) -// { -// s=p; // remember first position within local frame -// } -// if (e==-1 || mappedPositions[p]<=localFrame.getEnd()) -// { -// // update end pointer -// e=p; -// // compute local map -// mappedPositions[p] = localFrame.findIndex(mappedPositions[p]); -// } -// } -// } + // if (mappedPositions!=null) { + // int s=-1,e=-1; + // for (int p=0;p=localFrame.getStart()) + // { + // s=p; // remember first position within local frame + // } + // if (e==-1 || mappedPositions[p]<=localFrame.getEnd()) + // { + // // update end pointer + // e=p; + // // compute local map + // mappedPositions[p] = localFrame.findIndex(mappedPositions[p]); + // } + // } + // } return mappedPositions; } @@ -242,16 +258,16 @@ public abstract class MappableContactMatrix> { final int _column; final int _lcolumn; - if (localFrame==null) + if (localFrame == null) { throw new Error("Unimplemented when no local sequence given."); } // return a ContactListI for column // column is index into localFrame // 1. map column to corresponding column in matrix - final MappableContactMatrix us=this; - _lcolumn=localFrame.findPosition(column); - + final MappableContactMatrix us = this; + _lcolumn = localFrame.findPosition(column); + if (toSeq != null) { SequenceI lf = localFrame, uf = refSeq; @@ -287,11 +303,11 @@ public abstract class MappableContactMatrix> } else { - // no mapping + // no mapping _column = _lcolumn; } - // TODO - remove ? this may be a redundant check + // TODO - remove ? this may be a redundant check if (_column < 0 || ((toSeq != null && _column > toSeq.getToHighest()) || (toSeq == null && getHeight() <= _column))) { @@ -307,11 +323,11 @@ public abstract class MappableContactMatrix> int h = 0; for (int p = 0; p < matrixRange.length; p += 2) { - h += 1+Math.abs(matrixRange[p + 1] - matrixRange[p]); + h += 1 + Math.abs(matrixRange[p + 1] - matrixRange[p]); } final int rangeHeight = h; // 3. Construct ContactListImpl instance for just those segments. - + return new ContactListImpl(new ContactListProviderI() { @@ -403,6 +419,7 @@ public abstract class MappableContactMatrix> } return matrixRange[p] + mcolumn - h; } + @Override public Color getColourForGroup() { @@ -415,12 +432,13 @@ public abstract class MappableContactMatrix> /** * get a specific element of the contact matrix in its data-local coordinates - * rather than the mapped frame. Implementations are allowed to throw RunTimeExceptions if _column/i are out of bounds + * rather than the mapped frame. Implementations are allowed to throw + * RunTimeExceptions if _column/i are out of bounds * * @param _column * @param i * @return */ protected abstract double getElementAt(int _column, int i); - + } diff --git a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java index 0ba9584..b29c0d5 100644 --- a/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java +++ b/src/jalview/ws/datamodel/alphafold/PAEContactMatrix.java @@ -35,7 +35,8 @@ import jalview.util.MapList; import jalview.util.MapUtils; import jalview.ws.dbsources.EBIAlfaFold; -public class PAEContactMatrix extends MappableContactMatrix implements ContactMatrixI +public class PAEContactMatrix extends + MappableContactMatrix implements ContactMatrixI { int maxrow = 0, maxcol = 0; @@ -43,9 +44,9 @@ public class PAEContactMatrix extends MappableContactMatrix im float maxscore; - @SuppressWarnings("unchecked") - public PAEContactMatrix(SequenceI _refSeq, Map pae_obj) throws FileFormatException + public PAEContactMatrix(SequenceI _refSeq, Map pae_obj) + throws FileFormatException { setRefSeq(_refSeq); // convert the lists to primitive arrays and store @@ -93,17 +94,18 @@ public class PAEContactMatrix extends MappableContactMatrix im /** * new matrix with specific mapping to a reference sequence + * * @param newRefSeq * @param newFromMapList * @param elements2 - * @param grps2 + * @param grps2 */ - public PAEContactMatrix(SequenceI newRefSeq, - MapList newFromMapList, float[][] elements2, GroupSet grps2) + public PAEContactMatrix(SequenceI newRefSeq, MapList newFromMapList, + float[][] elements2, GroupSet grps2) { - this(newRefSeq,elements2); + this(newRefSeq, elements2); toSeq = newFromMapList; - grps= grps2; + grps = grps2; } /** @@ -144,7 +146,7 @@ public class PAEContactMatrix extends MappableContactMatrix im { elements[row][col++] = (float) ((Long) d).longValue(); } - + if (maxscore < elements[row][col - 1]) { maxscore = elements[row][col - 1]; @@ -213,20 +215,20 @@ public class PAEContactMatrix extends MappableContactMatrix im @Override public ContactListI getContactList(final int column) { -// final int _column; -// if (toSeq != null) -// { -// int[] word = toSeq.locateInTo(column, column); -// if (word == null) -// { -// return null; -// } -// _column = word[0]; -// } -// else -// { -// _column = column; -// } + // final int _column; + // if (toSeq != null) + // { + // int[] word = toSeq.locateInTo(column, column); + // if (word == null) + // { + // return null; + // } + // _column = word[0]; + // } + // else + // { + // _column = column; + // } if (column < 0 || column >= elements.length) { return null; @@ -263,6 +265,7 @@ public class PAEContactMatrix extends MappableContactMatrix im { return elements[_column][i]; } + @Override public float getMin() { @@ -278,17 +281,18 @@ public class PAEContactMatrix extends MappableContactMatrix im @Override public String getAnnotDescr() { - return "Predicted Alignment Error"+((refSeq==null) ? "" : (" for " + refSeq.getName())); + return "Predicted Alignment Error" + + ((refSeq == null) ? "" : (" for " + refSeq.getName())); } @Override public String getAnnotLabel() { StringBuilder label = new StringBuilder("PAE Matrix"); - //if (this.getReferenceSeq() != null) - //{ - // label.append(":").append(this.getReferenceSeq().getDisplayId(false)); - //} + // if (this.getReferenceSeq() != null) + // { + // label.append(":").append(this.getReferenceSeq().getDisplayId(false)); + // } return label.toString(); } @@ -311,39 +315,44 @@ public class PAEContactMatrix extends MappableContactMatrix im { return length; } - - public static void validateContactMatrixFile(String fileName) throws FileFormatException,IOException + + public static void validateContactMatrixFile(String fileName) + throws FileFormatException, IOException { - FileInputStream infile=null; - try { + FileInputStream infile = null; + try + { infile = new FileInputStream(new File(fileName)); } catch (Throwable t) { - new IOException("Couldn't open "+fileName,t); + new IOException("Couldn't open " + fileName, t); } - - - JSONObject paeDict=null; - try { + + JSONObject paeDict = null; + try + { paeDict = EBIAlfaFold.parseJSONtoPAEContactMatrix(infile); } catch (Throwable t) { - new FileFormatException("Couldn't parse "+fileName+" as a JSON dict or array containing a dict"); + new FileFormatException("Couldn't parse " + fileName + + " as a JSON dict or array containing a dict"); } - - PAEContactMatrix matrix = new PAEContactMatrix(new SequenceDummy("Predicted"), (Map)paeDict); - if (matrix.getWidth()<=0) + + PAEContactMatrix matrix = new PAEContactMatrix( + new SequenceDummy("Predicted"), (Map) paeDict); + if (matrix.getWidth() <= 0) { - throw new FileFormatException("No data in PAE matrix read from '"+fileName+"'"); + throw new FileFormatException( + "No data in PAE matrix read from '" + fileName + "'"); } } @Override - protected PAEContactMatrix newMappableContactMatrix( - SequenceI newRefSeq, MapList newFromMapList) + protected PAEContactMatrix newMappableContactMatrix(SequenceI newRefSeq, + MapList newFromMapList) { - PAEContactMatrix pae=new PAEContactMatrix(newRefSeq, newFromMapList, - elements, new GroupSet(grps)); + PAEContactMatrix pae = new PAEContactMatrix(newRefSeq, newFromMapList, + elements, new GroupSet(grps)); return pae; - } + } } diff --git a/src/jalview/ws/dbsources/EBIAlfaFold.java b/src/jalview/ws/dbsources/EBIAlfaFold.java index 5d88e89..b6fa642 100644 --- a/src/jalview/ws/dbsources/EBIAlfaFold.java +++ b/src/jalview/ws/dbsources/EBIAlfaFold.java @@ -497,7 +497,7 @@ public class EBIAlfaFold extends EbiFileRetrievedProxy ContactMatrixI matrix = new PAEContactMatrix(sm.getSequence(), (Map) pae_obj); - matrix.setGroupSet(GroupSet.makeGroups(matrix,5f, true)); + matrix.setGroupSet(GroupSet.makeGroups(matrix, 5f, true)); AlignmentAnnotation cmannot = sm.getSequence().addContactList(matrix); sm.getSequence().addAlignmentAnnotation(cmannot); diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java index 7126be6..0ec8f0b 100644 --- a/src/jalview/xml/binding/embl/EntrySetType.java +++ b/src/jalview/xml/binding/embl/EntrySetType.java @@ -5,7 +5,6 @@ // Generated on: 2023.05.13 at 06:58:42 PM BST // - 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; - /** - *

Java class for EntrySetType complex type. + *

+ * Java class for EntrySetType complex type. * - *

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

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

  * <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 entry;
+  @XmlElement(required = true)
+  protected List entry;
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link EntryType }
+   * 
+   * 
+   */
+  public List getEntry()
+  {
+    if (entry == null)
+    {
+      entry = new ArrayList();
     }
+    return this.entry;
+  }
 
 }
diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java
index 8b2e704..d90651c 100644
--- a/src/jalview/xml/binding/embl/EntryType.java
+++ b/src/jalview/xml/binding/embl/EntryType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for EntryType complex type.
+ * 

+ * Java class for EntryType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 secondaryAccession;
-    protected List projectAccession;
+@XmlType(
+  name = "EntryType",
+  propOrder =
+  { "secondaryAccession", "projectAccession", "description", "comment",
+      "keyword", "reference", "xref", "feature", "assembly", "contig",
+      "sequence" })
+public class EntryType
+{
+
+  protected List secondaryAccession;
+
+  protected List projectAccession;
+
+  @XmlElement(required = true)
+  protected String description;
+
+  protected String comment;
+
+  protected List keyword;
+
+  protected List reference;
+
+  protected List xref;
+
+  protected List 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List getProjectAccession()
+  {
+    if (projectAccession == null)
+    {
+      projectAccession = new ArrayList();
+    }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EntryType.Reference }
+   * 
+   * 
+   */
+  public List getReference()
+  {
+    if (reference == null)
+    {
+      reference = new ArrayList();
+    }
+    return this.reference;
+  }
+
+  /**
+   * Gets the value of the xref property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EntryType.Feature }
+   * 
+   * 
+   */
+  public List getFeature()
+  {
+    if (feature == null)
+    {
+      feature = new ArrayList();
+    }
+    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;
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="range" maxOccurs="unbounded">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "range" })
+  public static class Assembly
+  {
+
     @XmlElement(required = true)
-    protected String description;
-    protected String comment;
-    protected List keyword;
-    protected List reference;
-    protected List xref;
-    protected List 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 range;
 
     /**
-     * Gets the value of the secondaryAccession property.
+     * Gets the value of 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 set 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
+     * set method for the range property.
      * 
      * 

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

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link String }
+     * {@link EntryType.Assembly.Range }
      * 
      * 
      */
-    public List getSecondaryAccession() {
-        if (secondaryAccession == null) {
-            secondaryAccession = new ArrayList();
-        }
-        return this.secondaryAccession;
+    public List getRange()
+    {
+      if (range == null)
+      {
+        range = new ArrayList();
+      }
+      return this.range;
     }
 
     /**
-     * Gets the value of the projectAccession property.
-     * 
      * 

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

-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * 
-     *    getProjectAccession().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 

      * 
      * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
      */
-    public List getProjectAccession() {
-        if (projectAccession == null) {
-            projectAccession = new ArrayList();
+    @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;
-    }
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <choice maxOccurs="unbounded" minOccurs="0">
+   *           <element name="range">
+   *             <complexType>
+   *               <complexContent>
+   *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                   <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 </restriction>
+   *               </complexContent>
+   *             </complexType>
+   *           </element>
+   *           <element name="gap">
+   *             <complexType>
+   *               <complexContent>
+   *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 </restriction>
+   *               </complexContent>
+   *             </complexType>
+   *           </element>
+   *         </choice>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @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 rangeOrGap;
 
     /**
-     * Gets the value of the keyword property.
+     * Gets the value of the rangeOrGap property.
      * 
      * 

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

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

-     * 
-     * 
-     * 

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

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

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

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Reference }
+     * {@link EntryType.Contig.Range } {@link EntryType.Contig.Gap }
      * 
      * 
      */
-    public List getReference() {
-        if (reference == null) {
-            reference = new ArrayList();
-        }
-        return this.reference;
+    public List getRangeOrGap()
+    {
+      if (rangeOrGap == null)
+      {
+        rangeOrGap = new ArrayList();
+      }
+      return this.rangeOrGap;
     }
 
     /**
-     * Gets the value of the xref property.
-     * 
      * 

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

-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * 
-     *    getXref().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 

      * 
      * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link XrefType }
-     * 
-     * 
      */
-    public List getXref() {
-        if (xref == null) {
-            xref = new ArrayList();
+    @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.
-     * 
      * 

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

-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * 
-     *    getFeature().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 

      * 
      * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link EntryType.Feature }
-     * 
-     * 
      */
-    public List getFeature() {
-        if (feature == null) {
-            feature = new ArrayList();
+    @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;
-    }
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="taxon" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="lineage" minOccurs="0">
+   *                     <complexType>
+   *                       <complexContent>
+   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                           <sequence>
+   *                             <element name="taxon" maxOccurs="unbounded">
+   *                               <complexType>
+   *                                 <complexContent>
+   *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                                     <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                                   </restriction>
+   *                                 </complexContent>
+   *                               </complexType>
+   *                             </element>
+   *                           </sequence>
+   *                         </restriction>
+   *                       </complexContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *                 </sequence>
+   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @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 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 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.
+     * 

+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the xref property.
      * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getEntryVersion() {
-        return entryVersion;
-    }
-
-    /**
-     * Sets the value of the entryVersion property.
+     * 

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

      * 
-     * @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.
+     * 

+     * 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 getXref()
+    {
+      if (xref == null)
+      {
+        xref = new ArrayList();
+      }
+      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.
+     * 

+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the qualifier property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setMoleculeType(String value) {
-        this.moleculeType = value;
-    }
-
-    /**
-     * Gets the value of the sequenceLength property.
+     * 

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

      * 
-     * @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.
+     * 

+     * 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 getQualifier()
+    {
+      if (qualifier == null)
+      {
+        qualifier = new ArrayList();
+      }
+      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;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * 

+     * Java class for anonymous complex type.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
      * 
      * 
      * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       <sequence>
-     *         <element name="range" maxOccurs="unbounded">
+     *         <element name="lineage" minOccurs="0">
      *           <complexType>
      *             <complexContent>
      *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <sequence>
+     *                   <element name="taxon" maxOccurs="unbounded">
+     *                     <complexType>
+     *                       <complexContent>
+     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </restriction>
+     *                       </complexContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
      *               </restriction>
      *             </complexContent>
      *           </complexType>
      *         </element>
      *       </sequence>
+     *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
      *     </restriction>
      *   </complexContent>
      * </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;
+      }
+
+      /**
+       * 

+       * Java class for anonymous complex type.
+       * 
+       * 

+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
+       * 
+       * <complexType>
+       *   <complexContent>
+       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       <sequence>
+       *         <element name="taxon" maxOccurs="unbounded">
+       *           <complexType>
+       *             <complexContent>
+       *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *               </restriction>
+       *             </complexContent>
+       *           </complexType>
+       *         </element>
+       *       </sequence>
+       *     </restriction>
+       *   </complexContent>
+       * </complexType>
+       * 

+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "", propOrder = { "taxon" })
+      public static class Lineage
+      {
 
         @XmlElement(required = true)
-        protected List range;
+        protected List taxon;
 
         /**
-         * Gets the value of the range property.
+         * Gets the value of the taxon property.
          * 
          * 

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

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

          * 
          * 
          * 

          * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Assembly.Range }
-         * 
-         * 
-         */
-        public List getRange() {
-            if (range == null) {
-                range = new ArrayList();
-            }
-            return this.range;
-        }
-
-
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

+         * {@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 getTaxon()
+        {
+          if (taxon == null)
+          {
+            taxon = new ArrayList();
+          }
+          return this.taxon;
         }
 
-    }
-
-
-    /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <choice maxOccurs="unbounded" minOccurs="0">
-     *           <element name="range">
-     *             <complexType>
-     *               <complexContent>
-     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                   <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 </restriction>
-     *               </complexContent>
-     *             </complexType>
-     *           </element>
-     *           <element name="gap">
-     *             <complexType>
-     *               <complexContent>
-     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 </restriction>
-     *               </complexContent>
-     *             </complexType>
-     *           </element>
-     *         </choice>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @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 rangeOrGap;
-
         /**
-         * Gets the value of the rangeOrGap property.
-         * 
          * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Contig.Range }
-         * {@link EntryType.Contig.Gap }
-         * 
-         * 
-         */
-        public List getRangeOrGap() {
-            if (rangeOrGap == null) {
-                rangeOrGap = new ArrayList();
-            }
-            return this.rangeOrGap;
-        }
-
-
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
+         * The following schema fragment specifies the expected content
+         * contained within this class.
          * 
          * 
          * <complexType>
          *   <complexContent>
          *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
          *     </restriction>
          *   </complexContent>
          * </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;
+          }
 
         }
 
-
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @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;
-            }
-
-        }
+      }
 
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * 

+     * Java class for anonymous complex type.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
      * 
      * 
      * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       <sequence>
-     *         <element name="taxon" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="lineage" minOccurs="0">
-     *                     <complexType>
-     *                       <complexContent>
-     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           <sequence>
-     *                             <element name="taxon" maxOccurs="unbounded">
-     *                               <complexType>
-     *                                 <complexContent>
-     *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                                     <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                                   </restriction>
-     *                                 </complexContent>
-     *                               </complexType>
-     *                             </element>
-     *                           </sequence>
-     *                         </restriction>
-     *                       </complexContent>
-     *                     </complexType>
-     *                   </element>
-     *                 </sequence>
-     *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *                 </sequence>
-     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
+     *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
      *       </sequence>
      *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
      *     </restriction>
      *   </complexContent>
      * </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 xref;
-        protected List 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;
-        }
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+   *         <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="type" use="required">
+   *         <simpleType>
+   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             <enumeration value="submission"/>
+   *             <enumeration value="book"/>
+   *             <enumeration value="article"/>
+   *             <enumeration value="patent"/>
+   *             <enumeration value="thesis"/>
+   *             <enumeration value="unpublished"/>
+   *           </restriction>
+   *         </simpleType>
+   *       </attribute>
+   *       <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @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 author;
+
+    protected List applicant;
+
+    protected String consortium;
 
-        /**
-         * Gets the value of the xref property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link XrefType }
-         * 
-         * 
-         */
-        public List getXref() {
-            if (xref == null) {
-                xref = new ArrayList();
-            }
-            return this.xref;
-        }
+    @XmlSchemaType(name = "date")
+    protected XMLGregorianCalendar submissionDate;
 
-        /**
-         * Gets the value of the qualifier property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EntryType.Feature.Qualifier }
-         * 
-         * 
-         */
-        public List getQualifier() {
-            if (qualifier == null) {
-                qualifier = new ArrayList();
-            }
-            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;
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="lineage" minOccurs="0">
-         *           <complexType>
-         *             <complexContent>
-         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 <sequence>
-         *                   <element name="taxon" maxOccurs="unbounded">
-         *                     <complexType>
-         *                       <complexContent>
-         *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                         </restriction>
-         *                       </complexContent>
-         *                     </complexType>
-         *                   </element>
-         *                 </sequence>
-         *               </restriction>
-         *             </complexContent>
-         *           </complexType>
-         *         </element>
-         *       </sequence>
-         *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @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;
-            }
-
-
-            /**
-             * 
Java class for anonymous complex type.
-             * 
-             * 
The following schema fragment specifies the expected content contained within this class.
-             * 
-             * 
-             * <complexType>
-             *   <complexContent>
-             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       <sequence>
-             *         <element name="taxon" maxOccurs="unbounded">
-             *           <complexType>
-             *             <complexContent>
-             *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *               </restriction>
-             *             </complexContent>
-             *           </complexType>
-             *         </element>
-             *       </sequence>
-             *     </restriction>
-             *   </complexContent>
-             * </complexType>
-             * 

-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "", propOrder = {
-                "taxon"
-            })
-            public static class Lineage {
-
-                @XmlElement(required = true)
-                protected List taxon;
-
-                /**
-                 * Gets the value of the taxon property.
-                 * 
-                 * 

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

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

-                 * 
-                 * 
-                 * 

-                 * Objects of the following type(s) are allowed in the list
-                 * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
-                 * 
-                 * 
-                 */
-                public List getTaxon() {
-                    if (taxon == null) {
-                        taxon = new ArrayList();
-                    }
-                    return this.taxon;
-                }
-
-
-                /**
-                 * 
Java class for anonymous complex type.
-                 * 
-                 * 
The following schema fragment specifies the expected content contained within this class.
-                 * 
-                 * 
-                 * <complexType>
-                 *   <complexContent>
-                 *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-                 *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-                 *     </restriction>
-                 *   </complexContent>
-                 * </complexType>
-                 * 

-                 * 
-                 * 
-                 */
-                @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 xref;
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-         *       </sequence>
-         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the author property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
-     *         <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="type" use="required">
-     *         <simpleType>
-     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             <enumeration value="submission"/>
-     *             <enumeration value="book"/>
-     *             <enumeration value="article"/>
-     *             <enumeration value="patent"/>
-     *             <enumeration value="thesis"/>
-     *             <enumeration value="unpublished"/>
-     *           </restriction>
-     *         </simpleType>
-     *       </attribute>
-     *       <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getAuthor().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 author;
-        protected List 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 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 getAuthor()
+    {
+      if (author == null)
+      {
+        author = new ArrayList();
+      }
+      return this.author;
+    }
 
