From e148ab3317ddf2a3d8db98c89cbe0c68aedd1b47 Mon Sep 17 00:00:00 2001 From: Jim Procter Date: Thu, 15 Aug 2024 08:47:12 +0100 Subject: [PATCH] JAL-1551 spotless --- src/jalview/analysis/AAFrequency.java | 187 +- src/jalview/analysis/AlignSeq.java | 231 +- src/jalview/analysis/AlignmentAnnotationUtils.java | 3 +- src/jalview/analysis/AlignmentUtils.java | 68 +- src/jalview/analysis/ConnectivityException.java | 8 +- src/jalview/analysis/Finder.java | 2 +- src/jalview/analysis/PaSiMap.java | 43 +- src/jalview/analysis/TreeBuilder.java | 14 +- src/jalview/analysis/TreeModel.java | 10 +- src/jalview/analysis/ccAnalysis.java | 1004 +- .../analysis/scoremodels/DistanceScoreModel.java | 2 +- .../analysis/scoremodels/FeatureDistanceModel.java | 2 +- src/jalview/analysis/scoremodels/ScoreModels.java | 14 +- .../SecondaryStructureDistanceModel.java | 135 +- .../analysis/scoremodels/SimilarityParams.java | 2 +- src/jalview/api/AlignViewControllerI.java | 4 +- src/jalview/api/AlignViewportI.java | 17 +- src/jalview/api/ViewStyleI.java | 6 +- src/jalview/api/analysis/ScoreModelI.java | 30 +- src/jalview/api/analysis/SimilarityParamsI.java | 2 +- src/jalview/appletgui/AlignFrame.java | 4 +- src/jalview/bin/Cache.java | 9 +- src/jalview/bin/JalviewLite.java | 4 +- .../commands/JustifyLeftOrRightCommand.java | 6 +- src/jalview/controller/AlignViewController.java | 2 +- src/jalview/datamodel/Alignment.java | 5 +- src/jalview/datamodel/AlignmentAnnotation.java | 2 +- src/jalview/datamodel/BinaryNode.java | 18 +- src/jalview/datamodel/PDBEntry.java | 9 +- src/jalview/datamodel/Profile.java | 23 +- src/jalview/datamodel/ProfileI.java | 12 +- src/jalview/datamodel/SecondaryStructureCount.java | 9 +- src/jalview/datamodel/SequenceGroup.java | 145 +- src/jalview/ext/jmol/JalviewJmolBinding.java | 18 +- src/jalview/gui/AlignFrame.java | 14 +- src/jalview/gui/AlignViewport.java | 5 +- src/jalview/gui/AnnotationLabels.java | 40 +- src/jalview/gui/AppJmol.java | 18 +- src/jalview/gui/CalculationChooser.java | 37 +- src/jalview/gui/CutAndPasteTransfer.java | 12 +- src/jalview/gui/Desktop.java | 4 +- src/jalview/gui/FontChooser.java | 6 +- src/jalview/gui/PCAPanel.java | 13 +- src/jalview/gui/PaSiMapPanel.java | 80 +- src/jalview/gui/PairwiseAlignPanel.java | 73 +- src/jalview/gui/PopupMenu.java | 169 +- src/jalview/gui/ProgressBar.java | 2 +- src/jalview/gui/RotatableCanvas.java | 50 +- src/jalview/gui/SeqPanel.java | 3 +- src/jalview/gui/SliderPanel.java | 76 +- src/jalview/gui/StructureChooser.java | 14 +- src/jalview/gui/TreeCanvas.java | 29 +- src/jalview/gui/TreePanel.java | 27 +- .../ThreeDBStructureChooserQuerySource.java | 5 +- src/jalview/io/AnnotationFile.java | 8 +- src/jalview/jbgui/GAlignFrame.java | 202 +- src/jalview/jbgui/GCutAndPasteTransfer.java | 3 +- src/jalview/jbgui/GPCAPanel.java | 1 + src/jalview/jbgui/GPaSiMapPanel.java | 5 +- src/jalview/jbgui/GPreferences.java | 2 +- src/jalview/math/Matrix.java | 250 +- src/jalview/math/MatrixI.java | 173 +- src/jalview/math/MiscMath.java | 275 +- src/jalview/project/Jalview2XML.java | 80 +- src/jalview/renderer/AnnotationRenderer.java | 122 +- src/jalview/renderer/ResidueShader.java | 78 +- src/jalview/renderer/ResidueShaderI.java | 5 +- src/jalview/schemes/ClustalxColourScheme.java | 60 +- src/jalview/schemes/ResidueProperties.java | 18 +- .../structure/StructureSelectionManager.java | 26 +- src/jalview/util/Constants.java | 42 +- src/jalview/viewmodel/AlignmentViewport.java | 210 +- src/jalview/viewmodel/PaSiMapModel.java | 32 +- src/jalview/viewmodel/styles/ViewStyle.java | 44 +- .../workers/SecondaryStructureConsensusThread.java | 71 +- src/jalview/xml/binding/jalview/AlcodonFrame.java | 501 +- src/jalview/xml/binding/jalview/Annotation.java | 1482 +-- .../binding/jalview/AnnotationColourScheme.java | 432 +- .../xml/binding/jalview/AnnotationElement.java | 317 +- src/jalview/xml/binding/jalview/DoubleMatrix.java | 303 +- src/jalview/xml/binding/jalview/DoubleVector.java | 90 +- src/jalview/xml/binding/jalview/Feature.java | 568 +- .../xml/binding/jalview/FeatureMatcher.java | 248 +- .../xml/binding/jalview/FeatureMatcherSet.java | 272 +- src/jalview/xml/binding/jalview/FilterBy.java | 90 +- src/jalview/xml/binding/jalview/JalviewModel.java |13470 ++++++++++---------- .../xml/binding/jalview/JalviewUserColours.java | 1025 +- src/jalview/xml/binding/jalview/MapListType.java | 558 +- .../xml/binding/jalview/MapOnAMatrixType.java | 257 +- src/jalview/xml/binding/jalview/Mapping.java | 180 +- src/jalview/xml/binding/jalview/MatrixType.java | 606 +- src/jalview/xml/binding/jalview/NoValueColour.java | 90 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 1083 +- src/jalview/xml/binding/jalview/PcaDataType.java | 168 +- src/jalview/xml/binding/jalview/Pdbentry.java | 362 +- src/jalview/xml/binding/jalview/Property.java | 110 +- src/jalview/xml/binding/jalview/Sequence.java | 558 +- src/jalview/xml/binding/jalview/SequenceSet.java | 613 +- src/jalview/xml/binding/jalview/SequenceType.java | 229 +- src/jalview/xml/binding/jalview/ThresholdType.java | 37 +- src/jalview/xml/binding/jalview/VAMSAS.java | 156 +- .../binding/jalview/WebServiceParameterSet.java | 396 +- src/jalview/xml/binding/jalview/package-info.java | 4 +- test/jalview/analysis/AlignSeqTest.java | 16 +- test/jalview/analysis/AlignmentUtilsTests.java | 330 +- .../analysis/scoremodels/ScoreModelsTest.java | 2 +- .../SecondaryStructureDistanceModelTest.java | 266 +- test/jalview/commands/EditCommandTest.java | 49 +- test/jalview/gui/AssociatePDBFileTest.java | 25 +- test/jalview/gui/CalculationChooserTest.java | 42 +- test/jalview/project/Jalview2xmlTests.java | 10 +- test/jalview/renderer/ResidueShaderTest.java | 2 +- test/jalview/schemes/ClustalxColourSchemeTest.java | 1 + 113 files changed, 15129 insertions(+), 14253 deletions(-) diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java index 7278a80..ca619f9 100755 --- a/src/jalview/analysis/AAFrequency.java +++ b/src/jalview/analysis/AAFrequency.java @@ -192,13 +192,12 @@ public class AAFrequency // jalview.bin.Console.outPrintln(elapsed); } - public static final ProfilesI calculateSS(List list, int start, int end, String source) { return calculateSS(list, start, end, false, source); } - + public static final ProfilesI calculateSS(List sequences, int start, int end, boolean profile, String source) { @@ -220,28 +219,29 @@ public class AAFrequency { end = width; } - - ProfilesI reply = calculateSS(seqs, width, start, end, profile, source); + ProfilesI reply = calculateSS(seqs, width, start, end, profile, + source); return reply; } } - + public static final ProfilesI calculateSS(final SequenceI[] sequences, - int width, int start, int end, boolean saveFullProfile, String source) + int width, int start, int end, boolean saveFullProfile, + String source) { int seqCount = sequences.length; - + int seqWithSSCount = 0; - + ProfileI[] result = new ProfileI[width]; for (int column = start; column < end; column++) { - + int ssCount = 0; - + SecondaryStructureCount ssCounts = new SecondaryStructureCount(); for (int row = 0; row < seqCount; row++) @@ -252,29 +252,36 @@ public class AAFrequency "WARNING: Consensus skipping null sequence - possible race condition."); continue; } - + char c = sequences[row].getCharAt(column); - List annots = AlignmentUtils.getAlignmentAnnotationForSource(sequences[row], source); - if(annots!=null) { + List annots = AlignmentUtils + .getAlignmentAnnotationForSource(sequences[row], source); + if (annots != null) + { seqWithSSCount++; - for(AlignmentAnnotation aa:annots) { - if(aa!=null) { + for (AlignmentAnnotation aa : annots) + { + if (aa != null) + { ssCount++; } - - if (sequences[row].getLength() > column && !Comparison.isGap(c) && aa !=null) + + if (sequences[row].getLength() > column && !Comparison.isGap(c) + && aa != null) { - + int seqPosition = sequences[row].findPosition(column); - - char ss = AlignmentUtils.findSSAnnotationForGivenSeqposition( - aa, seqPosition); - if(ss == '*') { + + char ss = AlignmentUtils + .findSSAnnotationForGivenSeqposition(aa, seqPosition); + if (ss == '*') + { continue; - } - ssCounts.add(ss); + } + ssCounts.add(ss); } - else if(Comparison.isGap(c) && aa!=null) { + else if (Comparison.isGap(c) && aa != null) + { ssCounts.addGap(); } } @@ -284,9 +291,8 @@ public class AAFrequency int maxSSCount = ssCounts.getModalCount(); String maxSS = ssCounts.getSSForCount(maxSSCount); int gapCount = ssCounts.getGapCount(); - ProfileI profile = new Profile(maxSS, ssCount, gapCount, - maxSSCount, seqWithSSCount); - + ProfileI profile = new Profile(maxSS, ssCount, gapCount, maxSSCount, + seqWithSSCount); if (saveFullProfile) { @@ -394,67 +400,67 @@ public class AAFrequency // long elapsed = System.currentTimeMillis() - now; // jalview.bin.Console.outPrintln(-elapsed); } - - - public static void completeSSConsensus(AlignmentAnnotation ssConsensus, - ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps, - boolean showSequenceLogo, long nseq) - { - // long now = System.currentTimeMillis(); - if (ssConsensus == null || ssConsensus.annotations == null - || ssConsensus.annotations.length < endCol) - { - /* + + public static void completeSSConsensus(AlignmentAnnotation ssConsensus, + ProfilesI profiles, int startCol, int endCol, boolean ignoreGaps, + boolean showSequenceLogo, long nseq) + { + // long now = System.currentTimeMillis(); + if (ssConsensus == null || ssConsensus.annotations == null + || ssConsensus.annotations.length < endCol) + { + /* * called with a bad alignment annotation row * wait for it to be initialised properly */ - return; - } - - for (int i = startCol; i < endCol; i++) - { - ProfileI profile = profiles.get(i); - if (profile == null) - { - /* + return; + } + + for (int i = startCol; i < endCol; i++) + { + ProfileI profile = profiles.get(i); + if (profile == null) + { + /* * happens if sequences calculated over were * shorter than alignment width */ - ssConsensus.annotations[i] = null; - return; - } - - if(ssConsensus.getNoOfSequencesIncluded()<0) { - ssConsensus.setNoOfSequencesIncluded(profile.getSeqWithSSCount()); - } - - final int dp = getPercentageDp(nseq); - - float value = profile.getSSPercentageIdentity(ignoreGaps); - - String description = getSSTooltip(profile, value, showSequenceLogo, - ignoreGaps, dp); - - String modalSS = profile.getModalSS(); - if ("".equals(modalSS)) - { - modalSS = "-"; - } - else if (modalSS.length() > 1) - { - modalSS = "+"; - } - ssConsensus.annotations[i] = new Annotation(modalSS, description, - ' ', value); - } - - //Hide consensus with no data to display - if(ssConsensus.getNoOfSequencesIncluded()<1) - ssConsensus.visible = false; - - // long elapsed = System.currentTimeMillis() - now; - // jalview.bin.Console.outPrintln(-elapsed); - } + ssConsensus.annotations[i] = null; + return; + } + + if (ssConsensus.getNoOfSequencesIncluded() < 0) + { + ssConsensus.setNoOfSequencesIncluded(profile.getSeqWithSSCount()); + } + + final int dp = getPercentageDp(nseq); + + float value = profile.getSSPercentageIdentity(ignoreGaps); + + String description = getSSTooltip(profile, value, showSequenceLogo, + ignoreGaps, dp); + + String modalSS = profile.getModalSS(); + if ("".equals(modalSS)) + { + modalSS = "-"; + } + else if (modalSS.length() > 1) + { + modalSS = "+"; + } + ssConsensus.annotations[i] = new Annotation(modalSS, description, ' ', + value); + } + + // Hide consensus with no data to display + if (ssConsensus.getNoOfSequencesIncluded() < 1) + ssConsensus.visible = false; + + // long elapsed = System.currentTimeMillis() - now; + // jalview.bin.Console.outPrintln(-elapsed); + } /** * Derive the gap count annotation row. @@ -560,7 +566,7 @@ public class AAFrequency } return description; } - + static String getSSTooltip(ProfileI profile, float pid, boolean showSequenceLogo, boolean ignoreGaps, int dp) { @@ -616,27 +622,28 @@ public class AAFrequency { char[] symbols; int[] values; - + if (profile.getCounts() != null) { ResidueCount counts = profile.getCounts(); SymbolCounts symbolCounts = counts.getSymbolCounts(); symbols = symbolCounts.symbols; values = symbolCounts.values; - + } - else if(profile.getSSCounts() != null) + else if (profile.getSSCounts() != null) { SecondaryStructureCount counts = profile.getSSCounts(); // to do - SecondaryStructureCount.SymbolCounts symbolCounts = counts.getSymbolCounts(); + SecondaryStructureCount.SymbolCounts symbolCounts = counts + .getSymbolCounts(); symbols = symbolCounts.symbols; values = symbolCounts.values; } - else { + else + { return null; } - QuickSort.sort(values, symbols); int totalPercentage = 0; diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java index e806d2b..1a12681 100755 --- a/src/jalview/analysis/AlignSeq.java +++ b/src/jalview/analysis/AlignSeq.java @@ -58,10 +58,10 @@ public class AlignSeq private static final int DEFAULT_OPENCOST = 120; private static final int DEFAULT_EXTENDCOST = 20; - - private int GAP_OPEN_COST=DEFAULT_OPENCOST; - private int GAP_EXTEND_COST=DEFAULT_EXTENDCOST; + private int GAP_OPEN_COST = DEFAULT_OPENCOST; + + private int GAP_EXTEND_COST = DEFAULT_EXTENDCOST; private static final int GAP_INDEX = -1; @@ -100,11 +100,11 @@ public class AlignSeq int[] aseq1; int[] aseq2; - + /* * matches in alignment */ - int match=-1; + int match = -1; public String astr1 = ""; @@ -129,9 +129,9 @@ public class AlignSeq public float maxscore; - public float meanScore; //needed for PaSiMap + public float meanScore; // needed for PaSiMap - public int hypotheticMaxScore; // needed for PaSiMap + public int hypotheticMaxScore; // needed for PaSiMap int prev = 0; @@ -156,6 +156,7 @@ public class AlignSeq GAP_OPEN_COST = opencost; GAP_EXTEND_COST = extcost; } + public AlignSeq(SequenceI s1, SequenceI s2, String type) { seqInit(s1, s1.getSequenceAsString(), s2, s2.getSequenceAsString(), @@ -182,18 +183,18 @@ public class AlignSeq public AlignSeq(SequenceI s1, SequenceI s2, String type, int opencost, int extcost) { - this(s1,s2,type); - GAP_OPEN_COST=opencost; - GAP_EXTEND_COST=extcost; + this(s1, s2, type); + GAP_OPEN_COST = opencost; + GAP_EXTEND_COST = extcost; } public AlignSeq(SequenceI s12, String string1, SequenceI s22, String string2, String type2, int defaultOpencost, int defaultExtendcost) { - this(s12,string1,s22,string2,type2); - GAP_OPEN_COST=defaultOpencost; - GAP_EXTEND_COST=defaultExtendcost; + this(s12, string1, s22, string2, type2); + GAP_OPEN_COST = defaultOpencost; + GAP_EXTEND_COST = defaultExtendcost; } /** @@ -207,10 +208,10 @@ public class AlignSeq } /** - * returns the overall score of the alignment - * - * @return - */ + * returns the overall score of the alignment + * + * @return + */ public float getAlignmentScore() { return alignmentScore; @@ -333,27 +334,31 @@ public class AlignSeq s2.getDatasetSequence() == null ? s2 : s2.getDatasetSequence()); return alSeq2; } + /** * fraction of seq2 matched in the alignment + * * @return NaN or [0..1] */ public double getS2Coverage() { - if (match>=0) + if (match >= 0) { - return ((double)match)/((double)s2.getEnd()-s2.getStart()+1); + return ((double) match) / ((double) s2.getEnd() - s2.getStart() + 1); } return Double.NaN; } + /** * fraction of seq1 matched in the alignment + * * @return NaN or [0..1] */ public double getS1Coverage() { - if (match>=0) + if (match >= 0) { - return ((double)match)/((double)s1.getEnd()-s1.getStart()+1); + return ((double) match) / ((double) s1.getEnd() - s1.getStart() + 1); } return Double.NaN; } @@ -375,13 +380,14 @@ public class AlignSeq public void seqInit(SequenceI s1, String string1, SequenceI s2, String string2, String type) { - seqInit(s1,string1,s2,string2,type,GAP_OPEN_COST,GAP_EXTEND_COST); + seqInit(s1, string1, s2, string2, type, GAP_OPEN_COST, GAP_EXTEND_COST); } + public void seqInit(SequenceI s1, String string1, SequenceI s2, - String string2, String type, int opening,int extension) + String string2, String type, int opening, int extension) { - GAP_OPEN_COST=opening; - GAP_EXTEND_COST=extension; + GAP_OPEN_COST = opening; + GAP_EXTEND_COST = extension; this.s1 = s1; this.s2 = s2; setDefaultParams(type); @@ -473,13 +479,12 @@ public class AlignSeq aseq1 = new int[seq1.length + seq2.length]; aseq2 = new int[seq1.length + seq2.length]; - match=0; + match = 0; StringBuilder sb1 = new StringBuilder(aseq1.length); StringBuilder sb2 = new StringBuilder(aseq2.length); count = (seq1.length + seq2.length) - 1; - while (i > 0 && j > 0) { aseq1[count] = seq1[i]; @@ -523,12 +528,12 @@ public class AlignSeq { aseq2[count] = seq2[j]; sb2.append(s2str.charAt(j)); - if (aseq1[count]!=GAP_INDEX) { + if (aseq1[count] != GAP_INDEX) + { match++; } } - /* * we built the character strings backwards, so now * reverse them to convert to sequence strings @@ -570,7 +575,7 @@ public class AlignSeq int trace; maxscore = score[i][j] / 10f; - //prepare trailing gaps + // prepare trailing gaps while ((i < seq1.length - 1) || (j < seq2.length - 1)) { i++; @@ -587,20 +592,22 @@ public class AlignSeq count = (seq1.length + seq2.length) - 1; - //get trailing gaps + // get trailing gaps while ((i >= seq1.length) || (j >= seq2.length)) { if (i >= seq1.length) { - aseq1[count] = GAP_INDEX; - sb1.append("-"); - aseq2[count] = seq2[j]; - sb2.append(s2str.charAt(j)); - } else if (j >= seq2.length) { - aseq1[count] = seq1[i]; - sb1.append(s1str.charAt(i)); - aseq2[count] = GAP_INDEX; - sb2.append("-"); + aseq1[count] = GAP_INDEX; + sb1.append("-"); + aseq2[count] = seq2[j]; + sb2.append(s2str.charAt(j)); + } + else if (j >= seq2.length) + { + aseq1[count] = seq1[i]; + sb1.append(s1str.charAt(i)); + aseq2[count] = GAP_INDEX; + sb2.append("-"); } i--; j--; @@ -644,18 +651,20 @@ public class AlignSeq aseq2[count] = seq2[j]; sb2.append(s2str.charAt(j)); - //get initial gaps + // get initial gaps while (j > 0 || i > 0) { if (j > 0) { - j--; - sb1.append("-"); - sb2.append(s2str.charAt(j)); - } else if (i > 0) { - i--; - sb1.append(s1str.charAt(i)); - sb2.append("-"); + j--; + sb1.append("-"); + sb2.append(s2str.charAt(j)); + } + else if (i > 0) + { + i--; + sb1.append(s1str.charAt(i)); + sb2.append("-"); } } @@ -853,7 +862,7 @@ public class AlignSeq { int n = seq1.length; int m = seq2.length; - final int GAP_EX_COST=GAP_EXTEND_COST; + final int GAP_EX_COST = GAP_EXTEND_COST; final int GAP_OP_COST = GAP_OPEN_COST; // top left hand element score[0][0] = scoreMatrix.getPairwiseScore(s1str.charAt(0), @@ -871,8 +880,7 @@ public class AlignSeq float pairwiseScore = scoreMatrix.getPairwiseScore(s1str.charAt(0), s2str.charAt(j)); - score[0][j] = max(pairwiseScore * 10, -GAP_OP_COST, - -GAP_EX_COST); + score[0][j] = max(pairwiseScore * 10, -GAP_OP_COST, -GAP_EX_COST); traceback[0][j] = 1; } @@ -1076,13 +1084,15 @@ public class AlignSeq public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2, String type) { - return doGlobalNWAlignment(s1, s2, type, DEFAULT_OPENCOST,DEFAULT_EXTENDCOST); + return doGlobalNWAlignment(s1, s2, type, DEFAULT_OPENCOST, + DEFAULT_EXTENDCOST); } + public static AlignSeq doGlobalNWAlignment(SequenceI s1, SequenceI s2, - String type, int opencost,int extcost) + String type, int opencost, int extcost) { - - AlignSeq as = new AlignSeq(s1, s2, type,opencost,extcost); + + AlignSeq as = new AlignSeq(s1, s2, type, opencost, extcost); as.calcScoreMatrix(); as.traceAlignment(); @@ -1359,42 +1369,45 @@ public class AlignSeq } /** - * calculate the mean score of the alignment - * mean score is equal to the score of an alignmenet of two sequences with randomly shuffled AA sequence composited of the same AA as the two original sequences - * - */ + * calculate the mean score of the alignment mean score is equal to the score + * of an alignmenet of two sequences with randomly shuffled AA sequence + * composited of the same AA as the two original sequences + * + */ public void meanScore() { - int length = indelfreeAstr1.length(); //both have the