-        /**
-         * Gets the value of the author property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

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

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List getApplicant() {
-            if (applicant == null) {
-                applicant = new ArrayList();
-            }
-            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.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list {@link String }
+     * 
+     * 
+     */
+    public List getApplicant()
+    {
+      if (applicant == null)
+      {
+        applicant = new ArrayList();
+      }
+      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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link XrefType }
-         * 
-         * 
-         */
-        public List getXref() {
-            if (xref == null) {
-                xref = new ArrayList();
-            }
-            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.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list {@link XrefType
+     * }
+     * 
+     * 
+     */
+    public List getXref()
+    {
+      if (xref == null)
+      {
+        xref = new ArrayList();
+      }
+      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 71e220b..0bb5c59 100644
--- a/src/jalview/xml/binding/embl/ObjectFactory.java
+++ b/src/jalview/xml/binding/embl/ObjectFactory.java
@@ -5,155 +5,167 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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. 
- * 
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.
+ * 

+ * 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 e26f5ae..b3fad01 100644
--- a/src/jalview/xml/binding/embl/ROOT.java
+++ b/src/jalview/xml/binding/embl/ROOT.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 cb5eccf..03bbba4 100644
--- a/src/jalview/xml/binding/embl/XrefType.java
+++ b/src/jalview/xml/binding/embl/XrefType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for XrefType complex type.
+ * 

+ * Java class for XrefType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 60a5177..6b98b6a 100644
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 alcodon;
+
+  protected List alcodMap;
 
-    protected List alcodon;
-    protected List alcodMap;
+  /**
+   * Gets the value of the alcodon property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+   *       </sequence>
+   *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "mapping" })
+  public static class AlcodMap
+  {
+
+    @XmlElement(name = "Mapping", required = true)
+    protected Mapping mapping;
+
+    @XmlAttribute(name = "dnasq", required = true)
+    protected String dnasq;
 
     /**
-     * Gets the value of the alcodon property.
      * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link AlcodonFrame.AlcodMap }
+     * Sets the value of the mapping property.
      * 
+     * @param value
+     *          allowed object is {@link Mapping }
      * 
      */
-    public List getAlcodMap() {
-        if (alcodMap == null) {
-            alcodMap = new ArrayList();
-        }
-        return this.alcodMap;
+    public void setMapping(Mapping value)
+    {
+      this.mapping = value;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the dnasq property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
-     *       </sequence>
-     *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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).
+   * 
+   * 
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Alcodon
+  {
 
-        /**
-         * 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 }
      * 
-     * 
Java class for anonymous complex type.
+     */
+    public void setPos1(BigInteger value)
+    {
+      this.pos1 = value;
+    }
+
+    /**
+     * Gets the value of the pos2 property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link BigInteger }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 5e3d599..2feda64 100644
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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;
-    @XmlElement(required = true)
-    protected String label;
-    protected String description;
-    protected Annotation.ThresholdLine thresholdLine;
-    protected List contactmatrix;
-    protected List property;
-    @XmlAttribute(name = "graph", required = true)
-    protected boolean graph;
-    @XmlAttribute(name = "graphType")
-    protected Integer graphType;
-    @XmlAttribute(name = "sequenceRef")
-    protected String sequenceRef;
-    @XmlAttribute(name = "groupRef")
-    protected String groupRef;
-    @XmlAttribute(name = "graphColour")
-    protected Integer graphColour;
-    @XmlAttribute(name = "graphGroup")
-    protected Integer graphGroup;
-    @XmlAttribute(name = "graphHeight")
-    protected Integer graphHeight;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "scoreOnly")
-    protected Boolean scoreOnly;
-    @XmlAttribute(name = "score")
-    protected Double score;
-    @XmlAttribute(name = "visible")
-    protected Boolean visible;
-    @XmlAttribute(name = "centreColLabels")
-    protected Boolean centreColLabels;
-    @XmlAttribute(name = "scaleColLabels")
-    protected Boolean scaleColLabels;
-    @XmlAttribute(name = "showAllColLabels")
-    protected Boolean showAllColLabels;
-    @XmlAttribute(name = "autoCalculated")
-    protected Boolean autoCalculated;
-    @XmlAttribute(name = "belowAlignment")
-    protected Boolean belowAlignment;
-    @XmlAttribute(name = "calcId")
-    protected String calcId;
-
-    /**
-     * Gets the value of the annotationElement property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link MatrixType }
-     * 
-     * 
-     */
-    public List getContactmatrix() {
-        if (contactmatrix == null) {
-            contactmatrix = new ArrayList();
-        }
-        return this.contactmatrix;
-    }
-
-    /**
-     * Gets the value of the property property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Property }
-     * 
-     * 
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
-    }
-
-    /**
-     * Gets the value of the graph property.
-     * 
-     */
-    public boolean isGraph() {
-        return graph;
-    }
-
-    /**
-     * Sets the value of the graph property.
-     * 
-     */
-    public void setGraph(boolean value) {
-        this.graph = value;
-    }
-
-    /**
-     * Gets the value of the graphType property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getGraphType() {
-        return graphType;
-    }
+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;
 
-    /**
-     * 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 contactmatrix;
+
+  protected List property;
+
+  @XmlAttribute(name = "graph", required = true)
+  protected boolean graph;
+
+  @XmlAttribute(name = "graphType")
+  protected Integer graphType;
+
+  @XmlAttribute(name = "sequenceRef")
+  protected String sequenceRef;
+
+  @XmlAttribute(name = "groupRef")
+  protected String groupRef;
+
+  @XmlAttribute(name = "graphColour")
+  protected Integer graphColour;
+
+  @XmlAttribute(name = "graphGroup")
+  protected Integer graphGroup;
+
+  @XmlAttribute(name = "graphHeight")
+  protected Integer graphHeight;
+
+  @XmlAttribute(name = "id")
+  protected String id;
+
+  @XmlAttribute(name = "scoreOnly")
+  protected Boolean scoreOnly;
+
+  @XmlAttribute(name = "score")
+  protected Double score;
+
+  @XmlAttribute(name = "visible")
+  protected Boolean visible;
+
+  @XmlAttribute(name = "centreColLabels")
+  protected Boolean centreColLabels;
+
+  @XmlAttribute(name = "scaleColLabels")
+  protected Boolean scaleColLabels;
+
+  @XmlAttribute(name = "showAllColLabels")
+  protected Boolean showAllColLabels;
+
+  @XmlAttribute(name = "autoCalculated")
+  protected Boolean autoCalculated;
+
+  @XmlAttribute(name = "belowAlignment")
+  protected Boolean belowAlignment;
+
+  @XmlAttribute(name = "calcId")
+  protected String calcId;
+
+  /**
+   * Gets the value of the annotationElement property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class ThresholdLine
+  {
+
+    @XmlAttribute(name = "label")
+    protected String label;
 
-    /**
-     * 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;
-    }
-
-
-    /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class ThresholdLine {
-
-        @XmlAttribute(name = "label")
-        protected String label;
-        @XmlAttribute(name = "value")
-        protected Float value;
-        @XmlAttribute(name = "colour")
-        protected Integer colour;
-
-        /**
-         * Gets the value of the label property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getLabel() {
-            return label;
-        }
-
-        /**
-         * Sets the value of the label property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setLabel(String value) {
-            this.label = value;
-        }
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setValue(Float value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the colour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getColour() {
-            return colour;
-        }
-
-        /**
-         * Sets the value of the colour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setColour(Integer value) {
-            this.colour = value;
-        }
-
-    }
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index facd6dc..c820076 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for AnnotationColourScheme complex type.
+ * 

+ * Java class for AnnotationColourScheme complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 4aaf5ce..087667a 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 c1d812c..b42a170 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for DoubleMatrix complex type.
+ * 

+ * Java class for DoubleMatrix complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 row;
-    @XmlElement(name = "D")
-    protected DoubleVector d;
-    @XmlElement(name = "E")
-    protected DoubleVector e;
-    @XmlAttribute(name = "rows")
-    protected Integer rows;
-    @XmlAttribute(name = "columns")
-    protected Integer columns;
-
-    /**
-     * Gets the value of the row property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link DoubleVector }
-     * 
-     * 
-     */
-    public List getRow() {
-        if (row == null) {
-            row = new ArrayList();
-        }
-        return this.row;
-    }
-
-    /**
-     * Gets the value of the d property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public DoubleVector getD() {
-        return d;
-    }
-
-    /**
-     * Sets the value of the d property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public void setD(DoubleVector value) {
-        this.d = value;
-    }
-
-    /**
-     * Gets the value of the e property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public DoubleVector getE() {
-        return e;
-    }
-
-    /**
-     * Sets the value of the e property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public void setE(DoubleVector value) {
-        this.e = value;
-    }
-
-    /**
-     * Gets the value of the rows property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getRows() {
-        return rows;
-    }
-
-    /**
-     * Sets the value of the rows property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setRows(Integer value) {
-        this.rows = value;
-    }
-
-    /**
-     * Gets the value of the columns property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getColumns() {
-        return columns;
-    }
-
-    /**
-     * Sets the value of the columns property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setColumns(Integer value) {
-        this.columns = value;
+@XmlType(
+  name = "DoubleMatrix",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "row", "d", "e" })
+public class DoubleMatrix
+{
+
+  protected List row;
+
+  @XmlElement(name = "D")
+  protected DoubleVector d;
+
+  @XmlElement(name = "E")
+  protected DoubleVector e;
+
+  @XmlAttribute(name = "rows")
+  protected Integer rows;
+
+  @XmlAttribute(name = "columns")
+  protected Integer columns;
+
+  /**
+   * Gets the value of the row property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link DoubleVector }
+   * 
+   * 
+   */
+  public List getRow()
+  {
+    if (row == null)
+    {
+      row = new ArrayList();
     }
+    return this.row;
+  }
+
+  /**
+   * Gets the value of the d property.
+   * 
+   * @return possible object is {@link DoubleVector }
+   * 
+   */
+  public DoubleVector getD()
+  {
+    return d;
+  }
+
+  /**
+   * Sets the value of the d property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleVector }
+   * 
+   */
+  public void setD(DoubleVector value)
+  {
+    this.d = value;
+  }
+
+  /**
+   * Gets the value of the e property.
+   * 
+   * @return possible object is {@link DoubleVector }
+   * 
+   */
+  public DoubleVector getE()
+  {
+    return e;
+  }
+
+  /**
+   * Sets the value of the e property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleVector }
+   * 
+   */
+  public void setE(DoubleVector value)
+  {
+    this.e = value;
+  }
+
+  /**
+   * Gets the value of the rows property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getRows()
+  {
+    return rows;
+  }
+
+  /**
+   * Sets the value of the rows property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setRows(Integer value)
+  {
+    this.rows = value;
+  }
+
+  /**
+   * Gets the value of the columns property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getColumns()
+  {
+    return columns;
+  }
+
+  /**
+   * Sets the value of the columns property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setColumns(Integer value)
+  {
+    this.columns = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index a5ec2f9..3b449fe 100644
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for DoubleVector complex type.
+ * 

+ * Java class for DoubleVector complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 v;
+  @XmlElement(type = Double.class)
+  protected List v;
 
-    /**
-     * Gets the value of the v property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Double }
+   * 
+   * 
+   */
+  public List getV()
+  {
+    if (v == null)
+    {
+      v = new ArrayList();
     }
+    return this.v;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index 55198a7..afedb4c 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for feature complex type.
+ * 

+ * Java class for feature complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 otherData;
-    @XmlAttribute(name = "begin", required = true)
-    protected int begin;
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "description")
-    protected String description;
-    @XmlAttribute(name = "status")
-    protected String status;
-    @XmlAttribute(name = "featureGroup")
-    protected String featureGroup;
-    @XmlAttribute(name = "score")
-    protected Float score;
-
-    /**
-     * Gets the value of the otherData property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Feature.OtherData }
-     * 
-     * 
-     */
-    public List getOtherData() {
-        if (otherData == null) {
-            otherData = new ArrayList();
-        }
-        return this.otherData;
+@XmlType(
+  name = "feature",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "otherData" })
+public class Feature
+{
+
+  protected List otherData;
+
+  @XmlAttribute(name = "begin", required = true)
+  protected int begin;
+
+  @XmlAttribute(name = "end", required = true)
+  protected int end;
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
+
+  @XmlAttribute(name = "description")
+  protected String description;
+
+  @XmlAttribute(name = "status")
+  protected String status;
+
+  @XmlAttribute(name = "featureGroup")
+  protected String featureGroup;
+
+  @XmlAttribute(name = "score")
+  protected Float score;
+
+  /**
+   * Gets the value of the otherData property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class OtherData
+  {
+
+    @XmlAttribute(name = "key", required = true)
+    protected String key;
+
+    @XmlAttribute(name = "key2")
+    protected String key2;
+
+    @XmlAttribute(name = "value", required = true)
+    protected String value;
 
     /**
-     * Gets the value of the 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;
-    }
-
-
-    /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
+     *          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 99b0635..fa80569 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for FeatureMatcher complex type.
+ * 

+ * Java class for FeatureMatcher complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 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 attributeName;
 
-    /**
-     * Gets the value of the attributeName property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getAttributeName() {
-        if (attributeName == null) {
-            attributeName = new ArrayList();
-        }
-        return this.attributeName;
-    }
+  @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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List getAttributeName()
+  {
+    if (attributeName == null)
+    {
+      attributeName = new ArrayList();
     }
+    return this.attributeName;
+  }
 
-    /**
-     * 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 7fd9a50..45077af 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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
  * 
- * 
Java class for FeatureMatcherSet complex type.
+ * 

+ * Java class for FeatureMatcherSet complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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;
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+   *       </sequence>
+   *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "matcherSet" })
+  public static class CompoundMatcher
+  {
+
+    @XmlElement(namespace = "", required = true)
+    protected List matcherSet;
+
+    @XmlAttribute(name = "and", required = true)
+    protected boolean and;
 
     /**
-     * Gets the value of the 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.
+     * 

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

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

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link FeatureMatcherSet }
      * 
-     * @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 getMatcherSet()
+    {
+      if (matcherSet == null)
+      {
+        matcherSet = new ArrayList();
+      }
+      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;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
-     *       </sequence>
-     *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
+     * Sets the value of the and property.
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "matcherSet"
-    })
-    public static class CompoundMatcher {
-
-        @XmlElement(namespace = "", required = true)
-        protected List matcherSet;
-        @XmlAttribute(name = "and", required = true)
-        protected boolean and;
-
-        /**
-         * Gets the value of the matcherSet property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link FeatureMatcherSet }
-         * 
-         * 
-         */
-        public List getMatcherSet() {
-            if (matcherSet == null) {
-                matcherSet = new ArrayList();
-            }
-            return this.matcherSet;
-        }
-
-        /**
-         * Gets the value of the and property.
-         * 
-         */
-        public boolean isAnd() {
-            return and;
-        }
-
-        /**
-         * Sets the value of the and property.
-         * 
-         */
-        public void setAnd(boolean value) {
-            this.and = value;
-        }
-
+    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 0020675..76fc6cd 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -5,19 +5,21 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 
Java class for FilterBy.
+ * 

+ * Java class for FilterBy.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
  * 

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

+ * 
  * 
  * <simpleType name="FilterBy">
  *   <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 69b1022..94f9373 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for JalviewModel complex type.
+ * 

+ * Java class for JalviewModel complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 jSeq;
-    @XmlElement(name = "JGroup")
-    protected List jGroup;
-    @XmlElement(name = "Viewport")
-    protected List viewport;
-    @XmlElement(name = "UserColours")
-    protected List userColours;
-    protected List tree;
-    @XmlElement(name = "PcaViewer")
-    protected List pcaViewer;
-    @XmlElement(name = "FeatureSettings")
-    protected JalviewModel.FeatureSettings featureSettings;
-
-    /**
-     * Gets the value of the creationDate property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public XMLGregorianCalendar getCreationDate() {
-        return creationDate;
-    }
-
-    /**
-     * Sets the value of the creationDate property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setCreationDate(XMLGregorianCalendar value) {
-        this.creationDate = value;
+@XmlType(
+  name = "JalviewModel",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+      "userColours", "tree", "pcaViewer", "featureSettings" })
+public class JalviewModel
+{
+
+  @XmlElement(required = true)
+  @XmlSchemaType(name = "dateTime")
+  protected XMLGregorianCalendar creationDate;
+
+  @XmlElement(required = true)
+  protected String version;
+
+  @XmlElement(required = true)
+  protected VAMSAS vamsasModel;
+
+  @XmlElement(name = "JSeq")
+  protected List jSeq;
+
+  @XmlElement(name = "JGroup")
+  protected List jGroup;
+
+  @XmlElement(name = "Viewport")
+  protected List viewport;
+
+  @XmlElement(name = "UserColours")
+  protected List userColours;
+
+  protected List tree;
+
+  @XmlElement(name = "PcaViewer")
+  protected List pcaViewer;
+
+  @XmlElement(name = "FeatureSettings")
+  protected JalviewModel.FeatureSettings featureSettings;
+
+  /**
+   * Gets the value of the creationDate property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getCreationDate()
+  {
+    return creationDate;
+  }
+
+  /**
+   * Sets the value of the creationDate property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setCreationDate(XMLGregorianCalendar value)
+  {
+    this.creationDate = value;
+  }
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the vamsasModel property.
+   * 
+   * @return possible object is {@link VAMSAS }
+   * 
+   */
+  public VAMSAS getVamsasModel()
+  {
+    return vamsasModel;
+  }
+
+  /**
+   * Sets the value of the vamsasModel property.
+   * 
+   * @param value
+   *          allowed object is {@link VAMSAS }
+   * 
+   */
+  public void setVamsasModel(VAMSAS value)
+  {
+    this.vamsasModel = value;
+  }
+
+  /**
+   * Gets the value of the jSeq property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+   *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+   *                 </sequence>
+   *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+   *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="group" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "setting", "group" })
+  public static class FeatureSettings
+  {
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List setting;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List group;
 
     /**
-     * Gets the value of the jSeq property.
+     * Gets the value of the setting property.
      * 
      * 

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

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

      * 
      * 
      * 

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

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

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

      * 
      * 
      * 

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

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

-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * 
-     *    getViewport().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 

      * 
      * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Group
+    {
+
+      @XmlAttribute(name = "name", required = true)
+      protected String name;
+
+      @XmlAttribute(name = "display", required = true)
+      protected boolean display;
+
+      /**
+       * Gets the value of the name property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getName()
+      {
+        return name;
+      }
+
+      /**
+       * Sets the value of the name property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setName(String value)
+      {
+        this.name = value;
+      }
+
+      /**
+       * Gets the value of the display property.
+       * 
+       */
+      public boolean isDisplay()
+      {
+        return display;
+      }
+
+      /**
+       * Sets the value of the display property.
+       * 
+       */
+      public void setDisplay(boolean value)
+      {
+        this.display = value;
+      }
+
+    }
+
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
      * 

-     * 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.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
      * 
      */
-    public List getViewport() {
-        if (viewport == null) {
-            viewport = new ArrayList();
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+    public static class Setting
+    {
+
+      @XmlElement(namespace = "www.jalview.org")
+      protected List attributeName;
+
+      @XmlElement(namespace = "www.jalview.org")
+      protected FeatureMatcherSet matcherSet;
+
+      @XmlAttribute(name = "type", required = true)
+      protected String type;
+
+      @XmlAttribute(name = "colour", required = true)
+      protected int colour;
+
+      @XmlAttribute(name = "display", required = true)
+      protected boolean display;
+
+      @XmlAttribute(name = "order")
+      protected Float order;
+
+      @XmlAttribute(name = "mincolour")
+      protected Integer mincolour;
+
+      @XmlAttribute(name = "noValueColour")
+      protected NoValueColour noValueColour;
+
+      @XmlAttribute(name = "threshold")
+      protected Float threshold;
+
+      @XmlAttribute(name = "threshstate")
+      protected Integer threshstate;
+
+      @XmlAttribute(name = "max")
+      protected Float max;
+
+      @XmlAttribute(name = "min")
+      protected Float min;
+
+      @XmlAttribute(name = "colourByLabel")
+      protected Boolean colourByLabel;
+
+      @XmlAttribute(name = "autoScale")
+      protected Boolean autoScale;
+
+      /**
+       * Gets the value of the attributeName property.
+       * 
+       * 

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

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

+       * 
+       * 
+       * 

+       * Objects of the following type(s) are allowed in the list {@link String
+       * }
+       * 
+       * 
+       */
+      public List getAttributeName()
+      {
+        if (attributeName == null)
+        {
+          attributeName = new ArrayList();
+        }
+        return this.attributeName;
+      }
+
+      /**
+       * Gets the value of the matcherSet property.
+       * 
+       * @return possible object is {@link FeatureMatcherSet }
+       * 
+       */
+      public FeatureMatcherSet getMatcherSet()
+      {
+        return matcherSet;
+      }
+
+      /**
+       * Sets the value of the matcherSet property.
+       * 
+       * @param value
+       *          allowed object is {@link FeatureMatcherSet }
+       * 
+       */
+      public void setMatcherSet(FeatureMatcherSet value)
+      {
+        this.matcherSet = value;
+      }
+
+      /**
+       * Gets the value of the type property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getType()
+      {
+        return type;
+      }
+
+      /**
+       * Sets the value of the type property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setType(String value)
+      {
+        this.type = value;
+      }
+
+      /**
+       * Gets the value of the colour property.
+       * 
+       */
+      public int getColour()
+      {
+        return colour;
+      }
+
+      /**
+       * Sets the value of the colour property.
+       * 
+       */
+      public void setColour(int value)
+      {
+        this.colour = value;
+      }
+
+      /**
+       * Gets the value of the display property.
+       * 
+       */
+      public boolean isDisplay()
+      {
+        return display;
+      }
+
+      /**
+       * Sets the value of the display property.
+       * 
+       */
+      public void setDisplay(boolean value)
+      {
+        this.display = value;
+      }
+
+      /**
+       * Gets the value of the order property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getOrder()
+      {
+        return order;
+      }
+
+      /**
+       * Sets the value of the order property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setOrder(Float value)
+      {
+        this.order = value;
+      }
+
+      /**
+       * Gets the value of the mincolour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getMincolour()
+      {
+        return mincolour;
+      }
+
+      /**
+       * Sets the value of the mincolour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setMincolour(Integer value)
+      {
+        this.mincolour = value;
+      }
+
+      /**
+       * Gets the value of the noValueColour property.
+       * 
+       * @return possible object is {@link NoValueColour }
+       * 
+       */
+      public NoValueColour getNoValueColour()
+      {
+        if (noValueColour == null)
+        {
+          return NoValueColour.MIN;
         }
-        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;
+      }
+
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+   *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+  public static class JGroup
+  {
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List seq;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected AnnotationColourScheme annotationColours;
+
+    @XmlAttribute(name = "start")
+    protected Integer start;
+
+    @XmlAttribute(name = "end")
+    protected Integer end;
+
+    @XmlAttribute(name = "name")
+    protected String name;
+
+    @XmlAttribute(name = "colour")
+    protected String colour;
+
+    @XmlAttribute(name = "consThreshold")
+    protected Integer consThreshold;
+
+    @XmlAttribute(name = "pidThreshold")
+    protected Integer pidThreshold;
+
+    @XmlAttribute(name = "outlineColour")
+    protected Integer outlineColour;
+
+    @XmlAttribute(name = "displayBoxes")
+    protected Boolean displayBoxes;
+
+    @XmlAttribute(name = "displayText")
+    protected Boolean displayText;
+
+    @XmlAttribute(name = "colourText")
+    protected Boolean colourText;
+
+    @XmlAttribute(name = "textCol1")
+    protected Integer textCol1;
+
+    @XmlAttribute(name = "textCol2")
+    protected Integer textCol2;
+
+    @XmlAttribute(name = "textColThreshold")
+    protected Integer textColThreshold;
+
+    @XmlAttribute(name = "showUnconserved")
+    protected Boolean showUnconserved;
+
+    @XmlAttribute(name = "ignoreGapsinConsensus")
+    protected Boolean ignoreGapsinConsensus;
+
+    @XmlAttribute(name = "showConsensusHistogram")
+    protected Boolean showConsensusHistogram;
+
+    @XmlAttribute(name = "showSequenceLogo")
+    protected Boolean showSequenceLogo;
+
+    @XmlAttribute(name = "normaliseSequenceLogo")
+    protected Boolean normaliseSequenceLogo;
+
+    @XmlAttribute(name = "id")
+    protected String id;
+
     /**
-     * Gets the value of the userColours property.
+     * Gets the value of the seq property.
      * 
      * 

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

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

      * 
      * 
      * 

-     * 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 getUserColours() {
-        if (userColours == null) {
-            userColours = new ArrayList();
-        }
-        return this.userColours;
+    public List getSeq()
+    {
+      if (seq == null)
+      {
+        seq = new ArrayList();
+      }
+      return this.seq;
     }
 
     /**
-     * Gets the value of the tree property.
+     * Gets the value of the annotationColours property.
      * 
-     * 

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

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

+     */
+    public AnnotationColourScheme getAnnotationColours()
+    {
+      return annotationColours;
+    }
+
+    /**
+     * Sets the value of the annotationColours property.
      * 
+     * @param value
+     *          allowed object is {@link AnnotationColourScheme }
      * 
-     * 

-     * 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 getTree() {
-        if (tree == null) {
-            tree = new ArrayList();
-        }
-        return this.tree;
+    public Integer getStart()
+    {
+      return start;
     }
 
     /**
-     * Gets the value of the pcaViewer property.
+     * Sets the value of the start property.
      * 
-     * 

-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the pcaViewer property.
+     * @param value
+     *          allowed object is {@link Integer }
      * 
-     * 

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

+     */
+    public void setStart(Integer value)
+    {
+      this.start = value;
+    }
+
+    /**
+     * Gets the value of the end property.
      * 
+     * @return possible object is {@link Integer }
      * 
-     * 

-     * 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 getPcaViewer() {
-        if (pcaViewer == null) {
-            pcaViewer = new ArrayList();
-        }
-        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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Sets the value of the colour property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *                 </sequence>
-     *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="group" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 setting;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

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

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.FeatureSettings.Group }
-         * 
-         * 
-         */
-        public List getGroup() {
-            if (group == null) {
-                group = new ArrayList();
-            }
-            return this.group;
-        }
+    /**
+     * 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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Group {
-
-            @XmlAttribute(name = "name", required = true)
-            protected String name;
-            @XmlAttribute(name = "display", required = true)
-            protected boolean display;
-
-            /**
-             * Gets the value of the name property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getName() {
-                return name;
-            }
-
-            /**
-             * Sets the value of the name property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setName(String value) {
-                this.name = value;
-            }
-
-            /**
-             * Gets the value of the display property.
-             * 
-             */
-            public boolean isDisplay() {
-                return display;
-            }
-
-            /**
-             * Sets the value of the display property.
-             * 
-             */
-            public void setDisplay(boolean value) {
-                this.display = value;
-            }
+    /**
+     * Sets the value of the 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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-         *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-         *       </sequence>
-         *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-         *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "attributeName",
-            "matcherSet"
-        })
-        public static class Setting {
-
-            @XmlElement(namespace = "www.jalview.org")
-            protected List attributeName;
-            @XmlElement(namespace = "www.jalview.org")
-            protected FeatureMatcherSet matcherSet;
-            @XmlAttribute(name = "type", required = true)
-            protected String type;
-            @XmlAttribute(name = "colour", required = true)
-            protected int colour;
-            @XmlAttribute(name = "display", required = true)
-            protected boolean display;
-            @XmlAttribute(name = "order")
-            protected Float order;
-            @XmlAttribute(name = "mincolour")
-            protected Integer mincolour;
-            @XmlAttribute(name = "noValueColour")
-            protected NoValueColour noValueColour;
-            @XmlAttribute(name = "threshold")
-            protected Float threshold;
-            @XmlAttribute(name = "threshstate")
-            protected Integer threshstate;
-            @XmlAttribute(name = "max")
-            protected Float max;
-            @XmlAttribute(name = "min")
-            protected Float min;
-            @XmlAttribute(name = "colourByLabel")
-            protected Boolean colourByLabel;
-            @XmlAttribute(name = "autoScale")
-            protected Boolean autoScale;
-
-            /**
-             * Gets the value of the attributeName property.
-             * 
-             * 

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

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

-             * 
-             * 
-             * 

-             * Objects of the following type(s) are allowed in the list
-             * {@link String }
-             * 
-             * 
-             */
-            public List getAttributeName() {
-                if (attributeName == null) {
-                    attributeName = new ArrayList();
-                }
-                return this.attributeName;
-            }
-
-            /**
-             * Gets the value of the matcherSet property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link FeatureMatcherSet }
-             *     
-             */
-            public FeatureMatcherSet getMatcherSet() {
-                return matcherSet;
-            }
-
-            /**
-             * Sets the value of the matcherSet property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link FeatureMatcherSet }
-             *     
-             */
-            public void setMatcherSet(FeatureMatcherSet value) {
-                this.matcherSet = value;
-            }
-
-            /**
-             * Gets the value of the type property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getType() {
-                return type;
-            }
-
-            /**
-             * Sets the value of the type property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setType(String value) {
-                this.type = value;
-            }
-
-            /**
-             * Gets the value of the colour property.
-             * 
-             */
-            public int getColour() {
-                return colour;
-            }
-
-            /**
-             * Sets the value of the colour property.
-             * 
-             */
-            public void setColour(int value) {
-                this.colour = value;
-            }
-
-            /**
-             * Gets the value of the display property.
-             * 
-             */
-            public boolean isDisplay() {
-                return display;
-            }
-
-            /**
-             * Sets the value of the display property.
-             * 
-             */
-            public void setDisplay(boolean value) {
-                this.display = value;
-            }
-
-            /**
-             * Gets the value of the order property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getOrder() {
-                return order;
-            }
-
-            /**
-             * Sets the value of the order property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setOrder(Float value) {
-                this.order = value;
-            }
-
-            /**
-             * Gets the value of the mincolour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getMincolour() {
-                return mincolour;
-            }
-
-            /**
-             * Sets the value of the mincolour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setMincolour(Integer value) {
-                this.mincolour = value;
-            }
-
-            /**
-             * Gets the value of the noValueColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link NoValueColour }
-             *     
-             */
-            public NoValueColour getNoValueColour() {
-                if (noValueColour == null) {
-                    return NoValueColour.MIN;
-                } else {
-                    return noValueColour;
-                }
-            }
-
-            /**
-             * Sets the value of the noValueColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link NoValueColour }
-             *     
-             */
-            public void setNoValueColour(NoValueColour value) {
-                this.noValueColour = value;
-            }
-
-            /**
-             * Gets the value of the threshold property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getThreshold() {
-                return threshold;
-            }
-
-            /**
-             * Sets the value of the threshold property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setThreshold(Float value) {
-                this.threshold = value;
-            }
-
-            /**
-             * Gets the value of the threshstate property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getThreshstate() {
-                return threshstate;
-            }
-
-            /**
-             * Sets the value of the threshstate property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setThreshstate(Integer value) {
-                this.threshstate = value;
-            }
-
-            /**
-             * Gets the value of the max property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getMax() {
-                return max;
-            }
-
-            /**
-             * Sets the value of the max property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setMax(Float value) {
-                this.max = value;
-            }
-
-            /**
-             * Gets the value of the min property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getMin() {
-                return min;
-            }
-
-            /**
-             * Sets the value of the min property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setMin(Float value) {
-                this.min = value;
-            }
-
-            /**
-             * Gets the value of the colourByLabel property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isColourByLabel() {
-                return colourByLabel;
-            }
-
-            /**
-             * Sets the value of the colourByLabel property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setColourByLabel(Boolean value) {
-                this.colourByLabel = value;
-            }
-
-            /**
-             * Gets the value of the autoScale property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isAutoScale() {
-                return autoScale;
-            }
-
-            /**
-             * Sets the value of the autoScale property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setAutoScale(Boolean value) {
-                this.autoScale = value;
-            }
+    /**
+     * 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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the textCol1 property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link Integer }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List getSeq() {
-            if (seq == null) {
-                seq = new ArrayList();
-            }
-            return this.seq;
-        }
+    /**
+     * Gets the value of the textCol2 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol2()
+    {
+      return textCol2;
+    }
+
+    /**
+     * Sets the value of the textCol2 property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextCol2(Integer value)
+    {
+      this.textCol2 = value;
+    }
+
+    /**
+     * Gets the value of the textColThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextColThreshold()
+    {
+      return textColThreshold;
+    }
+
+    /**
+     * Sets the value of the textColThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextColThreshold(Integer value)
+    {
+      this.textColThreshold = value;
+    }
+
+    /**
+     * Gets the value of the showUnconserved property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowUnconserved()
+    {
+      return showUnconserved;
+    }
+
+    /**
+     * Sets the value of the showUnconserved property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowUnconserved(Boolean value)
+    {
+      this.showUnconserved = value;
+    }
+
+    /**
+     * Gets the value of the ignoreGapsinConsensus property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isIgnoreGapsinConsensus()
+    {
+      if (ignoreGapsinConsensus == null)
+      {
+        return true;
+      }
+      else
+      {
+        return ignoreGapsinConsensus;
+      }
+    }
+
+    /**
+     * Sets the value of the ignoreGapsinConsensus property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIgnoreGapsinConsensus(Boolean value)
+    {
+      this.ignoreGapsinConsensus = value;
+    }
+
+    /**
+     * Gets the value of the showConsensusHistogram property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowConsensusHistogram()
+    {
+      if (showConsensusHistogram == null)
+      {
+        return true;
+      }
+      else
+      {
+        return showConsensusHistogram;
+      }
+    }
+
+    /**
+     * Sets the value of the showConsensusHistogram property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowConsensusHistogram(Boolean value)
+    {
+      this.showConsensusHistogram = value;
+    }
+
+    /**
+     * Gets the value of the showSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowSequenceLogo()
+    {
+      if (showSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showSequenceLogo;
+      }
+    }
+
+    /**
+     * Sets the value of the showSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowSequenceLogo(Boolean value)
+    {
+      this.showSequenceLogo = value;
+    }
+
+    /**
+     * Gets the value of the normaliseSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isNormaliseSequenceLogo()
+    {
+      if (normaliseSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return normaliseSequenceLogo;
+      }
+    }
+
+    /**
+     * Sets the value of the normaliseSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setNormaliseSequenceLogo(Boolean value)
+    {
+      this.normaliseSequenceLogo = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setId(String value)
+    {
+      this.id = value;
+    }
+
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <extension base="{www.jalview.org}pdbentry">
+   *                 <sequence>
+   *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+   *                     <complexType>
+   *                       <simpleContent>
+   *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *                           <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         </extension>
+   *                       </simpleContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *               </extension>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="secondaryStructure" maxOccurs="unbounded">
+   *                     <complexType>
+   *                       <complexContent>
+   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         </restriction>
+   *                       </complexContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
+  public static class JSeq
+  {
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List features;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List pdbids;
+
+    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+    protected List hiddenSequences;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List rnaViewer;
+
+    @XmlAttribute(name = "colour")
+    protected Integer colour;
+
+    @XmlAttribute(name = "start", required = true)
+    protected int start;
+
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
+
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+
+    @XmlAttribute(name = "hidden")
+    protected Boolean hidden;
+
+    @XmlAttribute(name = "viewreference")
+    protected Boolean viewreference;
+
+    /**
+     * Gets the value of the features property.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

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

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

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

+     * 
+     * 
+     * 

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

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

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

+     * 
+     * 
+     * 

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

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

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

+     * 
+     * 
+     * 

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

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <extension base="{www.jalview.org}pdbentry">
+     *       <sequence>
+     *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <simpleContent>
+     *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </extension>
+     *             </simpleContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *     </extension>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = { "structureState" })
+    public static class Pdbids extends Pdbentry
+    {
+
+      @XmlElement(namespace = "www.jalview.org")
+      protected List structureState;
+
+      /**
+       * Gets the value of the structureState property.
+       * 
+       * 

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

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

+       * 
+       * 
+       * 

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

+       * Java class for anonymous complex type.
+       * 
+       * 

+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
+       * 
+       * <complexType>
+       *   <simpleContent>
+       *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+       *       <attGroup ref="{www.jalview.org}swingwindow"/>
+       *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+       *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </extension>
+       *   </simpleContent>
+       * </complexType>
+       * 

+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "", propOrder = { "value" })
+      public static class StructureState
+      {
+
+        @XmlValue
+        protected String value;
+
+        @XmlAttribute(name = "visible")
+        protected Boolean visible;
+
+        @XmlAttribute(name = "viewId")
+        protected String viewId;
+
+        @XmlAttribute(name = "alignwithAlignPanel")
+        protected Boolean alignwithAlignPanel;
+
+        @XmlAttribute(name = "colourwithAlignPanel")
+        protected Boolean colourwithAlignPanel;
+
+        @XmlAttribute(name = "colourByJmol")
+        protected Boolean colourByJmol;
+
+        @XmlAttribute(name = "type")
+        protected String type;
+
+        @XmlAttribute(name = "width")
+        protected Integer width;
+
+        @XmlAttribute(name = "height")
+        protected Integer height;
+
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
 
-        /**
-         * 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;
         }
 
+      }
+
+    }
+
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="secondaryStructure" maxOccurs="unbounded">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = { "secondaryStructure" })
+    public static class RnaViewer
+    {
+
+      @XmlElement(namespace = "www.jalview.org", required = true)
+      protected List secondaryStructure;
+
+      @XmlAttribute(name = "title")
+      protected String title;
+
+      @XmlAttribute(name = "viewId")
+      protected String viewId;
+
+      @XmlAttribute(name = "dividerLocation")
+      protected Integer dividerLocation;
+
+      @XmlAttribute(name = "selectedRna")
+      protected Integer selectedRna;
+
+      @XmlAttribute(name = "width")
+      protected Integer width;
+
+      @XmlAttribute(name = "height")
+      protected Integer height;
+
+      @XmlAttribute(name = "xpos")
+      protected Integer xpos;
+
+      @XmlAttribute(name = "ypos")
+      protected Integer ypos;
+
+      /**
+       * Gets the value of the secondaryStructure property.
+       * 
+       * 

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

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

+       * 
+       * 
+       * 

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

+       * Java class for anonymous complex type.
+       * 
+       * 

+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
+       * 
+       * <complexType>
+       *   <complexContent>
+       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </restriction>
+       *   </complexContent>
+       * </complexType>
+       * 

+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "")
+      public static class SecondaryStructure
+      {
+
+        @XmlAttribute(name = "title")
+        protected String title;
+
+        @XmlAttribute(name = "annotationId", required = true)
+        protected String annotationId;
+
+        @XmlAttribute(name = "gapped")
+        protected Boolean gapped;
+
+        @XmlAttribute(name = "viewerState")
+        protected String viewerState;
+
         /**
-         * Gets the value of the 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;
         }
 
+      }
+
+    }
+
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="sequencePoint" maxOccurs="unbounded">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="axis" maxOccurs="3" minOccurs="3">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="seqPointMin">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="seqPointMax">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
+  public static class PcaViewer
+  {
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List sequencePoint;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List axis;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected PcaDataType pcaData;
+
+    @XmlAttribute(name = "title")
+    protected String title;
+
+    @XmlAttribute(name = "scoreModelName")
+    protected String scoreModelName;
+
+    @XmlAttribute(name = "xDim")
+    protected Integer xDim;
+
+    @XmlAttribute(name = "yDim")
+    protected Integer yDim;
+
+    @XmlAttribute(name = "zDim")
+    protected Integer zDim;
+
+    @XmlAttribute(name = "bgColour")
+    protected Integer bgColour;
+
+    @XmlAttribute(name = "scaleFactor")
+    protected Float scaleFactor;
+
+    @XmlAttribute(name = "showLabels")
+    protected Boolean showLabels;
+
+    @XmlAttribute(name = "linkToAllViews")
+    protected Boolean linkToAllViews;
+
+    @XmlAttribute(name = "includeGaps")
+    protected Boolean includeGaps;
+
+    @XmlAttribute(name = "matchGaps")
+    protected Boolean matchGaps;
+
+    @XmlAttribute(name = "includeGappedColumns")
+    protected Boolean includeGappedColumns;
+
+    @XmlAttribute(name = "denominateByShortestLength")
+    protected Boolean denominateByShortestLength;
+
+    @XmlAttribute(name = "width")
+    protected Integer width;
+
+    @XmlAttribute(name = "height")
+    protected Integer height;
+
+    @XmlAttribute(name = "xpos")
+    protected Integer xpos;
+
+    @XmlAttribute(name = "ypos")
+    protected Integer ypos;
+
+    /**
+     * Gets the value of the sequencePoint property.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer.SequencePoint }
+     * 
+     * 
+     */
+    public List getSequencePoint()
+    {
+      if (sequencePoint == null)
+      {
+        sequencePoint = new ArrayList();
+      }
+      return this.sequencePoint;
+    }
+
+    /**
+     * Gets the value of the axis property.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer.Axis }
+     * 
+     * 
+     */
+    public List getAxis()
+    {
+      if (axis == null)
+      {
+        axis = new ArrayList();
+      }
+      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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Sets the value of the yDim property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Integer }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <extension base="{www.jalview.org}pdbentry">
-     *                 <sequence>
-     *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *                     <complexType>
-     *                       <simpleContent>
-     *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *                           <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         </extension>
-     *                       </simpleContent>
-     *                     </complexType>
-     *                   </element>
-     *                 </sequence>
-     *               </extension>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="secondaryStructure" maxOccurs="unbounded">
-     *                     <complexType>
-     *                       <complexContent>
-     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         </restriction>
-     *                       </complexContent>
-     *                     </complexType>
-     *                   </element>
-     *                 </sequence>
-     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 features;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List pdbids;
-        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-        protected List hiddenSequences;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List rnaViewer;
-        @XmlAttribute(name = "colour")
-        protected Integer colour;
-        @XmlAttribute(name = "start", required = true)
-        protected int start;
-        @XmlAttribute(name = "end", required = true)
-        protected int end;
-        @XmlAttribute(name = "id", required = true)
-        protected String id;
-        @XmlAttribute(name = "hidden")
-        protected Boolean hidden;
-        @XmlAttribute(name = "viewreference")
-        protected Boolean viewreference;
+    public Integer getZDim()
+    {
+      return zDim;
+    }
 
-        /**
-         * Gets the value of the features property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

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

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

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

-         * 
-         * 
-         * 

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

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

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

-         * 
-         * 
-         * 

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

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.JSeq.RnaViewer }
-         * 
-         * 
-         */
-        public List getRnaViewer() {
-            if (rnaViewer == null) {
-                rnaViewer = new ArrayList();
-            }
-            return this.rnaViewer;
-        }
+    /**
+     * Gets the value of the 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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <extension base="{www.jalview.org}pdbentry">
-         *       <sequence>
-         *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-         *           <complexType>
-         *             <simpleContent>
-         *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-         *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-         *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               </extension>
-         *             </simpleContent>
-         *           </complexType>
-         *         </element>
-         *       </sequence>
-         *     </extension>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "structureState"
-        })
-        public static class Pdbids
-            extends Pdbentry
-        {
+    /**
+     * Gets the value of the width property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getWidth()
+    {
+      return width;
+    }
 
-            @XmlElement(namespace = "www.jalview.org")
-            protected List structureState;
-
-            /**
-             * Gets the value of the structureState property.
-             * 
-             * 

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

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

-             * 
-             * 
-             * 

-             * Objects of the following type(s) are allowed in the list
-             * {@link JalviewModel.JSeq.Pdbids.StructureState }
-             * 
-             * 
-             */
-            public List getStructureState() {
-                if (structureState == null) {
-                    structureState = new ArrayList();
-                }
-                return this.structureState;
-            }
-
-
-            /**
-             * 
Java class for anonymous complex type.
-             * 
-             * 
The following schema fragment specifies the expected content contained within this class.
-             * 
-             * 
-             * <complexType>
-             *   <simpleContent>
-             *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-             *       <attGroup ref="{www.jalview.org}swingwindow"/>
-             *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-             *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     </extension>
-             *   </simpleContent>
-             * </complexType>
-             * 

-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "", propOrder = {
-                "value"
-            })
-            public static class StructureState {
-
-                @XmlValue
-                protected String value;
-                @XmlAttribute(name = "visible")
-                protected Boolean visible;
-                @XmlAttribute(name = "viewId")
-                protected String viewId;
-                @XmlAttribute(name = "alignwithAlignPanel")
-                protected Boolean alignwithAlignPanel;
-                @XmlAttribute(name = "colourwithAlignPanel")
-                protected Boolean colourwithAlignPanel;
-                @XmlAttribute(name = "colourByJmol")
-                protected Boolean colourByJmol;
-                @XmlAttribute(name = "type")
-                protected String type;
-                @XmlAttribute(name = "width")
-                protected Integer width;
-                @XmlAttribute(name = "height")
-                protected Integer height;
-                @XmlAttribute(name = "xpos")
-                protected Integer xpos;
-                @XmlAttribute(name = "ypos")
-                protected Integer ypos;
-
-                /**
-                 * Gets the value of the value property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getValue() {
-                    return value;
-                }
-
-                /**
-                 * Sets the value of the value property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setValue(String value) {
-                    this.value = value;
-                }
-
-                /**
-                 * Gets the value of the visible property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public Boolean isVisible() {
-                    return visible;
-                }
-
-                /**
-                 * Sets the value of the visible property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setVisible(Boolean value) {
-                    this.visible = value;
-                }
-
-                /**
-                 * Gets the value of the viewId property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getViewId() {
-                    return viewId;
-                }
-
-                /**
-                 * Sets the value of the viewId property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setViewId(String value) {
-                    this.viewId = value;
-                }
-
-                /**
-                 * Gets the value of the alignwithAlignPanel property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isAlignwithAlignPanel() {
-                    if (alignwithAlignPanel == null) {
-                        return true;
-                    } else {
-                        return alignwithAlignPanel;
-                    }
-                }
-
-                /**
-                 * Sets the value of the alignwithAlignPanel property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setAlignwithAlignPanel(Boolean value) {
-                    this.alignwithAlignPanel = value;
-                }
-
-                /**
-                 * Gets the value of the colourwithAlignPanel property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isColourwithAlignPanel() {
-                    if (colourwithAlignPanel == null) {
-                        return false;
-                    } else {
-                        return colourwithAlignPanel;
-                    }
-                }
-
-                /**
-                 * Sets the value of the colourwithAlignPanel property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setColourwithAlignPanel(Boolean value) {
-                    this.colourwithAlignPanel = value;
-                }
-
-                /**
-                 * Gets the value of the colourByJmol property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isColourByJmol() {
-                    if (colourByJmol == null) {
-                        return true;
-                    } else {
-                        return colourByJmol;
-                    }
-                }
-
-                /**
-                 * Sets the value of the colourByJmol property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setColourByJmol(Boolean value) {
-                    this.colourByJmol = value;
-                }
-
-                /**
-                 * Gets the value of the type property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getType() {
-                    return type;
-                }
-
-                /**
-                 * Sets the value of the type property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setType(String value) {
-                    this.type = value;
-                }
-
-                /**
-                 * Gets the value of the width property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getWidth() {
-                    return width;
-                }
-
-                /**
-                 * Sets the value of the width property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setWidth(Integer value) {
-                    this.width = value;
-                }
-
-                /**
-                 * Gets the value of the height property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getHeight() {
-                    return height;
-                }
-
-                /**
-                 * Sets the value of the height property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setHeight(Integer value) {
-                    this.height = value;
-                }
-
-                /**
-                 * Gets the value of the xpos property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getXpos() {
-                    return xpos;
-                }
-
-                /**
-                 * Sets the value of the xpos property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setXpos(Integer value) {
-                    this.xpos = value;
-                }
-
-                /**
-                 * Gets the value of the ypos property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getYpos() {
-                    return ypos;
-                }
-
-                /**
-                 * Sets the value of the ypos property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setYpos(Integer value) {
-                    this.ypos = value;
-                }
-
-            }
+    /**
+     * 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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="secondaryStructure" maxOccurs="unbounded">
-         *           <complexType>
-         *             <complexContent>
-         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               </restriction>
-         *             </complexContent>
-         *           </complexType>
-         *         </element>
-         *       </sequence>
-         *       <attGroup ref="{www.jalview.org}swingwindow"/>
-         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "secondaryStructure"
-        })
-        public static class RnaViewer {
-
-            @XmlElement(namespace = "www.jalview.org", required = true)
-            protected List secondaryStructure;
-            @XmlAttribute(name = "title")
-            protected String title;
-            @XmlAttribute(name = "viewId")
-            protected String viewId;
-            @XmlAttribute(name = "dividerLocation")
-            protected Integer dividerLocation;
-            @XmlAttribute(name = "selectedRna")
-            protected Integer selectedRna;
-            @XmlAttribute(name = "width")
-            protected Integer width;
-            @XmlAttribute(name = "height")
-            protected Integer height;
-            @XmlAttribute(name = "xpos")
-            protected Integer xpos;
-            @XmlAttribute(name = "ypos")
-            protected Integer ypos;
-
-            /**
-             * Gets the value of the secondaryStructure property.
-             * 
-             * 

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

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

-             * 
-             * 
-             * 

-             * Objects of the following type(s) are allowed in the list
-             * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-             * 
-             * 
-             */
-            public List getSecondaryStructure() {
-                if (secondaryStructure == null) {
-                    secondaryStructure = new ArrayList();
-                }
-                return this.secondaryStructure;
-            }
-
-            /**
-             * Gets the value of the title property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getTitle() {
-                return title;
-            }
-
-            /**
-             * Sets the value of the title property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setTitle(String value) {
-                this.title = value;
-            }
-
-            /**
-             * Gets the value of the viewId property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getViewId() {
-                return viewId;
-            }
-
-            /**
-             * Sets the value of the viewId property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setViewId(String value) {
-                this.viewId = value;
-            }
-
-            /**
-             * Gets the value of the dividerLocation property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getDividerLocation() {
-                return dividerLocation;
-            }
-
-            /**
-             * Sets the value of the dividerLocation property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setDividerLocation(Integer value) {
-                this.dividerLocation = value;
-            }
-
-            /**
-             * Gets the value of the selectedRna property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getSelectedRna() {
-                return selectedRna;
-            }
-
-            /**
-             * Sets the value of the selectedRna property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setSelectedRna(Integer value) {
-                this.selectedRna = value;
-            }
-
-            /**
-             * Gets the value of the width property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getWidth() {
-                return width;
-            }
-
-            /**
-             * Sets the value of the width property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setWidth(Integer value) {
-                this.width = value;
-            }
-
-            /**
-             * Gets the value of the height property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getHeight() {
-                return height;
-            }
-
-            /**
-             * Sets the value of the height property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setHeight(Integer value) {
-                this.height = value;
-            }
-
-            /**
-             * Gets the value of the xpos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getXpos() {
-                return xpos;
-            }
-
-            /**
-             * Sets the value of the xpos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setXpos(Integer value) {
-                this.xpos = value;
-            }
-
-            /**
-             * Gets the value of the ypos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getYpos() {
-                return ypos;
-            }
-
-            /**
-             * Sets the value of the ypos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setYpos(Integer value) {
-                this.ypos = value;
-            }
-
-
-            /**
-             * 
Java class for anonymous complex type.
-             * 
-             * 
The following schema fragment specifies the expected content contained within this class.
-             * 
-             * 
-             * <complexType>
-             *   <complexContent>
-             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     </restriction>
-             *   </complexContent>
-             * </complexType>
-             * 

-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "")
-            public static class SecondaryStructure {
-
-                @XmlAttribute(name = "title")
-                protected String title;
-                @XmlAttribute(name = "annotationId", required = true)
-                protected String annotationId;
-                @XmlAttribute(name = "gapped")
-                protected Boolean gapped;
-                @XmlAttribute(name = "viewerState")
-                protected String viewerState;
-
-                /**
-                 * Gets the value of the title property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getTitle() {
-                    return title;
-                }
-
-                /**
-                 * Sets the value of the title property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setTitle(String value) {
-                    this.title = value;
-                }
-
-                /**
-                 * Gets the value of the annotationId property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getAnnotationId() {
-                    return annotationId;
-                }
-
-                /**
-                 * Sets the value of the annotationId property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setAnnotationId(String value) {
-                    this.annotationId = value;
-                }
-
-                /**
-                 * Gets the value of the gapped property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public Boolean isGapped() {
-                    return gapped;
-                }
-
-                /**
-                 * Sets the value of the gapped property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setGapped(Boolean value) {
-                    this.gapped = value;
-                }
-
-                /**
-                 * Gets the value of the viewerState property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getViewerState() {
-                    return viewerState;
-                }
-
-                /**
-                 * Sets the value of the viewerState property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setViewerState(String value) {
-                    this.viewerState = value;
-                }
-
-            }
+    /**
+     * Gets the value of the xpos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXpos()
+    {
+      return xpos;
+    }
 
-        }
+    /**
+     * Sets the value of the xpos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setXpos(Integer value)
+    {
+      this.xpos = value;
+    }
 
+    /**
+     * Gets the value of the ypos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getYpos()
+    {
+      return ypos;
     }
 
+    /**
+     * Sets the value of the ypos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setYpos(Integer value)
+    {
+      this.ypos = value;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * 

+     * Java class for anonymous complex type.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
      * 
      * 
      * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="sequencePoint" maxOccurs="unbounded">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="axis" maxOccurs="3" minOccurs="3">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="seqPointMin">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="seqPointMax">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attGroup ref="{www.jalview.org}position"/>
      *     </restriction>
      *   </complexContent>
      * </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 sequencePoint;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List axis;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected PcaDataType pcaData;
-        @XmlAttribute(name = "title")
-        protected String title;
-        @XmlAttribute(name = "scoreModelName")
-        protected String scoreModelName;
-        @XmlAttribute(name = "xDim")
-        protected Integer xDim;
-        @XmlAttribute(name = "yDim")
-        protected Integer yDim;
-        @XmlAttribute(name = "zDim")
-        protected Integer zDim;
-        @XmlAttribute(name = "bgColour")
-        protected Integer bgColour;
-        @XmlAttribute(name = "scaleFactor")
-        protected Float scaleFactor;
-        @XmlAttribute(name = "showLabels")
-        protected Boolean showLabels;
-        @XmlAttribute(name = "linkToAllViews")
-        protected Boolean linkToAllViews;
-        @XmlAttribute(name = "includeGaps")
-        protected Boolean includeGaps;
-        @XmlAttribute(name = "matchGaps")
-        protected Boolean matchGaps;
-        @XmlAttribute(name = "includeGappedColumns")
-        protected Boolean includeGappedColumns;
-        @XmlAttribute(name = "denominateByShortestLength")
-        protected Boolean denominateByShortestLength;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
-
-        /**
-         * Gets the value of the sequencePoint property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.PcaViewer.SequencePoint }
-         * 
-         * 
-         */
-        public List getSequencePoint() {
-            if (sequencePoint == null) {
-                sequencePoint = new ArrayList();
-            }
-            return this.sequencePoint;
-        }
-
-        /**
-         * Gets the value of the axis property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.PcaViewer.Axis }
-         * 
-         * 
-         */
-        public List getAxis() {
-            if (axis == null) {
-                axis = new ArrayList();
-            }
-            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;
-        }
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}position"/>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SeqPointMax
+    {
+
+      @XmlAttribute(name = "xPos")
+      protected Float xPos;
+
+      @XmlAttribute(name = "yPos")
+      protected Float yPos;
+
+      @XmlAttribute(name = "zPos")
+      protected Float zPos;
+
+      /**
+       * Gets the value of the xPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getXPos()
+      {
+        return xPos;
+      }
+
+      /**
+       * Sets the value of the xPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setXPos(Float value)
+      {
+        this.xPos = value;
+      }
+
+      /**
+       * Gets the value of the yPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getYPos()
+      {
+        return yPos;
+      }
+
+      /**
+       * Sets the value of the yPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setYPos(Float value)
+      {
+        this.yPos = value;
+      }
+
+      /**
+       * Gets the value of the zPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getZPos()
+      {
+        return zPos;
+      }
+
+      /**
+       * Sets the value of the zPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setZPos(Float value)
+      {
+        this.zPos = value;
+      }
 
-        /**
-         * 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;
-        }
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}position"/>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SeqPointMin
+    {
+
+      @XmlAttribute(name = "xPos")
+      protected Float xPos;
+
+      @XmlAttribute(name = "yPos")
+      protected Float yPos;
+
+      @XmlAttribute(name = "zPos")
+      protected Float zPos;
+
+      /**
+       * Gets the value of the xPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getXPos()
+      {
+        return xPos;
+      }
+
+      /**
+       * Sets the value of the xPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setXPos(Float value)
+      {
+        this.xPos = value;
+      }
+
+      /**
+       * Gets the value of the yPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getYPos()
+      {
+        return yPos;
+      }
+
+      /**
+       * Sets the value of the yPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setYPos(Float value)
+      {
+        this.yPos = value;
+      }
+
+      /**
+       * Gets the value of the zPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getZPos()
+      {
+        return zPos;
+      }
+
+      /**
+       * Sets the value of the zPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setZPos(Float value)
+      {
+        this.zPos = value;
+      }
 
-        /**
-         * 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;
-        }
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}position"/>
+     *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SequencePoint
+    {
+
+      @XmlAttribute(name = "sequenceRef")
+      protected String sequenceRef;
+
+      @XmlAttribute(name = "xPos")
+      protected Float xPos;
+
+      @XmlAttribute(name = "yPos")
+      protected Float yPos;
+
+      @XmlAttribute(name = "zPos")
+      protected Float zPos;
+
+      /**
+       * Gets the value of the sequenceRef property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getSequenceRef()
+      {
+        return sequenceRef;
+      }
+
+      /**
+       * Sets the value of the sequenceRef property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setSequenceRef(String value)
+      {
+        this.sequenceRef = value;
+      }
+
+      /**
+       * Gets the value of the xPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getXPos()
+      {
+        return xPos;
+      }
+
+      /**
+       * Sets the value of the xPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setXPos(Float value)
+      {
+        this.xPos = value;
+      }
+
+      /**
+       * Gets the value of the yPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getYPos()
+      {
+        return yPos;
+      }
+
+      /**
+       * Sets the value of the yPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setYPos(Float value)
+      {
+        this.yPos = value;
+      }
+
+      /**
+       * Gets the value of the zPos property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getZPos()
+      {
+        return zPos;
+      }
+
+      /**
+       * Sets the value of the zPos property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setZPos(Float value)
+      {
+        this.zPos = value;
+      }
 
-        /**
-         * 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;
-        }
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence minOccurs="0">
+   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "title", "newick" })
+  public static class Tree
+  {
+
+    @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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Axis {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * 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;
+      }
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SeqPointMax {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * 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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SeqPointMin {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * 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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SequencePoint {
-
-            @XmlAttribute(name = "sequenceRef")
-            protected String sequenceRef;
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the sequenceRef property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getSequenceRef() {
-                return sequenceRef;
-            }
-
-            /**
-             * Sets the value of the sequenceRef property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setSequenceRef(String value) {
-                this.sequenceRef = value;
-            }
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    /**
+     * 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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Sets the value of the xpos property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Integer }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence minOccurs="0">
-     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+   *       </sequence>
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "userColourScheme" })
+  public static class UserColours
+  {
+
+    @XmlElement(
+      name = "UserColourScheme",
+      namespace = "www.jalview.org",
+      required = true)
+    protected JalviewUserColours userColourScheme;
+
+    @XmlAttribute(name = "id")
+    protected String id;
 
-        /**
-         * 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;
-        }
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+   *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </extension>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="overview" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
+  public static class Viewport
+  {
+
+    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+    protected AnnotationColourScheme annotationColours;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List hiddenColumns;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List calcIdParam;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected JalviewModel.Viewport.Overview overview;
+
+    @XmlAttribute(name = "conservationSelected")
+    protected Boolean conservationSelected;
+
+    @XmlAttribute(name = "pidSelected")
+    protected Boolean pidSelected;
+
+    @XmlAttribute(name = "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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the hiddenColumns property.
+     * 
+     * 

+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the hiddenColumns property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-     *       </sequence>
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getHiddenColumns().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 getHiddenColumns()
+    {
+      if (hiddenColumns == null)
+      {
+        hiddenColumns = new ArrayList();
+      }
+      return this.hiddenColumns;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the calcIdParam property.
+     * 
+     * 

+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the calcIdParam property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               </extension>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="overview" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getCalcIdParam().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 hiddenColumns;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List calcIdParam;
-        @XmlElement(namespace = "www.jalview.org")
-        protected JalviewModel.Viewport.Overview overview;
-        @XmlAttribute(name = "conservationSelected")
-        protected Boolean conservationSelected;
-        @XmlAttribute(name = "pidSelected")
-        protected Boolean pidSelected;
-        @XmlAttribute(name = "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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

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

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.Viewport.CalcIdParam }
-         * 
-         * 
-         */
-        public List getCalcIdParam() {
-            if (calcIdParam == null) {
-                calcIdParam = new ArrayList();
-            }
-            return this.calcIdParam;
-        }
-
-        /**
-         * Gets the value of the 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 getCalcIdParam()
+    {
+      if (calcIdParam == null)
+      {
+        calcIdParam = new ArrayList();
+      }
+      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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-         *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     </extension>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class CalcIdParam
-            extends WebServiceParameterSet
-        {
+    /**
+     * 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;
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class HiddenColumns {
-
-            @XmlAttribute(name = "start")
-            protected Integer start;
-            @XmlAttribute(name = "end")
-            protected Integer end;
-
-            /**
-             * Gets the value of the start property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getStart() {
-                return start;
-            }
-
-            /**
-             * Sets the value of the start property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setStart(Integer value) {
-                this.start = value;
-            }
-
-            /**
-             * Gets the value of the end property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getEnd() {
-                return end;
-            }
-
-            /**
-             * Sets the value of the end property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setEnd(Integer value) {
-                this.end = value;
-            }
+    /**
+     * Sets the value of the ypos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setYpos(Integer value)
+    {
+      this.ypos = value;
+    }
 
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </extension>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class CalcIdParam extends WebServiceParameterSet
+    {
+
+      @XmlAttribute(name = "calcId", required = true)
+      protected String calcId;
+
+      @XmlAttribute(name = "needsUpdate")
+      protected Boolean needsUpdate;
+
+      @XmlAttribute(name = "autoUpdate", required = true)
+      protected boolean autoUpdate;
+
+      /**
+       * Gets the value of the calcId property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getCalcId()
+      {
+        return calcId;
+      }
+
+      /**
+       * Sets the value of the calcId property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setCalcId(String value)
+      {
+        this.calcId = value;
+      }
+
+      /**
+       * Gets the value of the needsUpdate property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public boolean isNeedsUpdate()
+      {
+        if (needsUpdate == null)
+        {
+          return false;
         }
+        else
+        {
+          return needsUpdate;
+        }
+      }
+
+      /**
+       * Sets the value of the needsUpdate property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setNeedsUpdate(Boolean value)
+      {
+        this.needsUpdate = value;
+      }
+
+      /**
+       * Gets the value of the autoUpdate property.
+       * 
+       */
+      public boolean isAutoUpdate()
+      {
+        return autoUpdate;
+      }
+
+      /**
+       * Sets the value of the autoUpdate property.
+       * 
+       */
+      public void setAutoUpdate(boolean value)
+      {
+        this.autoUpdate = value;
+      }
 
+    }
 
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}swingwindow"/>
-         *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class Overview {
-
-            @XmlAttribute(name = "showHidden")
-            protected Boolean showHidden;
-            @XmlAttribute(name = "residueColour")
-            protected Integer residueColour;
-            @XmlAttribute(name = "gapColour")
-            protected Integer gapColour;
-            @XmlAttribute(name = "hiddenColour")
-            protected Integer hiddenColour;
-            @XmlAttribute(name = "title")
-            protected String title;
-            @XmlAttribute(name = "width")
-            protected Integer width;
-            @XmlAttribute(name = "height")
-            protected Integer height;
-            @XmlAttribute(name = "xpos")
-            protected Integer xpos;
-            @XmlAttribute(name = "ypos")
-            protected Integer ypos;
-
-            /**
-             * Gets the value of the showHidden property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isShowHidden() {
-                return showHidden;
-            }
-
-            /**
-             * Sets the value of the showHidden property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setShowHidden(Boolean value) {
-                this.showHidden = value;
-            }
-
-            /**
-             * Gets the value of the residueColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getResidueColour() {
-                return residueColour;
-            }
-
-            /**
-             * Sets the value of the residueColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setResidueColour(Integer value) {
-                this.residueColour = value;
-            }
-
-            /**
-             * Gets the value of the gapColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getGapColour() {
-                return gapColour;
-            }
-
-            /**
-             * Sets the value of the gapColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setGapColour(Integer value) {
-                this.gapColour = value;
-            }
-
-            /**
-             * Gets the value of the hiddenColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getHiddenColour() {
-                return hiddenColour;
-            }
-
-            /**
-             * Sets the value of the hiddenColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setHiddenColour(Integer value) {
-                this.hiddenColour = value;
-            }
-
-            /**
-             * Gets the value of the title property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getTitle() {
-                return title;
-            }
-
-            /**
-             * Sets the value of the title property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setTitle(String value) {
-                this.title = value;
-            }
-
-            /**
-             * Gets the value of the width property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getWidth() {
-                return width;
-            }
-
-            /**
-             * Sets the value of the width property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setWidth(Integer value) {
-                this.width = value;
-            }
-
-            /**
-             * Gets the value of the height property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getHeight() {
-                return height;
-            }
-
-            /**
-             * Sets the value of the height property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setHeight(Integer value) {
-                this.height = value;
-            }
-
-            /**
-             * Gets the value of the xpos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getXpos() {
-                return xpos;
-            }
-
-            /**
-             * Sets the value of the xpos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setXpos(Integer value) {
-                this.xpos = value;
-            }
-
-            /**
-             * Gets the value of the ypos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getYpos() {
-                return ypos;
-            }
-
-            /**
-             * Sets the value of the ypos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setYpos(Integer value) {
-                this.ypos = value;
-            }
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class HiddenColumns
+    {
+
+      @XmlAttribute(name = "start")
+      protected Integer start;
+
+      @XmlAttribute(name = "end")
+      protected Integer end;
+
+      /**
+       * Gets the value of the start property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getStart()
+      {
+        return start;
+      }
+
+      /**
+       * Sets the value of the start property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setStart(Integer value)
+      {
+        this.start = value;
+      }
+
+      /**
+       * Gets the value of the end property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getEnd()
+      {
+        return end;
+      }
+
+      /**
+       * Sets the value of the end property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setEnd(Integer value)
+      {
+        this.end = value;
+      }
 
-        }
+    }
+
+    /**
+     * 

+     * Java class for anonymous complex type.
+     * 
+     * 

+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Overview
+    {
+
+      @XmlAttribute(name = "showHidden")
+      protected Boolean showHidden;
+
+      @XmlAttribute(name = "residueColour")
+      protected Integer residueColour;
+
+      @XmlAttribute(name = "gapColour")
+      protected Integer gapColour;
+
+      @XmlAttribute(name = "hiddenColour")
+      protected Integer hiddenColour;
+
+      @XmlAttribute(name = "title")
+      protected String title;
+
+      @XmlAttribute(name = "width")
+      protected Integer width;
+
+      @XmlAttribute(name = "height")
+      protected Integer height;
+
+      @XmlAttribute(name = "xpos")
+      protected Integer xpos;
+
+      @XmlAttribute(name = "ypos")
+      protected Integer ypos;
+
+      /**
+       * Gets the value of the showHidden property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public Boolean isShowHidden()
+      {
+        return showHidden;
+      }
+
+      /**
+       * Sets the value of the showHidden property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setShowHidden(Boolean value)
+      {
+        this.showHidden = value;
+      }
+
+      /**
+       * Gets the value of the residueColour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getResidueColour()
+      {
+        return residueColour;
+      }
+
+      /**
+       * Sets the value of the residueColour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setResidueColour(Integer value)
+      {
+        this.residueColour = value;
+      }
+
+      /**
+       * Gets the value of the gapColour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getGapColour()
+      {
+        return gapColour;
+      }
+
+      /**
+       * Sets the value of the gapColour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setGapColour(Integer value)
+      {
+        this.gapColour = value;
+      }
+
+      /**
+       * Gets the value of the hiddenColour property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getHiddenColour()
+      {
+        return hiddenColour;
+      }
+
+      /**
+       * Sets the value of the hiddenColour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setHiddenColour(Integer value)
+      {
+        this.hiddenColour = value;
+      }
+
+      /**
+       * Gets the value of the title property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getTitle()
+      {
+        return title;
+      }
+
+      /**
+       * Sets the value of the title property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setTitle(String value)
+      {
+        this.title = value;
+      }
+
+      /**
+       * Gets the value of the width property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getWidth()
+      {
+        return width;
+      }
+
+      /**
+       * Sets the value of the width property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setWidth(Integer value)
+      {
+        this.width = value;
+      }
+
+      /**
+       * Gets the value of the height property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getHeight()
+      {
+        return height;
+      }
+
+      /**
+       * Sets the value of the height property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setHeight(Integer value)
+      {
+        this.height = value;
+      }
+
+      /**
+       * Gets the value of the xpos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getXpos()
+      {
+        return xpos;
+      }
+
+      /**
+       * Sets the value of the xpos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setXpos(Integer value)
+      {
+        this.xpos = value;
+      }
+
+      /**
+       * Gets the value of the ypos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getYpos()
+      {
+        return ypos;
+      }
+
+      /**
+       * Sets the value of the ypos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setYpos(Integer value)
+      {
+        this.ypos = value;
+      }
 
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index 70a9afb..e4b160f 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for JalviewUserColours complex type.
+ * 

+ * Java class for JalviewUserColours complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 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 colour;
+
+  @XmlElement(namespace = "")
+  protected List filter;
+
+  @XmlAttribute(name = "schemeName")
+  protected String schemeName;
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the colour property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+   *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "attributeName" })
+  public static class Colour
+  {
+
     @XmlElement(namespace = "")
-    protected List filter;
-    @XmlAttribute(name = "schemeName")
-    protected String schemeName;
+    protected List attributeName;
+
+    @XmlAttribute(name = "Name")
+    protected String name;
+
+    @XmlAttribute(name = "RGB", required = true)
+    protected String rgb;
+
+    @XmlAttribute(name = "minRGB")
+    protected String minRGB;
+
+    @XmlAttribute(name = "noValueColour")
+    protected NoValueColour noValueColour;
+
+    @XmlAttribute(name = "threshType")
+    protected ThresholdType threshType;
+
+    @XmlAttribute(name = "threshold")
+    protected Float threshold;
+
+    @XmlAttribute(name = "max")
+    protected Float max;
+
+    @XmlAttribute(name = "min")
+    protected Float min;
+
+    @XmlAttribute(name = "colourByLabel")
+    protected Boolean colourByLabel;
+
+    @XmlAttribute(name = "autoScale")
+    protected Boolean autoScale;
 
     /**
-     * Gets the value of the version property.
+     * Gets the value of the attributeName property.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list {@link String }
+     * 
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getVersion() {
-        return version;
+    public List getAttributeName()
+    {
+      if (attributeName == null)
+      {
+        attributeName = new ArrayList();
+      }
+      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.
      * 
-     * 

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

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

+     */
+    public String getRGB()
+    {
+      return rgb;
+    }
+
+    /**
+     * Sets the value of the rgb property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * 

-     * 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 getColour() {
-        if (colour == null) {
-            colour = new ArrayList();
-        }
-        return this.colour;
+    public String getMinRGB()
+    {
+      return minRGB;
     }
 
     /**
-     * Gets the value of the filter property.
+     * Sets the value of the minRGB property.
      * 
-     * 

-     * This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the filter property.
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * 

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

+     */
+    public void setMinRGB(String value)
+    {
+      this.minRGB = value;
+    }
+
+    /**
+     * Gets the value of the noValueColour property.
      * 
+     * @return possible object is {@link NoValueColour }
      * 
-     * 

-     * 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 getFilter() {
-        if (filter == null) {
-            filter = new ArrayList();
-        }
-        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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Sets the value of the threshold property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Float }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
-     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 attributeName;
-        @XmlAttribute(name = "Name")
-        protected String name;
-        @XmlAttribute(name = "RGB", required = true)
-        protected String rgb;
-        @XmlAttribute(name = "minRGB")
-        protected String minRGB;
-        @XmlAttribute(name = "noValueColour")
-        protected NoValueColour noValueColour;
-        @XmlAttribute(name = "threshType")
-        protected ThresholdType threshType;
-        @XmlAttribute(name = "threshold")
-        protected Float threshold;
-        @XmlAttribute(name = "max")
-        protected Float max;
-        @XmlAttribute(name = "min")
-        protected Float min;
-        @XmlAttribute(name = "colourByLabel")
-        protected Boolean colourByLabel;
-        @XmlAttribute(name = "autoScale")
-        protected Boolean autoScale;
-
-        /**
-         * Gets the value of the attributeName property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List getAttributeName() {
-            if (attributeName == null) {
-                attributeName = new ArrayList();
-            }
-            return this.attributeName;
-        }
-
-        /**
-         * Gets the value of the name property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getName() {
-            return name;
-        }
-
-        /**
-         * Sets the value of the name property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setName(String value) {
-            this.name = value;
-        }
-
-        /**
-         * Gets the value of the rgb property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getRGB() {
-            return rgb;
-        }
-
-        /**
-         * Sets the value of the rgb property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setRGB(String value) {
-            this.rgb = value;
-        }
-
-        /**
-         * Gets the value of the minRGB property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getMinRGB() {
-            return minRGB;
-        }
-
-        /**
-         * Sets the value of the minRGB property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setMinRGB(String value) {
-            this.minRGB = value;
-        }
-
-        /**
-         * Gets the value of the noValueColour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link NoValueColour }
-         *     
-         */
-        public NoValueColour getNoValueColour() {
-            if (noValueColour == null) {
-                return NoValueColour.MIN;
-            } else {
-                return noValueColour;
-            }
-        }
-
-        /**
-         * Sets the value of the noValueColour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link NoValueColour }
-         *     
-         */
-        public void setNoValueColour(NoValueColour value) {
-            this.noValueColour = value;
-        }
-
-        /**
-         * Gets the value of the threshType property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link ThresholdType }
-         *     
-         */
-        public ThresholdType getThreshType() {
-            return threshType;
-        }
-
-        /**
-         * Sets the value of the threshType property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link ThresholdType }
-         *     
-         */
-        public void setThreshType(ThresholdType value) {
-            this.threshType = value;
-        }
-
-        /**
-         * Gets the value of the threshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getThreshold() {
-            return threshold;
-        }
-
-        /**
-         * Sets the value of the threshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setThreshold(Float value) {
-            this.threshold = value;
-        }
-
-        /**
-         * Gets the value of the max property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getMax() {
-            return max;
-        }
-
-        /**
-         * Sets the value of the max property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setMax(Float value) {
-            this.max = value;
-        }
-
-        /**
-         * Gets the value of the min property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getMin() {
-            return min;
-        }
-
-        /**
-         * Sets the value of the min property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setMin(Float value) {
-            this.min = value;
-        }
-
-        /**
-         * Gets the value of the colourByLabel property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isColourByLabel() {
-            return colourByLabel;
-        }
-
-        /**
-         * Sets the value of the colourByLabel property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setColourByLabel(Boolean value) {
-            this.colourByLabel = value;
-        }
-
-        /**
-         * Gets the value of the autoScale property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isAutoScale() {
-            return autoScale;
-        }
-
-        /**
-         * Sets the value of the autoScale property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setAutoScale(Boolean value) {
-            this.autoScale = value;
-        }
+    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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Sets the value of the colourByLabel property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Boolean }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
-     *       </sequence>
-     *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    public void setColourByLabel(Boolean value)
+    {
+      this.colourByLabel = value;
+    }
+
+    /**
+     * Gets the value of the autoScale property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isAutoScale()
+    {
+      return autoScale;
+    }
+
+    /**
+     * Sets the value of the autoScale property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setAutoScale(Boolean value)
+    {
+      this.autoScale = value;
+    }
+
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+   *       </sequence>
+   *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "matcherSet" })
+  public static class Filter
+  {
+
+    @XmlElement(namespace = "", required = true)
+    protected FeatureMatcherSet matcherSet;
+
+    @XmlAttribute(name = "featureType", required = true)
+    protected String featureType;
+
+    /**
+     * Gets the value of the matcherSet property.
+     * 
+     * @return possible object is {@link FeatureMatcherSet }
+     * 
+     */
+    public FeatureMatcherSet getMatcherSet()
+    {
+      return matcherSet;
+    }
+
+    /**
+     * Sets the value of the matcherSet property.
+     * 
+     * @param value
+     *          allowed object is {@link FeatureMatcherSet }
+     * 
+     */
+    public void setMatcherSet(FeatureMatcherSet value)
+    {
+      this.matcherSet = value;
+    }
+
+    /**
+     * Gets the value of the featureType property.
      * 
+     * @return possible object is {@link String }
      * 
      */
-    @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 c0db23c..1f16680 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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
  * 
- * 
Java class for mapListType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * Java class for mapListType complex type.
+ * 
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 mapListFrom;
+
+  protected List mapListTo;
+
+  @XmlAttribute(name = "mapFromUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapFromUnit;
+
+  @XmlAttribute(name = "mapToUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapToUnit;
+
+  /**
+   * Gets the value of the mapListFrom property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class MapListFrom
+  {
+
+    @XmlAttribute(name = "start", required = true)
+    protected int start;
+
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
 
     /**
-     * Gets the value of the mapListFrom property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link MapListType.MapListTo }
-     * 
+     * Sets the value of the start property.
      * 
      */
-    public List getMapListTo() {
-        if (mapListTo == null) {
-            mapListTo = new ArrayList();
-        }
-        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;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class MapListTo
+  {
+
+    @XmlAttribute(name = "start", required = true)
+    protected int start;
+
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
+
     /**
-     * Gets the value of the 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;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
+     * 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;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
+     * 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 8cd3dbf..69bf01d 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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).
+ * 
  * 
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 ac79fa8..b9767e2 100644
--- a/src/jalview/xml/binding/jalview/MatrixType.java
+++ b/src/jalview/xml/binding/jalview/MatrixType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for MatrixType complex type.
+ * 

+ * Java class for MatrixType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <complexType name="MatrixType">
@@ -48,311 +49,317 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MatrixType", propOrder = {
-    "elements",
-    "groups",
-    "newick",
-    "property",
-    "mapping"
-})
-public class MatrixType {
-
-    @XmlElement(required = true)
-    protected String elements;
-    protected List groups;
-    protected List newick;
-    protected List property;
-    protected MapListType mapping;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "rows", required = true)
-    protected BigInteger rows;
-    @XmlAttribute(name = "cols", required = true)
-    protected BigInteger cols;
-    @XmlAttribute(name = "treeMethod")
-    protected String treeMethod;
-    @XmlAttribute(name = "cutHeight")
-    protected Double cutHeight;
-    @XmlAttribute(name = "id")
-    protected String id;
-
-    /**
-     * Gets the value of the elements property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getElements() {
-        return elements;
-    }
+@XmlType(
+  name = "MatrixType",
+  propOrder =
+  { "elements", "groups", "newick", "property", "mapping" })
+public class MatrixType
+{
 
-    /**
-     * Sets the value of the elements property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setElements(String value) {
-        this.elements = value;
-    }
+  @XmlElement(required = true)
+  protected String elements;
 
-    /**
-     * Gets the value of the groups property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

-     * 
-     * 
-     * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Property }
-     * 
-     * 
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
-    }
+  protected List property;
 
-    /**
-     * Gets the value of the mapping property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link MapListType }
-     *     
-     */
-    public MapListType getMapping() {
-        return mapping;
-    }
+  protected MapListType mapping;
 
-    /**
-     * Sets the value of the mapping property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link MapListType }
-     *     
-     */
-    public void setMapping(MapListType value) {
-        this.mapping = value;
-    }
+  @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 = "rows", required = true)
+  protected BigInteger rows;
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  @XmlAttribute(name = "cols", required = true)
+  protected BigInteger cols;
 
-    /**
-     * Gets the value of the rows property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getRows() {
-        return rows;
-    }
+  @XmlAttribute(name = "treeMethod")
+  protected String treeMethod;
 
-    /**
-     * Sets the value of the rows property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setRows(BigInteger value) {
-        this.rows = value;
-    }
+  @XmlAttribute(name = "cutHeight")
+  protected Double cutHeight;
 
-    /**
-     * Gets the value of the cols property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getCols() {
-        return cols;
-    }
+  @XmlAttribute(name = "id")
+  protected String id;
 
-    /**
-     * 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 elements property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getElements()
+  {
+    return elements;
+  }
 
-    /**
-     * Gets the value of the treeMethod property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getTreeMethod() {
-        return treeMethod;
-    }
+  /**
+   * Sets the value of the elements property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setElements(String value)
+  {
+    this.elements = value;
+  }
 
-    /**
-     * Sets the value of the treeMethod property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setTreeMethod(String value) {
-        this.treeMethod = value;
+  /**
+   * Gets the value of the groups property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Property }
+   * 
+   * 
+   */
+  public List getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList();
     }
+    return this.property;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Gets the value of the mapping property.
+   * 
+   * @return possible object is {@link MapListType }
+   * 
+   */
+  public MapListType getMapping()
+  {
+    return mapping;
+  }
 
-    /**
-     * 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 mapping property.
+   * 
+   * @param value
+   *          allowed object is {@link MapListType }
+   * 
+   */
+  public void setMapping(MapListType value)
+  {
+    this.mapping = 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 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 e77537f..eeeed22 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -5,19 +5,21 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 
Java class for NoValueColour.
+ * 

+ * Java class for NoValueColour.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
  * 

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

+ * 
  * 
  * <simpleType name="NoValueColour">
  *   <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 031d125..993adae7 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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. 
- * 
An ObjectFactory allows you to programatically 
- * construct new instances of the Java representation 
- * for XML content. The Java representation of XML 
- * content can consist of schema derived interfaces 
- * and classes representing the binding of schema 
- * type definitions, element declarations and model 
- * groups.  Factory methods for each of these are 
- * provided in this class.
+ * This object contains factory methods for each Java content interface and Java
+ * element interface generated in the jalview.xml.binding.jalview package.
+ * 

+ * An ObjectFactory allows you to programatically construct new instances of the
+ * Java representation for XML content. The Java representation of XML content
+ * can consist of schema derived interfaces and classes representing the binding
+ * of schema type definitions, element declarations and model groups. Factory
+ * methods for each of these are provided in this class.
  * 
  */
 @XmlRegistry
-public class ObjectFactory {
-
-    private final static QName _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 createWebServiceParameterSet(WebServiceParameterSet value) {
-        return new JAXBElement(_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 createJalviewModel(JalviewModel value) {
-        return new JAXBElement(_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 createJalviewUserColours(JalviewUserColours value) {
-        return new JAXBElement(_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 createWebServiceParameterSet(
+          WebServiceParameterSet value)
+  {
+    return new JAXBElement(
+            _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 createJalviewModel(JalviewModel value)
+  {
+    return new JAXBElement(_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 createJalviewUserColours(
+          JalviewUserColours value)
+  {
+    return new JAXBElement(_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 9f8962f..2ff7a55 100644
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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
+ * 
  * 
- * 
Java class for PcaDataType complex type.
+ * 

+ * Java class for PcaDataType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 bd170de..f0fd2f3 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for pdbentry complex type.
+ * 

+ * Java class for pdbentry complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 property;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "type")
-    protected String type;
-    @XmlAttribute(name = "file")
-    protected String file;
-
-    /**
-     * Gets the value of the property property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Pdbentry.Property }
-     * 
-     * 
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
+@XmlType(
+  name = "pdbentry",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "property" })
+@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
+public class Pdbentry
+{
+
+  protected List property;
+
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
+
+  @XmlAttribute(name = "type")
+  protected String type;
+
+  @XmlAttribute(name = "file")
+  protected String file;
+
+  /**
+   * Gets the value of the property property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Property
+  {
+
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
+
+    @XmlAttribute(name = "value", required = true)
+    protected String value;
 
     /**
-     * Gets the value of the 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;
-    }
-
-
-    /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
+     *          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 25a297e..b70e665 100644
--- a/src/jalview/xml/binding/jalview/Property.java
+++ b/src/jalview/xml/binding/jalview/Property.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for property complex type.
+ * 

+ * Java class for property complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 b9739cd..a5923e1 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 dbRef;
-    @XmlAttribute(name = "dsseqid")
-    protected String dsseqid;
-    @XmlAttribute(name = "biotype")
-    protected String biotype;
+  @XmlElement(name = "DBRef")
+  protected List dbRef;
+
+  @XmlAttribute(name = "dsseqid")
+  protected String dsseqid;
+
+  @XmlAttribute(name = "biotype")
+  protected String biotype;
+
+  /**
+   * Gets the value of the dbRef property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @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.
      * 
-     * 

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

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

+     */
+    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 }
      * 
-     * 

-     * 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 getDBRef() {
-        if (dbRef == null) {
-            dbRef = new ArrayList();
-        }
-        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;
+      }
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Sets the value of the locus property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Boolean }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 a091950..f08b225 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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;
-    @XmlElement(name = "Annotation")
-    protected List annotation;
-    protected List sequenceSetProperties;
-    @XmlElement(name = "AlcodonFrame")
-    protected List alcodonFrame;
-    @XmlAttribute(name = "gapChar", required = true)
-    protected String gapChar;
-    @XmlAttribute(name = "datasetId")
-    protected String datasetId;
+  @XmlElement(name = "Sequence")
+  protected List sequence;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Sequence }
-     * 
-     * 
-     */
-    public List getSequence() {
-        if (sequence == null) {
-            sequence = new ArrayList();
-        }
-        return this.sequence;
+  @XmlElement(name = "Annotation")
+  protected List annotation;
+
+  protected List sequenceSetProperties;
+
+  @XmlElement(name = "AlcodonFrame")
+  protected List alcodonFrame;
+
+  @XmlAttribute(name = "gapChar", required = true)
+  protected String gapChar;
+
+  @XmlAttribute(name = "datasetId")
+  protected String datasetId;
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class SequenceSetProperties
+  {
+
+    @XmlAttribute(name = "key")
+    protected String key;
+
+    @XmlAttribute(name = "value")
+    protected String value;
 
     /**
-     * Gets the value of the 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;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     * 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 3ccb382..44e606d 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for SequenceType complex type.
+ * 

+ * Java class for SequenceType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 9afd22b..ad0ea1e 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -5,18 +5,20 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 
Java class for ThresholdType.
+ * 

+ * Java class for ThresholdType.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
  * 

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

+ * 
  * 
  * <simpleType name="ThresholdType">
  *   <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 3e17b63..099af84 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for VAMSAS complex type.
+ * 

+ * Java class for VAMSAS complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 tree;
 
-    @XmlElement(name = "Tree")
-    protected List tree;
-    @XmlElement(name = "SequenceSet")
-    protected List sequenceSet;
+  @XmlElement(name = "SequenceSet")
+  protected List sequenceSet;
 
-    /**
-     * Gets the value of the tree property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link SequenceSet
+   * }
+   * 
+   * 
+   */
+  public List getSequenceSet()
+  {
+    if (sequenceSet == null)
+    {
+      sequenceSet = new ArrayList();
     }
+    return this.sequenceSet;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index dcc30ed..4374c83 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:41 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for WebServiceParameterSet complex type.
+ * 

+ * Java class for WebServiceParameterSet complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 serviceURL;
-    @XmlElement(namespace = "", required = true)
-    protected String parameters;
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
-
-    /**
-     * Gets the value of the version property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getVersion() {
-        return version;
-    }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setVersion(String value) {
-        this.version = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * Gets the value of the serviceURL property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getServiceURL() {
-        if (serviceURL == null) {
-            serviceURL = new ArrayList();
-        }
-        return this.serviceURL;
-    }
-
-    /**
-     * Gets the value of the parameters property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getParameters() {
-        return parameters;
-    }
-
-    /**
-     * Sets the value of the parameters property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setParameters(String value) {
-        this.parameters = value;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
+    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
+public class WebServiceParameterSet
+{
+
+  @XmlElement(name = "Version", namespace = "")
+  protected String version;
+
+  @XmlElement(namespace = "")
+  protected String description;
+
+  @XmlElement(namespace = "", required = true)
+  @XmlSchemaType(name = "anyURI")
+  protected List serviceURL;
+
+  @XmlElement(namespace = "", required = true)
+  protected String parameters;
+
+  @XmlAttribute(name = "name", required = true)
+  protected String name;
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the serviceURL property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List getServiceURL()
+  {
+    if (serviceURL == null)
+    {
+      serviceURL = new ArrayList();
     }
+    return this.serviceURL;
+  }
+
+  /**
+   * Gets the value of the parameters property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getParameters()
+  {
+    return parameters;
+  }
+
+  /**
+   * Sets the value of the parameters property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setParameters(String value)
+  {
+    this.parameters = value;
+  }
+
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index 3e94a3f..65d49d5 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: 2023.05.13 at 06:58:41 PM BST 
 //
 
-@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(
+  namespace = "www.vamsas.ac.uk/jalview/version2",
+  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.jalview;
diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java
index d43091a..c5980b3 100644
--- a/src/jalview/xml/binding/uniprot/CitationType.java
+++ b/src/jalview/xml/binding/uniprot/CitationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for citationType complex type.
+ * 

+ * Java class for citationType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link DbReferenceType }
-     * 
-     * 
-     */
-    public List getDbReference() {
-        if (dbReference == null) {
-            dbReference = new ArrayList();
-        }
-        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 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList();
+    }
+    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 87a8e48..d7f0cdb 100644
--- a/src/jalview/xml/binding/uniprot/CofactorType.java
+++ b/src/jalview/xml/binding/uniprot/CofactorType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for cofactorType complex type.
+ * 

+ * Java class for cofactorType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of 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 set method
+   * for the evidence property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java
index 2e6218f..0477736 100644
--- a/src/jalview/xml/binding/uniprot/CommentType.java
+++ b/src/jalview/xml/binding/uniprot/CommentType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for commentType complex type.
+ * 

+ * Java class for commentType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 physiologicalReaction;
-    protected List cofactor;
-    protected List subcellularLocation;
-    protected CommentType.Conflict conflict;
-    protected List link;
-    protected List event;
-    protected List isoform;
-    protected List interactant;
-    @XmlElement(defaultValue = "false")
-    protected Boolean organismsDiffer;
-    protected Integer experiments;
-    protected CommentType.Disease disease;
-    protected List location;
-    protected List 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 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 physiologicalReaction;
 
-    /**
-     * Gets the value of the redoxPotential property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.RedoxPotential }
-     *     
-     */
-    public CommentType.RedoxPotential getRedoxPotential() {
-        return redoxPotential;
-    }
+  protected List 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 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 link;
+
+  protected List event;
+
+  protected List isoform;
+
+  protected List interactant;
+
+  @XmlElement(defaultValue = "false")
+  protected Boolean organismsDiffer;
+
+  protected Integer experiments;
+
+  protected CommentType.Disease disease;
+
+  protected List location;
+
+  protected List 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 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link SubcellularLocationType }
+   * 
+   * 
+   */
+  public List getSubcellularLocation()
+  {
+    if (subcellularLocation == null)
+    {
+      subcellularLocation = new ArrayList();
+    }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link InteractantType }
+   * 
+   * 
+   */
+  public List getInteractant()
+  {
+    if (interactant == null)
+    {
+      interactant = new ArrayList();
+    }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link LocationType }
+   * 
+   * 
+   */
+  public List getLocation()
+  {
+    if (location == null)
+    {
+      location = new ArrayList();
+    }
+    return this.location;
+  }
+
+  /**
+   * Gets the value of 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 set method
+   * for the text property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List getText()
+  {
+    if (text == null)
+    {
+      text = new ArrayList();
+    }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "max", "text" })
+  public static class Absorption
+  {
+
+    protected EvidencedStringType max;
+
+    protected List 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.
      * 
      * 

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

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

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link PhysiologicalReactionType }
+     * {@link EvidencedStringType }
      * 
      * 
      */
-    public List getPhysiologicalReaction() {
-        if (physiologicalReaction == null) {
-            physiologicalReaction = new ArrayList();
-        }
-        return this.physiologicalReaction;
+    public List getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="sequence" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="resource" use="required">
+   *                   <simpleType>
+   *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *                       <enumeration value="EMBL-CDS"/>
+   *                       <enumeration value="EMBL"/>
+   *                     </restriction>
+   *                   </simpleType>
+   *                 </attribute>
+   *                 <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attribute name="type" use="required">
+   *         <simpleType>
+   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             <enumeration value="frameshift"/>
+   *             <enumeration value="erroneous initiation"/>
+   *             <enumeration value="erroneous termination"/>
+   *             <enumeration value="erroneous gene model prediction"/>
+   *             <enumeration value="erroneous translation"/>
+   *             <enumeration value="miscellaneous discrepancy"/>
+   *           </restriction>
+   *         </simpleType>
+   *       </attribute>
+   *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * 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 getCofactor() {
-        if (cofactor == null) {
-            cofactor = new ArrayList();
-        }
-        return this.cofactor;
+    public CommentType.Conflict.Sequence getSequence()
+    {
+      return sequence;
     }
 
     /**
-     * Gets the value of the subcellularLocation property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * 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 getSubcellularLocation() {
-        if (subcellularLocation == null) {
-            subcellularLocation = new ArrayList();
-        }
-        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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * 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 getLink() {
-        if (link == null) {
-            link = new ArrayList();
-        }
-        return this.link;
+    public void setType(String value)
+    {
+      this.type = value;
     }
 
     /**
-     * Gets the value of the event property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * 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 getEvent() {
-        if (event == null) {
-            event = new ArrayList();
-        }
-        return this.event;
+    public String getRef()
+    {
+      return ref;
     }
 
     /**
-     * Gets the value of the isoform property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * 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 getIsoform() {
-        if (isoform == null) {
-            isoform = new ArrayList();
-        }
-        return this.isoform;
+    public void setRef(String value)
+    {
+      this.ref = value;
     }
 
     /**
-     * Gets the value of the interactant property.
-     * 
      * 

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

-     * For example, to add a new item, do as follows:
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
      * 
-     *    getInteractant().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="resource" use="required">
+     *         <simpleType>
+     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             <enumeration value="EMBL-CDS"/>
+     *             <enumeration value="EMBL"/>
+     *           </restriction>
+     *         </simpleType>
+     *       </attribute>
+     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 

      * 
      * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link InteractantType }
-     * 
-     * 
      */
-    public List getInteractant() {
-        if (interactant == null) {
-            interactant = new ArrayList();
-        }
-        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;
-    }
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+   *       </sequence>
+   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * 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 getLocation() {
-        if (location == null) {
-            location = new ArrayList();
-        }
-        return this.location;
+    public String getName()
+    {
+      return name;
     }
 
     /**
-     * Gets the value of 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 set method for the text property.
-     * 
-     * 

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

-     * 
-     * 
-     * 

-     * 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 getText() {
-        if (text == null) {
-            text = new ArrayList();
-        }
-        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;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "km", "vmax", "text" })
+  public static class Kinetics
+  {
+
+    @XmlElement(name = "KM")
+    protected List km;
+
+    @XmlElement(name = "Vmax")
+    protected List vmax;
+
+    protected List text;
+
     /**
-     * Gets the value of the evidence property.
+     * Gets the value of the km property.
      * 
      * 

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

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

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
+     * {@link EvidencedStringType }
      * 
      * 
      */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+    public List getKM()
+    {
+      if (km == null)
+      {
+        km = new ArrayList();
+      }
+      return this.km;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the vmax property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getVmax().add(newItem);
      * 

      * 
      * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "max",
-        "text"
-    })
-    public static class Absorption {
-
-        protected EvidencedStringType max;
-        protected List 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getText() {
-            if (text == null) {
-                text = new ArrayList();
-            }
-            return this.text;
-        }
-
-    }
-
-
-    /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="sequence" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="resource" use="required">
-     *                   <simpleType>
-     *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *                       <enumeration value="EMBL-CDS"/>
-     *                       <enumeration value="EMBL"/>
-     *                     </restriction>
-     *                   </simpleType>
-     *                 </attribute>
-     *                 <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *       <attribute name="type" use="required">
-     *         <simpleType>
-     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             <enumeration value="frameshift"/>
-     *             <enumeration value="erroneous initiation"/>
-     *             <enumeration value="erroneous termination"/>
-     *             <enumeration value="erroneous gene model prediction"/>
-     *             <enumeration value="erroneous translation"/>
-     *             <enumeration value="miscellaneous discrepancy"/>
-     *           </restriction>
-     *         </simpleType>
-     *       </attribute>
-     *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     * 

+     * 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;
-        }
-
-
-        /**
-         * 
Java class for anonymous complex type.
-         * 
-         * 
The following schema fragment specifies the expected content contained within this class.
-         * 
-         * 
-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="resource" use="required">
-         *         <simpleType>
-         *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-         *             <enumeration value="EMBL-CDS"/>
-         *             <enumeration value="EMBL"/>
-         *           </restriction>
-         *         </simpleType>
-         *       </attribute>
-         *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 

-         * 
-         * 
-         */
-        @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 getVmax()
+    {
+      if (vmax == null)
+      {
+        vmax = new ArrayList();
+      }
+      return this.vmax;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of 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
+     * set method for the text property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-     *       </sequence>
-     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getText().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Link
+  {
+
+    @XmlAttribute(name = "uri", required = true)
+    @XmlSchemaType(name = "anyURI")
+    protected String uri;
 
     /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     * 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 km;
-        @XmlElement(name = "Vmax")
-        protected List vmax;
-        protected List text;
-
-        /**
-         * Gets the value of the km property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getKM() {
-            if (km == null) {
-                km = new ArrayList();
-            }
-            return this.km;
-        }
-
-        /**
-         * Gets the value of the vmax property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getVmax() {
-            if (vmax == null) {
-                vmax = new ArrayList();
-            }
-            return this.vmax;
-        }
-
-        /**
-         * Gets the value of 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 set method for the text property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getText() {
-            if (text == null) {
-                text = new ArrayList();
-            }
-            return this.text;
-        }
-
+    public String getUri()
+    {
+      return uri;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "text" })
+  public static class PhDependence
+  {
+
+    @XmlElement(required = true)
+    protected List text;
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of 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
+     * set method for the text property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getText().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 text;
-
-        /**
-         * Gets the value of 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 set method for the text property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getText() {
-            if (text == null) {
-                text = new ArrayList();
-            }
-            return this.text;
-        }
-
+    public List getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "text" })
+  public static class RedoxPotential
+  {
+
+    @XmlElement(required = true)
+    protected List text;
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the text property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getText().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 text;
-
-        /**
-         * Gets the value of 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 set method for the text property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getText() {
-            if (text == null) {
-                text = new ArrayList();
-            }
-            return this.text;
-        }
-
+    public List getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList();
+      }
+      return this.text;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "text" })
+  public static class TemperatureDependence
+  {
+
+    @XmlElement(required = true)
+    protected List text;
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the text property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getText().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 text;
-
-        /**
-         * Gets the value of 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 set method for the text property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getText() {
-            if (text == null) {
-                text = new ArrayList();
-            }
-            return this.text;
-        }
-
+    public List getText()
+    {
+      if (text == null)
+      {
+        text = new ArrayList();
+      }
+      return this.text;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java
index d0c560f..719344b 100644
--- a/src/jalview/xml/binding/uniprot/ConsortiumType.java
+++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for consortiumType complex type.
+ * 

+ * Java class for consortiumType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 506eafa..184f424 100644
--- a/src/jalview/xml/binding/uniprot/DbReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for dbReferenceType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * Java class for dbReferenceType complex type.
+ * 
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 property;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "evidence")
-    protected List 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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link PropertyType }
-     * 
-     * 
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
-    }
+  protected List 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 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link PropertyType }
+   * 
+   * 
+   */
+  public List getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList();
     }
+    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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of 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 set method
+   * for the evidence property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java
index d13e87e..72de883 100644
--- a/src/jalview/xml/binding/uniprot/Entry.java
+++ b/src/jalview/xml/binding/uniprot/Entry.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 accession;
-    @XmlElement(required = true)
-    protected List name;
-    @XmlElement(required = true)
-    protected ProteinType protein;
-    protected List gene;
-    @XmlElement(required = true)
-    protected OrganismType organism;
-    protected List organismHost;
-    protected List geneLocation;
-    @XmlElement(required = true)
-    protected List reference;
-    @XmlElement(nillable = true)
-    protected List comment;
-    protected List dbReference;
-    @XmlElement(required = true)
-    protected ProteinExistenceType proteinExistence;
-    protected List keyword;
-    protected List feature;
-    protected List 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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getAccession() {
-        if (accession == null) {
-            accession = new ArrayList();
-        }
-        return this.accession;
-    }
+public class Entry
+{
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getName() {
-        if (name == null) {
-            name = new ArrayList();
-        }
-        return this.name;
-    }
+  @XmlElement(required = true)
+  protected List accession;
 
-    /**
-     * Gets the value of the protein property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link ProteinType }
-     *     
-     */
-    public ProteinType getProtein() {
-        return protein;
-    }
+  @XmlElement(required = true)
+  protected List 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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link GeneType }
-     * 
-     * 
-     */
-    public List getGene() {
-        if (gene == null) {
-            gene = new ArrayList();
-        }
-        return this.gene;
-    }
+  protected List 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 organismHost;
 
-    /**
-     * Gets the value of the organismHost property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link OrganismType }
-     * 
-     * 
-     */
-    public List getOrganismHost() {
-        if (organismHost == null) {
-            organismHost = new ArrayList();
-        }
-        return this.organismHost;
-    }
+  protected List geneLocation;
 
-    /**
-     * Gets the value of the geneLocation property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link GeneLocationType }
-     * 
-     * 
-     */
-    public List getGeneLocation() {
-        if (geneLocation == null) {
-            geneLocation = new ArrayList();
-        }
-        return this.geneLocation;
-    }
+  @XmlElement(required = true)
+  protected List reference;
 
-    /**
-     * Gets the value of the reference property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link ReferenceType }
-     * 
-     * 
-     */
-    public List getReference() {
-        if (reference == null) {
-            reference = new ArrayList();
-        }
-        return this.reference;
-    }
+  @XmlElement(nillable = true)
+  protected List comment;
 
-    /**
-     * Gets the value of the comment property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link CommentType }
-     * 
-     * 
-     */
-    public List getComment() {
-        if (comment == null) {
-            comment = new ArrayList();
-        }
-        return this.comment;
-    }
+  protected List dbReference;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link DbReferenceType }
-     * 
-     * 
-     */
-    public List getDbReference() {
-        if (dbReference == null) {
-            dbReference = new ArrayList();
-        }
-        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 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 feature;
 
-    /**
-     * Gets the value of 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 set method for the keyword property.
-     * 
-     * 

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link KeywordType }
-     * 
-     * 
-     */
-    public List getKeyword() {
-        if (keyword == null) {
-            keyword = new ArrayList();
-        }
-        return this.keyword;
-    }
+  protected List evidence;
 
-    /**
-     * Gets the value of the feature property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link FeatureType }
-     * 
-     * 
-     */
-    public List getFeature() {
-        if (feature == null) {
-            feature = new ArrayList();
-        }
-        return this.feature;
-    }
+  @XmlElement(required = true)
+  protected SequenceType sequence;
 
-    /**
-     * Gets the value of 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 set method for the evidence property.
-     * 
-     * 

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link EvidenceType }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List getAccession()
+  {
+    if (accession == null)
+    {
+      accession = new ArrayList();
     }
-
-    /**
-     * 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList();
     }
-
-    /**
-     * 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link GeneType }
+   * 
+   * 
+   */
+  public List getGene()
+  {
+    if (gene == null)
+    {
+      gene = new ArrayList();
     }
-
-    /**
-     * 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link OrganismType }
+   * 
+   * 
+   */
+  public List getOrganismHost()
+  {
+    if (organismHost == null)
+    {
+      organismHost = new ArrayList();
     }
-
-    /**
-     * 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link GeneLocationType }
+   * 
+   * 
+   */
+  public List getGeneLocation()
+  {
+    if (geneLocation == null)
+    {
+      geneLocation = new ArrayList();
     }
-
-    /**
-     * Gets the value of the version property.
-     * 
-     */
-    public int getVersion() {
-        return version;
+    return this.geneLocation;
+  }
+
+  /**
+   * Gets the value of the reference property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link ReferenceType }
+   * 
+   * 
+   */
+  public List getReference()
+  {
+    if (reference == null)
+    {
+      reference = new ArrayList();
     }
-
-    /**
-     * 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList();
+    }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link FeatureType
+   * }
+   * 
+   * 
+   */
+  public List getFeature()
+  {
+    if (feature == null)
+    {
+      feature = new ArrayList();
+    }
+    return this.feature;
+  }
+
+  /**
+   * Gets the value of 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 set method
+   * for the evidence property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidenceType }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    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 765bbad..ec9fdcd 100644
--- a/src/jalview/xml/binding/uniprot/EventType.java
+++ b/src/jalview/xml/binding/uniprot/EventType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for eventType complex type.
+ * 

+ * Java class for eventType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 4297a04..d40163d 100644
--- a/src/jalview/xml/binding/uniprot/EvidenceType.java
+++ b/src/jalview/xml/binding/uniprot/EvidenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for evidenceType complex type.
+ * 

+ * Java class for evidenceType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 f2b903b..4b4c3a2 100644
--- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java
+++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for evidencedStringType complex type.
+ * 

+ * Java class for evidencedStringType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    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 902430d..791aa0e 100644
--- a/src/jalview/xml/binding/uniprot/FeatureType.java
+++ b/src/jalview/xml/binding/uniprot/FeatureType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for featureType complex type.
+ * 

+ * Java class for featureType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getVariation() {
-        if (variation == null) {
-            variation = new ArrayList();
-        }
-        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 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List getVariation()
+  {
+    if (variation == null)
+    {
+      variation = new ArrayList();
     }
+    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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    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 bd93656..f3d2973 100644
--- a/src/jalview/xml/binding/uniprot/GeneLocationType.java
+++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for geneLocationType complex type.
+ * 

+ * Java class for geneLocationType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 name;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+  protected List name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link StatusType }
-     * 
-     * 
-     */
-    public List getName() {
-        if (name == null) {
-            name = new ArrayList();
-        }
-        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 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link StatusType
+   * }
+   * 
+   * 
+   */
+  public List getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList();
     }
+    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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of 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 set method
+   * for the evidence property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java
index 945ced2..b8cec80 100644
--- a/src/jalview/xml/binding/uniprot/GeneNameType.java
+++ b/src/jalview/xml/binding/uniprot/GeneNameType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for geneNameType complex type.
+ * 

+ * Java class for geneNameType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    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 060e9f1..3b2300b 100644
--- a/src/jalview/xml/binding/uniprot/GeneType.java
+++ b/src/jalview/xml/binding/uniprot/GeneType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for geneType complex type.
+ * 

+ * Java class for geneType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 name;
+  @XmlElement(required = true)
+  protected List name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link GeneNameType }
+   * 
+   * 
+   */
+  public List getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList();
     }
+    return this.name;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java
index 956457c..f22b4c8 100644
--- a/src/jalview/xml/binding/uniprot/ImportedFromType.java
+++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for importedFromType complex type.
+ * 

+ * Java class for importedFromType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 7e93624..8902f68 100644
--- a/src/jalview/xml/binding/uniprot/InteractantType.java
+++ b/src/jalview/xml/binding/uniprot/InteractantType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for interactantType complex type.
+ * 

+ * Java class for interactantType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 9724599..c3f1d0a 100644
--- a/src/jalview/xml/binding/uniprot/IsoformType.java
+++ b/src/jalview/xml/binding/uniprot/IsoformType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for isoformType complex type.
+ * 

+ * Java class for isoformType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 id;
-    @XmlElement(required = true)
-    protected List name;
-    @XmlElement(required = true)
-    protected IsoformType.Sequence sequence;
-    protected List text;
+  @XmlElement(required = true)
+  protected List id;
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getId() {
-        if (id == null) {
-            id = new ArrayList();
-        }
-        return this.id;
+  @XmlElement(required = true)
+  protected List name;
+
+  @XmlElement(required = true)
+  protected IsoformType.Sequence sequence;
+
+  protected List text;
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link IsoformType.Name }
-     * 
-     * 
-     */
-    public List getName() {
-        if (name == null) {
-            name = new ArrayList();
-        }
-        return this.name;
+  /**
+   * Gets the value of the name property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link IsoformType.Name }
+   * 
+   * 
+   */
+  public List getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList();
+    }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Name
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List 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.
      * 
      * 

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

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

      * 
      * 
      * 

-     * 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 getText() {
-        if (text == null) {
-            text = new ArrayList();
-        }
-        return this.text;
+    public List getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList();
+      }
+      return this.evidence;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="type" use="required">
+   *         <simpleType>
+   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             <enumeration value="not described"/>
+   *             <enumeration value="described"/>
+   *             <enumeration value="displayed"/>
+   *             <enumeration value="external"/>
+   *           </restriction>
+   *         </simpleType>
+   *       </attribute>
+   *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class Sequence
+  {
+
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+
+    @XmlAttribute(name = "ref")
+    protected String ref;
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the type property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * 
-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
-     * 

+     */
+    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 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList();
-            }
-            return this.evidence;
-        }
-
+    public void setType(String value)
+    {
+      this.type = value;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the ref property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="type" use="required">
-     *         <simpleType>
-     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             <enumeration value="not described"/>
-     *             <enumeration value="described"/>
-     *             <enumeration value="displayed"/>
-     *             <enumeration value="external"/>
-     *           </restriction>
-     *         </simpleType>
-     *       </attribute>
-     *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 5763865..0c10761 100644
--- a/src/jalview/xml/binding/uniprot/KeywordType.java
+++ b/src/jalview/xml/binding/uniprot/KeywordType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for keywordType complex type.
+ * 

+ * Java class for keywordType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    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 0af69c5..1aa1925 100644
--- a/src/jalview/xml/binding/uniprot/LocationType.java
+++ b/src/jalview/xml/binding/uniprot/LocationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for locationType complex type.
+ * 

+ * Java class for locationType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 6bc898d..3b6d294 100644
--- a/src/jalview/xml/binding/uniprot/MoleculeType.java
+++ b/src/jalview/xml/binding/uniprot/MoleculeType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for moleculeType complex type.
+ * 

+ * Java class for moleculeType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 c68a0dd..89496ec 100644
--- a/src/jalview/xml/binding/uniprot/NameListType.java
+++ b/src/jalview/xml/binding/uniprot/NameListType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for nameListType complex type.
+ * 

+ * Java class for nameListType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 consortiumOrPerson;
+  @XmlElements({
+      @XmlElement(name = "consortium", type = ConsortiumType.class),
+      @XmlElement(name = "person", type = PersonType.class) })
+  protected List consortiumOrPerson;
 
-    /**
-     * Gets the value of the consortiumOrPerson property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link ConsortiumType }
-     * {@link PersonType }
-     * 
-     * 
-     */
-    public List getConsortiumOrPerson() {
-        if (consortiumOrPerson == null) {
-            consortiumOrPerson = new ArrayList();
-        }
-        return this.consortiumOrPerson;
+  /**
+   * Gets the value of the consortiumOrPerson property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link ConsortiumType } {@link PersonType }
+   * 
+   * 
+   */
+  public List getConsortiumOrPerson()
+  {
+    if (consortiumOrPerson == null)
+    {
+      consortiumOrPerson = new ArrayList();
     }
+    return this.consortiumOrPerson;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java
index 67c20b8..07967eb 100644
--- a/src/jalview/xml/binding/uniprot/ObjectFactory.java
+++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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. 
- * 
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.
+ * 

+ * 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 createCopyright(String value) {
-        return new JAXBElement(_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 createCopyright(String value)
+  {
+    return new JAXBElement(_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 6306288..de03ff2 100644
--- a/src/jalview/xml/binding/uniprot/OrganismNameType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for organismNameType complex type.
+ * 

+ * Java class for organismNameType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 6d110c1..b053df8 100644
--- a/src/jalview/xml/binding/uniprot/OrganismType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for organismType complex type.
+ * 

+ * Java class for organismType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 name;
-    @XmlElement(required = true)
-    protected List dbReference;
-    protected OrganismType.Lineage lineage;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link OrganismNameType }
-     * 
-     * 
-     */
-    public List getName() {
-        if (name == null) {
-            name = new ArrayList();
-        }
-        return this.name;
+@XmlType(
+  name = "organismType",
+  propOrder =
+  { "name", "dbReference", "lineage" })
+public class OrganismType
+{
+
+  @XmlElement(required = true)
+  protected List name;
+
+  @XmlElement(required = true)
+  protected List dbReference;
+
+  protected OrganismType.Lineage lineage;
+
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
+
+  /**
+   * Gets the value of the name property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link OrganismNameType }
+   * 
+   * 
+   */
+  public List getName()
+  {
+    if (name == null)
+    {
+      name = new ArrayList();
     }
-
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link DbReferenceType }
-     * 
-     * 
-     */
-    public List getDbReference() {
-        if (dbReference == null) {
-            dbReference = new ArrayList();
-        }
-        return this.dbReference;
+    return this.name;
+  }
+
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList();
     }
-
-    /**
-     * 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @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 taxon;
 
     /**
-     * Gets the value of the evidence property.
+     * Gets the value of the taxon property.
      * 
      * 

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

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

      * 
      * 
      * 

-     * 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 getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+    public List getTaxon()
+    {
+      if (taxon == null)
+      {
+        taxon = new ArrayList();
+      }
+      return this.taxon;
     }
 
-
-    /**
-     * 
Java class for anonymous complex type.
-     * 
-     * 
The following schema fragment specifies the expected content contained within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "taxon"
-    })
-    public static class Lineage {
-
-        @XmlElement(required = true)
-        protected List taxon;
-
-        /**
-         * Gets the value of the taxon property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
-         * 
-         */
-        public List getTaxon() {
-            if (taxon == null) {
-                taxon = new ArrayList();
-            }
-            return this.taxon;
-        }
-
-    }
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java
index bdc6631..0887b7b 100644
--- a/src/jalview/xml/binding/uniprot/PersonType.java
+++ b/src/jalview/xml/binding/uniprot/PersonType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for personType complex type.
+ * 

+ * Java class for personType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 36c5d97..e8cea36 100644
--- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
+++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for physiologicalReactionType complex type.
+ * 

+ * Java class for physiologicalReactionType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of 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 set method
+   * for the evidence property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java
index f867ab3..3383f53 100644
--- a/src/jalview/xml/binding/uniprot/PositionType.java
+++ b/src/jalview/xml/binding/uniprot/PositionType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for positionType complex type.
+ * 

+ * Java class for positionType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

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

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of 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 set method
+   * for the evidence property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java
index f54fa28..e651a3b 100644
--- a/src/jalview/xml/binding/uniprot/PropertyType.java
+++ b/src/jalview/xml/binding/uniprot/PropertyType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for propertyType complex type.
+ * 

+ * Java class for propertyType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 f106f83..f3d61ee 100644
--- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for proteinExistenceType complex type.
+ * 

+ * Java class for proteinExistenceType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 6f4c235..13fe5aa 100644
--- a/src/jalview/xml/binding/uniprot/ProteinType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for proteinType complex type.
+ * 

+ * Java class for proteinType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 alternativeName;
+
+  protected List submittedName;
+
+  protected EvidencedStringType allergenName;
+
+  protected EvidencedStringType biotechName;
+
+  protected List cdAntigenName;
+
+  protected List innName;
+
+  protected List domain;
+
+  protected List 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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.AlternativeName }
+   * 
+   * 
+   */
+  public List getAlternativeName()
+  {
+    if (alternativeName == null)
+    {
+      alternativeName = new ArrayList();
+    }
+    return this.alternativeName;
+  }
+
+  /**
+   * Gets the value of 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 set method
+   * for the submittedName property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.SubmittedName }
+   * 
+   * 
+   */
+  public List getSubmittedName()
+  {
+    if (submittedName == null)
+    {
+      submittedName = new ArrayList();
+    }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List getCdAntigenName()
+  {
+    if (cdAntigenName == null)
+    {
+      cdAntigenName = new ArrayList();
+    }
+    return this.cdAntigenName;
+  }
+
+  /**
+   * Gets the value of 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 set method
+   * for the innName property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List getInnName()
+  {
+    if (innName == null)
+    {
+      innName = new ArrayList();
+    }
+    return this.innName;
+  }
+
+  /**
+   * Gets the value of 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 set method
+   * for the domain property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.Domain }
+   * 
+   * 
+   */
+  public List getDomain()
+  {
+    if (domain == null)
+    {
+      domain = new ArrayList();
+    }
+    return this.domain;
+  }
+
+  /**
+   * Gets the value of 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 set method
+   * for the component property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link ProteinType.Component }
+   * 
+   * 
+   */
+  public List getComponent()
+  {
+    if (component == null)
+    {
+      component = new ArrayList();
+    }
+    return this.component;
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+   *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+  public static class AlternativeName
+  {
+
+    protected EvidencedStringType fullName;
+
+    protected List shortName;
+
+    protected List 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.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

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

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

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

+     * 
+     * 
+     * 

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

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "recommendedName", "alternativeName", "submittedName", "allergenName",
+        "biotechName", "cdAntigenName", "innName" })
+  public static class Component
+  {
 
     protected ProteinType.RecommendedName recommendedName;
+
     protected List alternativeName;
+
     protected List submittedName;
+
     protected EvidencedStringType allergenName;
+
     protected EvidencedStringType biotechName;
+
     protected List cdAntigenName;
+
     protected List innName;
-    protected List domain;
-    protected List 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.
      * 
      * 

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

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

      * 
      * 
@@ -126,26 +558,29 @@ public class ProteinType {
      * 
      * 
      */
-    public List getAlternativeName() {
-        if (alternativeName == null) {
-            alternativeName = new ArrayList();
-        }
-        return this.alternativeName;
+    public List getAlternativeName()
+    {
+      if (alternativeName == null)
+      {
+        alternativeName = new ArrayList();
+      }
+      return this.alternativeName;
     }
 
     /**
      * Gets the value of 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 set 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
+     * set method for the submittedName property.
      * 
      * 

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

      * 
      * 
@@ -155,74 +590,75 @@ public class ProteinType {
      * 
      * 
      */
-    public List getSubmittedName() {
-        if (submittedName == null) {
-            submittedName = new ArrayList();
-        }
-        return this.submittedName;
+    public List getSubmittedName()
+    {
+      if (submittedName == null)
+      {
+        submittedName = new ArrayList();
+      }
+      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.
      * 
      * 

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

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

      * 
      * 
@@ -232,26 +668,29 @@ public class ProteinType {
      * 
      * 
      */
-    public List getCdAntigenName() {
-        if (cdAntigenName == null) {
-            cdAntigenName = new ArrayList();
-        }
-        return this.cdAntigenName;
+    public List getCdAntigenName()
+    {
+      if (cdAntigenName == null)
+      {
+        cdAntigenName = new ArrayList();
+      }
+      return this.cdAntigenName;
     }
 
     /**
      * Gets the value of 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 set 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
+     * set method for the innName property.
      * 
      * 

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

      * 
      * 
@@ -261,849 +700,472 @@ public class ProteinType {
      * 
      * 
      */
-    public List getInnName() {
-        if (innName == null) {
-            innName = new ArrayList();
-        }
-        return this.innName;
+    public List getInnName()
+    {
+      if (innName == null)
+      {
+        innName = new ArrayList();
+      }
+      return this.innName;
+    }
+
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "recommendedName", "alternativeName", "submittedName", "allergenName",
+        "biotechName", "cdAntigenName", "innName" })
+  public static class Domain
+  {
+
+    protected ProteinType.RecommendedName recommendedName;
+
+    protected List alternativeName;
+
+    protected List submittedName;
+
+    protected EvidencedStringType allergenName;
+
+    protected EvidencedStringType biotechName;
+
+    protected List cdAntigenName;
+
+    protected List 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.
      * 
      * 

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

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

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.Domain }
+     * {@link ProteinType.AlternativeName }
      * 
      * 
      */
-    public List getDomain() {
-        if (domain == null) {
-            domain = new ArrayList();
-        }
-        return this.domain;
+    public List getAlternativeName()
+    {
+      if (alternativeName == null)
+      {
+        alternativeName = new ArrayList();
+      }
+      return this.alternativeName;
     }
 
     /**
-     * Gets the value of the component property.
+     * Gets the value of 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 set 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
+     * set method for the submittedName property.
      * 
      * 

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

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link ProteinType.Component }
+     * {@link ProteinType.SubmittedName }
      * 
      * 
      */
-    public List getComponent() {
-        if (component == null) {
-            component = new ArrayList();
-        }
-        return this.component;
+    public List getSubmittedName()
+    {
+      if (submittedName == null)
+      {
+        submittedName = new ArrayList();
+      }
+      return this.submittedName;
     }
 
+    /**
+     * Gets the value of the allergenName property.
+     * 
+     * @return possible object is {@link EvidencedStringType }
+     * 
+     */
+    public EvidencedStringType getAllergenName()
+    {
+      return allergenName;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Sets the value of the allergenName property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link EvidencedStringType }
      * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     */
+    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 shortName;
-        protected List 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getShortName() {
-            if (shortName == null) {
-                shortName = new ArrayList();
-            }
-            return this.shortName;
-        }
-
-        /**
-         * Gets the value of the ecNumber property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getEcNumber() {
-            if (ecNumber == null) {
-                ecNumber = new ArrayList();
-            }
-            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.
+     * 
+     * 

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

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

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link EvidencedStringType }
+     * 
+     * 
+     */
+    public List getCdAntigenName()
+    {
+      if (cdAntigenName == null)
+      {
+        cdAntigenName = new ArrayList();
+      }
+      return this.cdAntigenName;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the innName property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getInnName().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 alternativeName;
-        protected List submittedName;
-        protected EvidencedStringType allergenName;
-        protected EvidencedStringType biotechName;
-        protected List cdAntigenName;
-        protected List 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.AlternativeName }
-         * 
-         * 
-         */
-        public List getAlternativeName() {
-            if (alternativeName == null) {
-                alternativeName = new ArrayList();
-            }
-            return this.alternativeName;
-        }
-
-        /**
-         * Gets the value of 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 set method for the submittedName property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.SubmittedName }
-         * 
-         * 
-         */
-        public List getSubmittedName() {
-            if (submittedName == null) {
-                submittedName = new ArrayList();
-            }
-            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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getCdAntigenName() {
-            if (cdAntigenName == null) {
-                cdAntigenName = new ArrayList();
-            }
-            return this.cdAntigenName;
-        }
-
-        /**
-         * Gets the value of 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 set method for the innName property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getInnName() {
-            if (innName == null) {
-                innName = new ArrayList();
-            }
-            return this.innName;
-        }
+    public List getInnName()
+    {
+      if (innName == null)
+      {
+        innName = new ArrayList();
+      }
+      return this.innName;
+    }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+   *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" })
+  public static class RecommendedName
+  {
+
+    @XmlElement(required = true)
+    protected EvidencedStringType fullName;
+
+    protected List shortName;
+
+    protected List 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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the shortName property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getShortName().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 alternativeName;
-        protected List submittedName;
-        protected EvidencedStringType allergenName;
-        protected EvidencedStringType biotechName;
-        protected List cdAntigenName;
-        protected List 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.AlternativeName }
-         * 
-         * 
-         */
-        public List getAlternativeName() {
-            if (alternativeName == null) {
-                alternativeName = new ArrayList();
-            }
-            return this.alternativeName;
-        }
-
-        /**
-         * Gets the value of 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 set method for the submittedName property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link ProteinType.SubmittedName }
-         * 
-         * 
-         */
-        public List getSubmittedName() {
-            if (submittedName == null) {
-                submittedName = new ArrayList();
-            }
-            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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getCdAntigenName() {
-            if (cdAntigenName == null) {
-                cdAntigenName = new ArrayList();
-            }
-            return this.cdAntigenName;
-        }
-
-        /**
-         * Gets the value of 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 set method for the innName property.
-         * 
-         * 

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getInnName() {
-            if (innName == null) {
-                innName = new ArrayList();
-            }
-            return this.innName;
-        }
-
+    public List getShortName()
+    {
+      if (shortName == null)
+      {
+        shortName = new ArrayList();
+      }
+      return this.shortName;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the ecNumber property.
+     * 
+     * 

+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the ecNumber property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getEcNumber().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 shortName;
-        protected List 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getShortName() {
-            if (shortName == null) {
-                shortName = new ArrayList();
-            }
-            return this.shortName;
-        }
-
-        /**
-         * Gets the value of the ecNumber property.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getEcNumber() {
-            if (ecNumber == null) {
-                ecNumber = new ArrayList();
-            }
-            return this.ecNumber;
-        }
+    public List getEcNumber()
+    {
+      if (ecNumber == null)
+      {
+        ecNumber = new ArrayList();
+      }
+      return this.ecNumber;
+    }
+
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "fullName", "ecNumber" })
+  public static class SubmittedName
+  {
+
+    @XmlElement(required = true)
+    protected EvidencedStringType fullName;
+
+    protected List 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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the ecNumber property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getEcNumber().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link EvidencedStringType }
-         * 
-         * 
-         */
-        public List getEcNumber() {
-            if (ecNumber == null) {
-                ecNumber = new ArrayList();
-            }
-            return this.ecNumber;
-        }
-
+    public List getEcNumber()
+    {
+      if (ecNumber == null)
+      {
+        ecNumber = new ArrayList();
+      }
+      return this.ecNumber;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java
index 2ea12e3..9fbb9da 100644
--- a/src/jalview/xml/binding/uniprot/ReactionType.java
+++ b/src/jalview/xml/binding/uniprot/ReactionType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for reactionType complex type.
+ * 

+ * Java class for reactionType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 dbReference;
-    @XmlAttribute(name = "evidence")
-    protected List 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 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 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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link DbReferenceType }
+   * 
+   * 
+   */
+  public List getDbReference()
+  {
+    if (dbReference == null)
+    {
+      dbReference = new ArrayList();
     }
+    return this.dbReference;
+  }
 
-    /**
-     * Gets the value of 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 set method for the evidence property.
-     * 
-     * 

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        return this.evidence;
+  /**
+   * Gets the value of 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 set method
+   * for the evidence property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    return this.evidence;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java
index cc21c86..d1562a1 100644
--- a/src/jalview/xml/binding/uniprot/ReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/ReferenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for referenceType complex type.
+ * 

+ * Java class for referenceType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 scope;
-    protected SourceDataType source;
-    @XmlAttribute(name = "evidence")
-    protected List 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.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
-     * 
-     */
-    public List getScope() {
-        if (scope == null) {
-            scope = new ArrayList();
-        }
-        return this.scope;
-    }
+  @XmlElement(required = true)
+  protected List 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 evidence;
 
-    /**
-     * Gets the value of 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 set method for the evidence property.
-     * 
-     * 

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Integer }
-     * 
-     * 
-     */
-    public List getEvidence() {
-        if (evidence == null) {
-            evidence = new ArrayList();
-        }
-        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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
+   * 
+   */
+  public List getScope()
+  {
+    if (scope == null)
+    {
+      scope = new ArrayList();
     }
+    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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Integer }
+   * 
+   * 
+   */
+  public List getEvidence()
+  {
+    if (evidence == null)
+    {
+      evidence = new ArrayList();
     }
+    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 4c6c67c..f9b4daa 100644
--- a/src/jalview/xml/binding/uniprot/SequenceType.java
+++ b/src/jalview/xml/binding/uniprot/SequenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for sequenceType complex type.
+ * 

+ * Java class for sequenceType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 370323c..4c92560 100644
--- a/src/jalview/xml/binding/uniprot/SourceDataType.java
+++ b/src/jalview/xml/binding/uniprot/SourceDataType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for sourceDataType complex type.
+ * 

+ * Java class for sourceDataType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 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 strainOrPlasmidOrTransposon;
+
+  /**
+   * Gets the value of 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 set method
+   * for the strainOrPlasmidOrTransposon property.
+   * 
+   * 

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

+   * 
+   * 
+   * 

+   * 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 getStrainOrPlasmidOrTransposon()
+  {
+    if (strainOrPlasmidOrTransposon == null)
+    {
+      strainOrPlasmidOrTransposon = new ArrayList();
+    }
+    return this.strainOrPlasmidOrTransposon;
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Plasmid
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List 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.
      * 
      * 

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

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

      * 
      * 
      * 

-     * 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 getStrainOrPlasmidOrTransposon() {
-        if (strainOrPlasmidOrTransposon == null) {
-            strainOrPlasmidOrTransposon = new ArrayList();
-        }
-        return this.strainOrPlasmidOrTransposon;
+    public List getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList();
+      }
+      return this.evidence;
     }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Strain
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List evidence;
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the value property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * 
-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
-     * 

+     */
+    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 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList();
-            }
-            return this.evidence;
-        }
-
+    public void setValue(String value)
+    {
+      this.value = value;
     }
 
-
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the evidence property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
+     * getEvidence().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList();
-            }
-            return this.evidence;
-        }
+    public List getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList();
+      }
+      return this.evidence;
+    }
+
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Tissue
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List 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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the evidence property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
+     * getEvidence().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList();
-            }
-            return this.evidence;
-        }
+    public List getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList();
+      }
+      return this.evidence;
+    }
 
+  }
+
+  /**
+   * 

+   * Java class for anonymous complex type.
+   * 
+   * 

+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
+   * 
+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 

+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "", propOrder = { "value" })
+  public static class Transposon
+  {
+
+    @XmlValue
+    protected String value;
+
+    @XmlAttribute(name = "evidence")
+    protected List 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;
+    }
 
     /**
-     * 
Java class for anonymous complex type.
+     * Gets the value of the evidence property.
      * 
-     * 
The following schema fragment specifies the expected content contained within this class.
+     * 

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

+     * For example, to add a new item, do as follows:
      * 
      * 
-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
+     * getEvidence().add(newItem);
      * 

      * 
      * 
+     * 

+     * 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 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.
-         * 
-         * 

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

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

-         * 
-         * 
-         * 

-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
-         * 
-         */
-        public List getEvidence() {
-            if (evidence == null) {
-                evidence = new ArrayList();
-            }
-            return this.evidence;
-        }
-
+    public List getEvidence()
+    {
+      if (evidence == null)
+      {
+        evidence = new ArrayList();
+      }
+      return this.evidence;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java
index 886f33f..2e92ca6 100644
--- a/src/jalview/xml/binding/uniprot/SourceType.java
+++ b/src/jalview/xml/binding/uniprot/SourceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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).
  * 
- * 
Java class for sourceType complex type.
+ * 

+ * Java class for sourceType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 919bc93..220c009 100644
--- a/src/jalview/xml/binding/uniprot/StatusType.java
+++ b/src/jalview/xml/binding/uniprot/StatusType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for statusType complex type.
+ * 

+ * Java class for statusType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 18da1a7..f8adfde 100644
--- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
+++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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.
  * 
- * 
Java class for subcellularLocationType complex type.
+ * 

+ * Java class for subcellularLocationType complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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 location;
+
+  protected List topology;
 
-    @XmlElement(required = true)
-    protected List location;
-    protected List topology;
-    protected List orientation;
+  protected List orientation;
 
-    /**
-     * Gets the value of the location property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List getLocation()
+  {
+    if (location == null)
+    {
+      location = new ArrayList();
     }
+    return this.location;
+  }
 
-    /**
-     * Gets the value of the topology property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List getTopology()
+  {
+    if (topology == null)
+    {
+      topology = new ArrayList();
     }
+    return this.topology;
+  }
 
-    /**
-     * Gets the value of the orientation property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

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

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list
+   * {@link EvidencedStringType }
+   * 
+   * 
+   */
+  public List getOrientation()
+  {
+    if (orientation == null)
+    {
+      orientation = new ArrayList();
     }
+    return this.orientation;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java
index cb1c9d3..283ba1f 100644
--- a/src/jalview/xml/binding/uniprot/Uniprot.java
+++ b/src/jalview/xml/binding/uniprot/Uniprot.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.05.13 at 06:58:42 PM BST 
 //
 
-
 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;
 
-
 /**
- * 
Java class for anonymous complex type.
+ * 

+ * Java class for anonymous complex type.
  * 
- * 
The following schema fragment specifies the expected content contained within this class.
+ * 

+ * The following schema fragment specifies the expected content contained within
+ * this class.
  * 
  * 
  * <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;
-    protected String copyright;
+  @XmlElement(required = true)
+  protected List entry;
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * 

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

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

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link Entry }
-     * 
-     * 
-     */
-    public List getEntry() {
-        if (entry == null) {
-            entry = new ArrayList();
-        }
-        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.
+   * 
+   * 

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

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

+   * 
+   * 
+   * 

+   * Objects of the following type(s) are allowed in the list {@link Entry }
+   * 
+   * 
+   */
+  public List getEntry()
+  {
+    if (entry == null)
+    {
+      entry = new ArrayList();
     }
+    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 dbe9ff7..eb7f47a 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: 2023.05.13 at 06:58:42 PM BST 
 //
 
-@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 c56a947..2970ccf 100755
--- a/src/mc_view/PDBChain.java
+++ b/src/mc_view/PDBChain.java
@@ -703,7 +703,8 @@ public class PDBChain
               dsq.addAlignmentAnnotation(ana);
               if (cm != null && cm instanceof MappableContactMatrixI)
               {
-                dsq.addContactListFor(ana, ((MappableContactMatrixI) cm).liftOver(dsq,sqmpping));
+                dsq.addContactListFor(ana, ((MappableContactMatrixI) cm)
+                        .liftOver(dsq, sqmpping));
               }
             }
             else
@@ -718,8 +719,8 @@ 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 0f3ea96..f017662 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -2605,25 +2605,29 @@ public class AlignmentUtilsTests
     assertSame(seq, cds1.getDatasetSequence());
   }
 
-
   @Test(groups = "Functional")
   public void testAddReferenceAnnotations()
   {
-    SequenceI longseq= new Sequence("longA","ASDASDASDASDAASDASDASDASDA");
+    SequenceI longseq = new Sequence("longA", "ASDASDASDASDAASDASDASDASDA");
     Annotation[] aa = new Annotation[longseq.getLength()];
-    
-    for (int p=0;p tipEntries = new TreeMap<>();
     Map> candidates = new LinkedHashMap<>();
@@ -2633,9 +2637,9 @@ public class AlignmentUtilsTests
     AlignmentUtils.addReferenceAnnotations(candidates, ourAl, null);
 
     assertNotNull(ourAl.getAlignmentAnnotation());
-    assertEquals(ourAl.getAlignmentAnnotation().length,2);
-    
-    for (AlignmentAnnotation alan:ourAl.getAlignmentAnnotation())
+    assertEquals(ourAl.getAlignmentAnnotation().length, 2);
+
+    for (AlignmentAnnotation alan : ourAl.getAlignmentAnnotation())
     {
       verifyExpectedSequenceAnnotation(alan);
     }
@@ -2643,12 +2647,14 @@ public class AlignmentUtilsTests
     // now simulate copy/paste to new alignment
     SequenceI[] newSeqAl = new SequenceI[2];
     // copy sequences but no annotation
-    newSeqAl[0]=new Sequence(ourAl.getSequenceAt(0),ourAl.getSequenceAt(0).getAnnotation());
-    newSeqAl[1]=new Sequence(ourAl.getSequenceAt(1),ourAl.getSequenceAt(1).getAnnotation());
-    
+    newSeqAl[0] = new Sequence(ourAl.getSequenceAt(0),
+            ourAl.getSequenceAt(0).getAnnotation());
+    newSeqAl[1] = new Sequence(ourAl.getSequenceAt(1),
+            ourAl.getSequenceAt(1).getAnnotation());
+
     Alignment newAl = new Alignment(newSeqAl);
     // delete annotation
-    for (SequenceI sq:newAl.getSequences())
+    for (SequenceI sq : newAl.getSequences())
     {
       sq.setAlignmentAnnotation(new AlignmentAnnotation[0]);
     }
@@ -2656,28 +2662,37 @@ public class AlignmentUtilsTests
     SequenceGroup sg = new SequenceGroup(Arrays.asList(newSeqAl));
     sg.setStartRes(0);
     sg.setEndRes(newAl.getWidth());
-    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0], newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
-    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1], newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
-    for (AlignmentAnnotation alan:newAl.getAlignmentAnnotation())
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[0],
+            newSeqAl[0].getDatasetSequence().getAnnotation()[0], sg);
+    AlignmentUtils.addReferenceAnnotationTo(newAl, newSeqAl[1],
+            newSeqAl[1].getDatasetSequence().getAnnotation()[0], sg);
+    for (AlignmentAnnotation alan : newAl.getAlignmentAnnotation())
     {
       verifyExpectedSequenceAnnotation(alan);
     }
   }
-  
+
   /**
-   * helper - tests annotation is mapped to position it was originally created for
+   * helper - tests annotation is mapped to position it was originally created
+   * for
+   * 
    * @param alan
    */
   private void verifyExpectedSequenceAnnotation(AlignmentAnnotation alan)
   {
-    for (int c=0;c=alan.sequenceRef.getLength() || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
+        assertEquals("Misaligned annotation at " + c,
+                (float) alan.sequenceRef.findPosition(c), a.value);
+      }
+      else
+      {
+        assertTrue("Unexpected Null at position " + c,
+                c >= alan.sequenceRef.getLength()
+                        || Comparison.isGap(alan.sequenceRef.getCharAt(c)));
       }
     }
   }
@@ -2707,15 +2722,17 @@ public class AlignmentUtilsTests
     AlignmentAnnotation alan = al.findAnnotations(sq, null, cm_aan.label)
             .iterator().next();
     ContactMatrixI t_cm = al.getContactMatrixFor(alan);
-    assertNotNull("No contact map for the transferred annotation row.",t_cm);
+    assertNotNull("No contact map for the transferred annotation row.",
+            t_cm);
     assertTrue(t_cm instanceof SeqDistanceContactMatrix);
-    assertTrue(((SeqDistanceContactMatrix)t_cm).hasReferenceSeq());
-    
+    assertTrue(((SeqDistanceContactMatrix) t_cm).hasReferenceSeq());
+
     ContactListI cl = al.getContactListFor(alan, 1);
     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 9550a21..0e80368 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(groups = { "Functional" })
+  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 pae_obj = (List) 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) 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 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(groups={"Functional"})
-    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 pae_obj = (List) Platform.parseJSON(new FileInputStream(testPAE));
-      if (pae_obj == null)
-      {
-        Assert.fail("JSON PAE file did not parse properly.");
-      }
-      ContactMatrixI matrix = new PAEContactMatrix(target,
-              (Map) 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 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();
-        groups.add(clusterer.getTopNode());
-      }
-      int n=1;
-      for (BinaryNode root:groups)
+      groups = new ArrayList();
+      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/datamodel/PAEContactMatrixTest.java b/test/jalview/datamodel/PAEContactMatrixTest.java
index 9b95164..8cc2ec4 100644
--- a/test/jalview/datamodel/PAEContactMatrixTest.java
+++ b/test/jalview/datamodel/PAEContactMatrixTest.java
@@ -22,162 +22,188 @@ public class PAEContactMatrixTest
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
   }
 
-  static float[][] PAEdata = {
-      {1.0f,2.0f,3.0f,4.0f,5.0f},
-      {2.0f,1.0f,2.0f,3.0f,4.0f},
-      {3.0f,2.0f,1.0f,2.0f,3.0f},
-      {4.0f,3.0f,2.0f,1.0f,2.0f},
-      {5.0f,4.0f,3.0f,2.0f,1.0f}};
-  
+  static float[][] PAEdata = { { 1.0f, 2.0f, 3.0f, 4.0f, 5.0f },
+      { 2.0f, 1.0f, 2.0f, 3.0f, 4.0f },
+      { 3.0f, 2.0f, 1.0f, 2.0f, 3.0f },
+      { 4.0f, 3.0f, 2.0f, 1.0f, 2.0f },
+      { 5.0f, 4.0f, 3.0f, 2.0f, 1.0f } };
+
   /**
    * test associations for a PAE matrix
    */
   @Test(groups = { "Functional" })
   public void testSeqAssociatedPAEMatrix()
   {
-    Sequence seq = new Sequence("Seq","ASDQE");
-    AlignmentAnnotation aa = seq.addContactList(new PAEContactMatrix(seq, PAEdata));
+    Sequence seq = new Sequence("Seq", "ASDQE");
+    AlignmentAnnotation aa = seq
+            .addContactList(new PAEContactMatrix(seq, PAEdata));
     assertNotNull(seq.getContactListFor(aa, 0));
-    assertEquals(seq.getContactListFor(aa, 0).getContactAt(0),1.0);
+    assertEquals(seq.getContactListFor(aa, 0).getContactAt(0), 1.0);
     assertNotNull(seq.getContactListFor(aa, 1));
-    assertEquals(seq.getContactListFor(aa, 1).getContactAt(1),1.0);
+    assertEquals(seq.getContactListFor(aa, 1).getContactAt(1), 1.0);
     assertNotNull(seq.getContactListFor(aa, 2));
-    assertEquals(seq.getContactListFor(aa, 2).getContactAt(2),1.0);
+    assertEquals(seq.getContactListFor(aa, 2).getContactAt(2), 1.0);
     assertNotNull(seq.getContactListFor(aa, 3));
-    assertEquals(seq.getContactListFor(aa, 3).getContactAt(3),1.0);
+    assertEquals(seq.getContactListFor(aa, 3).getContactAt(3), 1.0);
     assertNotNull(seq.getContactListFor(aa, 4));
-    assertEquals(seq.getContactListFor(aa, 4).getContactAt(4),1.0);
-    
-    assertNotNull(seq.getContactListFor(aa, seq.getEnd()-1));
+    assertEquals(seq.getContactListFor(aa, 4).getContactAt(4), 1.0);
+
+    assertNotNull(seq.getContactListFor(aa, seq.getEnd() - 1));
     assertNull(seq.getContactListFor(aa, seq.getEnd()));
-    
+
     ContactListI cm = seq.getContactListFor(aa, seq.getStart());
-    assertEquals(cm.getContactAt(seq.getStart()),1d);
-    verifyPAEmatrix(seq, aa, 0,0,4);
-    
-    
+    assertEquals(cm.getContactAt(seq.getStart()), 1d);
+    verifyPAEmatrix(seq, aa, 0, 0, 4);
+
     // Now associated with sequence not starting at 1
-    seq = new Sequence("Seq/5-9","ASDQE");
+    seq = new Sequence("Seq/5-9", "ASDQE");
     ContactMatrixI paematrix = new PAEContactMatrix(seq, PAEdata);
     aa = seq.addContactList(paematrix);
     assertNotNull(aa);
-    // individual annotation elements need to be distinct for Matrix associated rows
-    Annotation ae5=aa.getAnnotationForPosition(5);
-    Annotation ae6=aa.getAnnotationForPosition(6);
+    // individual annotation elements need to be distinct for Matrix associated
+    // rows
+    Annotation ae5 = aa.getAnnotationForPosition(5);
+    Annotation ae6 = aa.getAnnotationForPosition(6);
     assertNotNull(ae5);
     assertNotNull(ae6);
-    assertTrue(ae5!=ae6);
-    
+    assertTrue(ae5 != ae6);
+
     cm = seq.getContactListFor(aa, 0);
-    assertEquals(cm.getContactAt(0),1d);
+    assertEquals(cm.getContactAt(0), 1d);
     verifyPAEmatrix(seq, aa, 0, 0, 4);
 
     // test clustering
     paematrix.setGroupSet(GroupSet.makeGroups(paematrix, 0.1f, false));
-    
+
     // remap - test the MappableContactMatrix.liftOver method
-    SequenceI newseq = new Sequence("Seq","ASDQEASDQEASDQE");
-    Mapping sqmap = new Mapping(seq, new MapList(new int[] {5,8,10,10},new int[] { 5,9}, 1, 1));
+    SequenceI newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+    Mapping sqmap = new Mapping(seq,
+            new MapList(new int[]
+            { 5, 8, 10, 10 }, new int[] { 5, 9 }, 1, 1));
     assertTrue(paematrix instanceof MappableContactMatrixI);
-    
-    MappableContactMatrixI remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
+
+    MappableContactMatrixI remapped = ((MappableContactMatrixI) paematrix)
+            .liftOver(newseq, sqmap);
     assertTrue(remapped instanceof PAEContactMatrix);
-    
+
     AlignmentAnnotation newaa = newseq.addContactList(remapped);
-    assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(1)));
-    assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(4)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(5)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(6)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(7)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(8)));
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
     // no mapping for position 9
-    assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(9)));
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
     // last column
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
 
     // verify MappedPositions includes discontinuity
-    int[] mappedCl = newseq.getContactListFor(newaa, 5).getMappedPositionsFor(0, 4);
-    assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
-    
-    // make it harder. 
-    
+    int[] mappedCl = newseq.getContactListFor(newaa, 5)
+            .getMappedPositionsFor(0, 4);
+    assertEquals(4, mappedCl.length,
+            "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
+    // make it harder.
+
     SequenceI alseq = newseq.getSubSequence(6, 10);
     alseq.insertCharAt(2, 2, '-');
-    AlignmentI alForSeq=new Alignment(new SequenceI[] { alseq });
-    newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa, null);
+    AlignmentI alForSeq = new Alignment(new SequenceI[] { alseq });
+    newaa = AlignmentUtils.addReferenceAnnotationTo(alForSeq, alseq, newaa,
+            null);
     ContactListI alcl = alForSeq.getContactListFor(newaa, 1);
     assertNotNull(alcl);
     mappedCl = alcl.getMappedPositionsFor(0, 4);
     assertNotNull(mappedCl);
-    assertEquals(4,mappedCl.length,"getMappedPositionsFor doesn't support discontinuous mappings to contactList");
-    
+    assertEquals(4, mappedCl.length,
+            "getMappedPositionsFor doesn't support discontinuous mappings to contactList");
+
     // remap2 - test with original matrix map from 1-5 remapped to 5-9
-    
-    seq = new Sequence("Seq/1-5","ASDQE");
+
+    seq = new Sequence("Seq/1-5", "ASDQE");
     paematrix = new PAEContactMatrix(seq, PAEdata);
     assertTrue(paematrix instanceof MappableContactMatrixI);
     aa = seq.addContactList(paematrix);
-    
-    newseq = new Sequence("Seq","ASDQEASDQEASDQE");
-    sqmap = new Mapping(seq, new MapList(new int[] {5,9},new int[] { 1,5}, 1, 1));
-    
-    remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
+
+    newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+    sqmap = new Mapping(seq,
+            new MapList(new int[]
+            { 5, 9 }, new int[] { 1, 5 }, 1, 1));
+
+    remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
     assertTrue(remapped instanceof PAEContactMatrix);
-    
-    
+
     newaa = newseq.addContactList(remapped);
     verify_mapping(newseq, newaa);
 
     // remap3 - remap2 but mapping sense in liftover is reversed
-    
-    seq = new Sequence("Seq/1-5","ASDQE");
+
+    seq = new Sequence("Seq/1-5", "ASDQE");
     paematrix = new PAEContactMatrix(seq, PAEdata);
     assertTrue(paematrix instanceof MappableContactMatrixI);
     aa = seq.addContactList(paematrix);
-    
-    newseq = new Sequence("Seq","ASDQEASDQEASDQE");
-    sqmap = new Mapping(newseq, new MapList(new int[] { 1,5},new int[] {5,9},1, 1));
-    
-    remapped = ((MappableContactMatrixI)paematrix).liftOver(newseq, sqmap);
+
+    newseq = new Sequence("Seq", "ASDQEASDQEASDQE");
+    sqmap = new Mapping(newseq,
+            new MapList(new int[]
+            { 1, 5 }, new int[] { 5, 9 }, 1, 1));
+
+    remapped = ((MappableContactMatrixI) paematrix).liftOver(newseq, sqmap);
     assertTrue(remapped instanceof PAEContactMatrix);
-    
-    
+
     newaa = newseq.addContactList(remapped);
     verify_mapping(newseq, newaa);
   }
+
   /**
-   * checks that the PAE matrix is located at positions 1-9 in newseq, and columns are not truncated.
+   * checks that the PAE matrix is located at positions 1-9 in newseq, and
+   * columns are not truncated.
+   * 
    * @param newseq
    * @param newaa
    */
   private void verify_mapping(SequenceI newseq, AlignmentAnnotation newaa)
   {
-  assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(1)));
-    assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(4)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(5)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(6)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(7)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(8)));
-    assertNotNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(9)));
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(1)));
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(4)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(5)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(6)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(7)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(8)));
+    assertNotNull(
+            newseq.getContactListFor(newaa, -1 + newseq.findIndex(9)));
     // last column should be null this time
-    assertNull(newseq.getContactListFor(newaa, -1+newseq.findIndex(10)));
-    
+    assertNull(newseq.getContactListFor(newaa, -1 + newseq.findIndex(10)));
+
     verifyPAEmatrix(newseq, newaa, 4, 4, 8);
   }
 
-  private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa, int topl, int rowl, int rowr)
+  private void verifyPAEmatrix(SequenceI seq, AlignmentAnnotation aa,
+          int topl, int rowl, int rowr)
   {
     int[] mappedCl;
-    for (int f=rowl;f<=rowr;f++) {
+    for (int f = rowl; f <= rowr; f++)
+    {
       ContactListI clist = seq.getContactListFor(aa, f);
-      assertNotNull(clist,"No ContactListI for position "+(f));
-      assertEquals(clist.getContactAt(0), (double) f-topl+1,"for column "+f+" relative to "+topl);
+      assertNotNull(clist, "No ContactListI for position " + (f));
+      assertEquals(clist.getContactAt(0), (double) f - topl + 1,
+              "for column " + f + " relative to " + topl);
       mappedCl = clist.getMappedPositionsFor(0, 0);
       assertNotNull(mappedCl);
-      assertEquals(mappedCl[0],mappedCl[1]);
-      assertEquals(mappedCl[0],seq.findIndex(seq.getStart()+topl));
-      assertEquals(clist.getContactAt(f-topl),1d, "for column and row "+f+" relative to "+topl);
-    }    
+      assertEquals(mappedCl[0], mappedCl[1]);
+      assertEquals(mappedCl[0], seq.findIndex(seq.getStart() + topl));
+      assertEquals(clist.getContactAt(f - topl), 1d,
+              "for column and row " + f + " relative to " + topl);
+    }
   }
 
 }
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/SeqPanelTest.java b/test/jalview/gui/SeqPanelTest.java
index f905ef2..6a27b51 100644
--- a/test/jalview/gui/SeqPanelTest.java
+++ b/test/jalview/gui/SeqPanelTest.java
@@ -920,7 +920,7 @@ public class SeqPanelTest
     }
     assertEquals(dna.length(), 51200);
     AlignFrame alignFrame = new FileLoader()
-            .LoadFileWaitTillLoaded("dna "+dna, DataSourceType.PASTE);
+            .LoadFileWaitTillLoaded("dna " + dna, DataSourceType.PASTE);
     SeqPanel testee = alignFrame.alignPanel.getSeqPanel();
     AlignViewport av = alignFrame.getViewport();
     av.setScaleAboveWrapped(true);
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/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index d038c78..37ef069 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -247,9 +247,8 @@ 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))
@@ -268,9 +267,8 @@ 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,
@@ -1568,30 +1566,34 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     }
     PAEContactMatrix dummyMat = new PAEContactMatrix(sq, paevals);
     String content = ContactMatrix.contactToFloatString(dummyMat);
-    Assert.assertTrue(content.contains("\t1.")); // at least one element must be 1
-    float[][] vals = ContactMatrix.fromFloatStringToContacts(content, sq.getLength(), sq.getLength());
-    assertEquals(vals[3][4],paevals[3][4]);
-    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat,0.5f, false));
+    Assert.assertTrue(content.contains("\t1.")); // at least one element must be
+                                                 // 1
+    float[][] vals = ContactMatrix.fromFloatStringToContacts(content,
+            sq.getLength(), sq.getLength());
+    assertEquals(vals[3][4], paevals[3][4]);
+    dummyMat.setGroupSet(GroupSet.makeGroups(dummyMat, 0.5f, false));
     Assert.assertNotSame(dummyMat.getNewick(), "");
     AlignmentAnnotation paeCm = sq.addContactList(dummyMat);
     al.addAnnotation(paeCm);
     // verify store/restore of group bitsets
-    for (BitSet  gp:dummyMat.getGroups())
+    for (BitSet gp : dummyMat.getGroups())
     {
       StringBuilder sb = new StringBuilder();
-      for (long val:gp.toLongArray())
+      for (long val : gp.toLongArray())
       {
-        if (sb.length()>0) {
+        if (sb.length() > 0)
+        {
           sb.append(",");
         }
         sb.append(val);
       }
       String[] longvals = sb.toString().split(",");
       long[] newlongvals = new long[longvals.length];
-      for (int lv=0;lv= 0; i--)
     {
       ContactListI oldCM = dummyMat.getContactList(i),
               newCM = restoredMat.getContactList(i);
       for (int j = oldCM.getContactHeight(); j >= 0; j--)
       {
-        double old_j=oldCM.getContactAt(j);
-        double new_j=newCM.getContactAt(j);
-        Assert.assertEquals(old_j,new_j);
+        double old_j = oldCM.getContactAt(j);
+        double new_j = newCM.getContactAt(j);
+        Assert.assertEquals(old_j, new_j);
       }
     }
     Assert.assertEquals(restoredMat.hasGroups(), dummyMat.hasGroups());
     Assert.assertEquals(restoredMat.getGroups(), dummyMat.getGroups());
     Assert.assertEquals(restoredMat.hasTree(), dummyMat.hasTree());
-    Assert.assertEquals( restoredMat.getNewick(),dummyMat.getNewick());
-    
-    
+    Assert.assertEquals(restoredMat.getNewick(), dummyMat.getNewick());
+
   }
 
 }
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