same length - //create HashMap for counting residues in each sequence + int length = indelfreeAstr1.length(); // both have the same length + // create HashMap for counting residues in each sequence HashMap seq1ResCount = new HashMap(); HashMap seq2ResCount = new HashMap(); - // for both sequences (String indelfreeAstr1 or 2) create a key for the residue and add 1 each time its encountered - for (char residue: indelfreeAstr1.toCharArray()) + // for both sequences (String indelfreeAstr1 or 2) create a key for the + // residue and add 1 each time its encountered + for (char residue : indelfreeAstr1.toCharArray()) { seq1ResCount.putIfAbsent(residue, 0); seq1ResCount.replace(residue, seq1ResCount.get(residue) + 1); } - for (char residue: indelfreeAstr2.toCharArray()) + for (char residue : indelfreeAstr2.toCharArray()) { seq2ResCount.putIfAbsent(residue, 0); seq2ResCount.replace(residue, seq2ResCount.get(residue) + 1); } - // meanscore = for each residue pair get the number of appearance and add (countA * countB * pairwiseScore(AB)) + // meanscore = for each residue pair get the number of appearance and add + // (countA * countB * pairwiseScore(AB)) // divide the meanscore by the sequence length afterwards float _meanscore = 0; for (char resA : seq1ResCount.keySet()) { for (char resB : seq2ResCount.keySet()) { - int countA = seq1ResCount.get(resA); - int countB = seq2ResCount.get(resB); + int countA = seq1ResCount.get(resA); + int countB = seq2ResCount.get(resB); float scoreAB = scoreMatrix.getPairwiseScore(resA, resB); - _meanscore += countA * countB * scoreAB; + _meanscore += countA * countB * scoreAB; } } _meanscore /= length; @@ -1407,21 +1420,23 @@ public class AlignSeq } /** - * calculate the hypothetic max score using the self-alignment of the sequences - */ + * calculate the hypothetic max score using the self-alignment of the + * sequences + */ public void hypotheticMaxScore() { int _hmsA = 0; int _hmsB = 0; - for (char residue: indelfreeAstr1.toCharArray()) + for (char residue : indelfreeAstr1.toCharArray()) { _hmsA += scoreMatrix.getPairwiseScore(residue, residue); } - for (char residue: indelfreeAstr2.toCharArray()) + for (char residue : indelfreeAstr2.toCharArray()) { _hmsB += scoreMatrix.getPairwiseScore(residue, residue); } - this.hypotheticMaxScore = (_hmsA < _hmsB) ? _hmsA : _hmsB; // take the lower self alignment + this.hypotheticMaxScore = (_hmsA < _hmsB) ? _hmsA : _hmsB; // take the lower + // self alignment } @@ -1431,27 +1446,30 @@ public class AlignSeq } /** - * create strings based of astr1 and astr2 but without gaps - */ + * create strings based of astr1 and astr2 but without gaps + */ public void getIndelfreeAstr() { - int n = astr1.length(); // both have the same length + int n = astr1.length(); // both have the same length for (int i = 0; i < n; i++) { - if (Character.isLetter(astr1.charAt(i)) && Character.isLetter(astr2.charAt(i))) // if both sequences dont have a gap -> add to indelfreeAstr + if (Character.isLetter(astr1.charAt(i)) + && Character.isLetter(astr2.charAt(i))) // if both sequences dont + // have a gap -> add to + // indelfreeAstr { - this.indelfreeAstr1 += astr1.charAt(i); - this.indelfreeAstr2 += astr2.charAt(i); + this.indelfreeAstr1 += astr1.charAt(i); + this.indelfreeAstr2 += astr2.charAt(i); } } } /** - * calculates the overall score of the alignment - * preprescore = sum of all scores - all penalties - * if preprescore < 1 ~ alignmentScore = Float.NaN > - * alignmentScore = ((preprescore - meanScore) / (hypotheticMaxScore - meanScore)) * coverage - */ + * calculates the overall score of the alignment preprescore = sum of all + * scores - all penalties if preprescore < 1 ~ alignmentScore = Float.NaN > + * alignmentScore = ((preprescore - meanScore) / (hypotheticMaxScore - + * meanScore)) * coverage + */ public void scoreAlignment() { @@ -1475,36 +1493,51 @@ public class AlignSeq char char2 = indelfreeAstr2.charAt(i); boolean aIsLetter = Character.isLetter(char1); boolean bIsLetter = Character.isLetter(char2); - if (aIsLetter && bIsLetter) // if pair -> get score + if (aIsLetter && bIsLetter) // if pair -> get score { score += scoreMatrix.getPairwiseScore(char1, char2); - } else if (!aIsLetter && !bIsLetter) { // both are gap -> skip - } else if ((!aIsLetter && aGapOpen) || (!bIsLetter && bGapOpen)) { // one side gapopen -> score - gap_extend - score -= GAP_EXTEND_COST; - } else { // no gap open -> score - gap_open - score -= GAP_OPEN_COST; + } + else if (!aIsLetter && !bIsLetter) + { // both are gap -> skip + } + else if ((!aIsLetter && aGapOpen) || (!bIsLetter && bGapOpen)) + { // one side gapopen -> score - gap_extend + score -= GAP_EXTEND_COST; + } + else + { // no gap open -> score - gap_open + score -= GAP_OPEN_COST; } // adjust GapOpen status in both sequences aGapOpen = (!aIsLetter) ? true : false; bGapOpen = (!bIsLetter) ? true : false; } - float preprescore = score; // if this score < 1 --> alignment score = Float.NaN - score = (score - this.meanScore) / (this.hypotheticMaxScore - this.meanScore); - int[] _max = MiscMath.findMax(new int[]{astr1.replace("-","").length(), astr2.replace("-","").length()}); // {index of max, max} - float coverage = (float) n / (float) _max[1]; // indelfreeAstr length / longest sequence length - float prescore = score; // only debug + float preprescore = score; // if this score < 1 --> alignment score = + // Float.NaN + score = (score - this.meanScore) + / (this.hypotheticMaxScore - this.meanScore); + int[] _max = MiscMath + .findMax(new int[] + { astr1.replace("-", "").length(), + astr2.replace("-", "").length() }); // {index of max, max} + float coverage = (float) n / (float) _max[1]; // indelfreeAstr length / + // longest sequence length + float prescore = score; // only debug score *= coverage; - //System.out.println(String.format("prepre-score: %f, pre-score: %f, longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore, _max[1], score, this.meanScore, this.hypotheticMaxScore)); + // System.out.println(String.format("prepre-score: %f, pre-score: %f, + // longlength: %d\nscore: %1.16f, mean: %f, max: %d", preprescore, prescore, + // _max[1], score, this.meanScore, this.hypotheticMaxScore)); float minScore = 0f; this.alignmentScore = (score <= minScore) ? Float.NaN : score; } public void setScoreMatrix(ScoreMatrix sm) { - if (sm != null) { - scoreMatrix = sm; - } + if (sm != null) + { + scoreMatrix = sm; + } } } diff --git a/src/jalview/analysis/AlignmentAnnotationUtils.java b/src/jalview/analysis/AlignmentAnnotationUtils.java index cf2f5bb..15514ef 100644 --- a/src/jalview/analysis/AlignmentAnnotationUtils.java +++ b/src/jalview/analysis/AlignmentAnnotationUtils.java @@ -273,8 +273,7 @@ public class AlignmentAnnotationUtils }); } } - - + /** * Returns a BitSet (possibly empty) of those graphGroups for line graph * annotations, which have at least one member annotation row marked visible. diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index f5927ab..31670fd 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -84,7 +84,7 @@ public class AlignmentUtils { private static final int CODON_LENGTH = 3; - private static final String SEQUENCE_VARIANT = "sequence_variant:"; + private static final String SEQUENCE_VARIANT = "sequence_variant:"; /* * the 'id' attribute is provided for variant features fetched from @@ -1542,13 +1542,15 @@ public class AlignmentUtils } } } - - - public static boolean isSSAnnotationPresent( Map> annotations) { - + + public static boolean isSSAnnotationPresent( + Map> annotations) + { + for (SequenceI seq : annotations.keySet()) { - if(isSecondaryStructurePresent(annotations.get(seq).toArray(new AlignmentAnnotation[0]))) + if (isSecondaryStructurePresent( + annotations.get(seq).toArray(new AlignmentAnnotation[0]))) { return true; } @@ -1645,7 +1647,7 @@ public class AlignmentUtils } } } - + /** * Shows or hides auto calculated annotations for a sequence group. * @@ -1689,8 +1691,7 @@ public class AlignmentUtils } } } - - + public static AlignmentAnnotation getFirstSequenceAnnotationOfType( AlignmentI al, int graphType) { @@ -2898,8 +2899,9 @@ public class AlignmentUtils } return true; } - - public static boolean isSecondaryStructurePresent(AlignmentAnnotation[] annotations) + + public static boolean isSecondaryStructurePresent( + AlignmentAnnotation[] annotations) { boolean ssPresent = false; @@ -2920,7 +2922,7 @@ public class AlignmentUtils return ssPresent; } - + public static Color getSecondaryStructureAnnotationColour(char symbol) { @@ -2940,8 +2942,8 @@ public class AlignmentUtils return Color.white; } - public static char findSSAnnotationForGivenSeqposition(AlignmentAnnotation aa, - int seqPosition) + public static char findSSAnnotationForGivenSeqposition( + AlignmentAnnotation aa, int seqPosition) { char ss = '*'; @@ -2966,8 +2968,7 @@ public class AlignmentUtils return ss; } - - + public static List extractSSSourceInAlignmentAnnotation( AlignmentAnnotation[] annotations) { @@ -2998,7 +2999,7 @@ public class AlignmentUtils return ssSources; } - + public static String extractSSSourceFromAnnotationDescription( AlignmentAnnotation aa) { @@ -3009,13 +3010,13 @@ public class AlignmentUtils if (label.equals(aa.label)) { - if (aa.getProperty(Constants.SS_PROVIDER_PROPERTY) != null) + if (aa.getProperty(Constants.SS_PROVIDER_PROPERTY) != null) { - + return aa.getProperty(Constants.SS_PROVIDER_PROPERTY); - + } - + // For JPred if (Constants.SS_ANNOTATION_FROM_JPRED_LABEL.equals(aa.label)) { @@ -3026,7 +3027,8 @@ public class AlignmentUtils // For input with secondary structure if (Constants.SS_ANNOTATION_LABEL.equals(aa.label) - && aa.description != null && Constants.SS_ANNOTATION_LABEL.equals(aa.description)) + && aa.description != null + && Constants.SS_ANNOTATION_LABEL.equals(aa.description)) { return (Constants.SECONDARY_STRUCTURE_LABELS.get(aa.label)); @@ -3052,11 +3054,13 @@ public class AlignmentUtils String entryProvider = entry.getProvider(); if (entryProvider == null) { - // No provider - so this is either an old Jalview project, or not retrieved from recognised source + // No provider - so this is either an old Jalview project, or not + // retrieved from recognised source entryProvider = "PDB"; } - // Should (re)use a standard mechanism for extracting the PDB ID as it is written 1QWXTUV:CHAIN + // Should (re)use a standard mechanism for extracting the PDB ID as it + // is written 1QWXTUV:CHAIN // Trim the string from first occurrence of colon String entryID = entry.getId(); int index = entryID.indexOf(':'); @@ -3070,7 +3074,8 @@ public class AlignmentUtils } - // TODO: shouldn't need to extract from description what the originating ID is for this annotation! + // TODO: shouldn't need to extract from description what the + // originating ID is for this annotation! if (entryProvider == "PDB" && aa.description.toLowerCase() .contains("secondary structure for " + entryID.toLowerCase())) @@ -3095,8 +3100,8 @@ public class AlignmentUtils return null; } - - //to do set priority for labels + + // to do set priority for labels public static List getAlignmentAnnotationForSource( SequenceI seq, String ssSource) { @@ -3118,9 +3123,9 @@ public class AlignmentUtils for (AlignmentAnnotation annot : aa) { - String ssSourceForAnnot = extractSSSourceFromAnnotationDescription(annot); - if (ssSourceForAnnot != null && ssSource - .equals(ssSourceForAnnot)) + String ssSourceForAnnot = extractSSSourceFromAnnotationDescription( + annot); + if (ssSourceForAnnot != null && ssSource.equals(ssSourceForAnnot)) { ssAnnots.add(annot); } @@ -3170,7 +3175,8 @@ public class AlignmentUtils * * @param selectedSSSource * @param aa - * @return true if aa is from a provider or all providers as specified by selectedSSSource + * @return true if aa is from a provider or all providers as specified by + * selectedSSSource */ public static boolean isSecondaryStructureFrom(String selectedSSSource, AlignmentAnnotation aa) diff --git a/src/jalview/analysis/ConnectivityException.java b/src/jalview/analysis/ConnectivityException.java index 9915f2a..5f371c8 100644 --- a/src/jalview/analysis/ConnectivityException.java +++ b/src/jalview/analysis/ConnectivityException.java @@ -23,7 +23,9 @@ package jalview.analysis; public class ConnectivityException extends RuntimeException { private String sequence; + private int connection; + private byte dim; public ConnectivityException(String sequence, int connection, byte dim) @@ -31,9 +33,11 @@ public class ConnectivityException extends RuntimeException this("Insufficient number of connections", sequence, connection, dim); } - public ConnectivityException(String message, String sequence, int connection, byte dim) + public ConnectivityException(String message, String sequence, + int connection, byte dim) { - super(String.format("%s for %s (%d, should be %d or more)", message, sequence, connection, dim)); + super(String.format("%s for %s (%d, should be %d or more)", message, + sequence, connection, dim)); this.sequence = sequence; this.connection = connection; this.dim = dim; diff --git a/src/jalview/analysis/Finder.java b/src/jalview/analysis/Finder.java index c84c69a..32d4cf3 100644 --- a/src/jalview/analysis/Finder.java +++ b/src/jalview/analysis/Finder.java @@ -606,7 +606,7 @@ public class Finder implements FinderI } else { - //allFeatures = sf.getAllFeatures(null); + // allFeatures = sf.getAllFeatures(null); allFeatures = sf.getAllFeatures(); } // so we can check we are advancing when debugging diff --git a/src/jalview/analysis/PaSiMap.java b/src/jalview/analysis/PaSiMap.java index 48ec899..295bb89 100755 --- a/src/jalview/analysis/PaSiMap.java +++ b/src/jalview/analysis/PaSiMap.java @@ -38,7 +38,8 @@ import java.util.Hashtable; /** * Performs Principal Component Analysis on given sequences - * @AUTHOR MorellThomas + * + * @AUTHOR MorellThomas */ public class PaSiMap implements Runnable { @@ -72,14 +73,17 @@ public class PaSiMap implements Runnable * @param sm * @param options */ - public PaSiMap(AlignmentViewport sequences, ScoreModelI sm, PairwiseAlignPanel pap) + public PaSiMap(AlignmentViewport sequences, ScoreModelI sm, + PairwiseAlignPanel pap) { this.seqs = sequences; - if (sm!=null && sm instanceof ScoreMatrix) + if (sm != null && sm instanceof ScoreMatrix) { this.scoreMatrix = ((ScoreMatrix) sm); - } else { + } + else + { this.scoreMatrix = null; } @@ -108,7 +112,8 @@ public class PaSiMap implements Runnable * DOCUMENT ME! * @param mm * DOCUMENT ME! - * @param factor ~ is 1 + * @param factor + * ~ is 1 * * @return DOCUMENT ME! */ @@ -164,8 +169,8 @@ public class PaSiMap implements Runnable } /** - * Answers a formatted text report of the PaSiMap calculation results (matrices - * and eigenvalues) suitable for display + * Answers a formatted text report of the PaSiMap calculation results + * (matrices and eigenvalues) suitable for display * * @return */ @@ -197,23 +202,27 @@ public class PaSiMap implements Runnable /** * Performs the PaSiMap calculation * - * creates a new gui/PairwiseAlignPanel with the input sequences (AlignmentViewport) - * uses analysis/AlignSeq to creatue the pairwise alignments and calculate the AlignmentScores (float for each pair) - * gets all float[][] scores from the gui/PairwiseAlignPanel - * checks the connections for each sequence with AlignmentViewport seqs.calculateConnectivity(float[][] scores, int dim) (from analysis/Connectivity) -- throws an Exception if insufficient - * creates a math/MatrixI pairwiseScores of the float[][] scores - * copys the scores and fills the diagonal to create a symmetric matrix using math/Matrix.fillDiagonal() - * performs the analysis/ccAnalysis with the symmetric matrix - * gets the eigenmatrix and the eigenvalues using math/Matrix.tqli() + * creates a new gui/PairwiseAlignPanel with the input sequences + * (AlignmentViewport) uses analysis/AlignSeq to creatue the pairwise + * alignments and calculate the AlignmentScores (float for each pair) gets all + * float[][] scores from the gui/PairwiseAlignPanel checks the connections for + * each sequence with AlignmentViewport seqs.calculateConnectivity(float[][] + * scores, int dim) (from analysis/Connectivity) -- throws an Exception if + * insufficient creates a math/MatrixI pairwiseScores of the float[][] scores + * copys the scores and fills the diagonal to create a symmetric matrix using + * math/Matrix.fillDiagonal() performs the analysis/ccAnalysis with the + * symmetric matrix gets the eigenmatrix and the eigenvalues using + * math/Matrix.tqli() */ @Override public void run() { try { - //alignment = new PairwiseAlignPanel(seqs, true, 100, 5); + // alignment = new PairwiseAlignPanel(seqs, true, 100, 5); alignment.calculate(scoreMatrix); - float[][] scores = alignment.getAlignmentScores(); //bigger index first -- eg scores[14][13] + float[][] scores = alignment.getAlignmentScores(); // bigger index first + // -- eg scores[14][13] SequenceI[] iseqs = alignment.getInputSequences(); Connectivity.getConnectivity(iseqs, scores, dim); diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java index e713525..156657a 100644 --- a/src/jalview/analysis/TreeBuilder.java +++ b/src/jalview/analysis/TreeBuilder.java @@ -43,6 +43,7 @@ public abstract class TreeBuilder extends TreeEngine public static final String NEIGHBOUR_JOINING = "NJ"; protected SequenceI[] sequences; + protected List labels; public AlignmentView seqData; @@ -78,7 +79,7 @@ public abstract class TreeBuilder extends TreeEngine } init(seqStrings, start, end); - + computeTree(sm, scoreParameters); } @@ -87,7 +88,6 @@ public abstract class TreeBuilder extends TreeEngine return sequences; } - /** * * @return true if tree has real distances @@ -129,7 +129,7 @@ public abstract class TreeBuilder extends TreeEngine labels = new ArrayList(); sequences = sm.expandSeqData(sequences, seqData, scoreOptions, labels); noseqs = sequences.length; - + distances = sm.findDistances(seqData, scoreOptions); makeLeaves(); @@ -186,14 +186,14 @@ public abstract class TreeBuilder extends TreeEngine SequenceNode sn = new SequenceNode(); sn.setElement(sequences[i]); - - if (labels.size()==noseqs) + + if (labels.size() == noseqs) { sn.setLabel(labels.get(i)); } - + sn.setName(sequences[i].getName()); - + node.addElement(sn); BitSet bs = new BitSet(); bs.set(i); diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java index e29eb95..2d2248d 100644 --- a/src/jalview/analysis/TreeModel.java +++ b/src/jalview/analysis/TreeModel.java @@ -87,11 +87,15 @@ public class TreeModel if (leafAnnotations != null) { // leaf names are seuqence ID + annotation for display - // leaf links are annotationId <> annotation object for import from project + // leaf links are annotationId <> annotation object for import from + // project // --> need to resolve before passing for display // ==> do leafs need to be renamed after import ? - // ==> implies the 'nodeLabel' business needs to be callable independently of score function - } else { + // ==> implies the 'nodeLabel' business needs to be callable independently + // of score function + } + else + { associateLeavesToSequences(seqs); } } diff --git a/src/jalview/analysis/ccAnalysis.java b/src/jalview/analysis/ccAnalysis.java index 4922a54..265a3f4 100755 --- a/src/jalview/analysis/ccAnalysis.java +++ b/src/jalview/analysis/ccAnalysis.java @@ -55,11 +55,11 @@ import org.apache.commons.math3.linear.SingularValueDecomposition; /** * A class to model rectangular matrices of double values and operations on them */ -public class ccAnalysis +public class ccAnalysis { - private byte dim = 0; //dimensions + private byte dim = 0; // dimensions - private MatrixI scoresOld; //input scores + private MatrixI scoresOld; // input scores public ccAnalysis(MatrixI scores, byte dim) { @@ -68,29 +68,33 @@ public class ccAnalysis { for (int j = 0; j < scores.width(); j++) { - if (!Double.isNaN(scores.getValue(i,j))) - { - scores.setValue(i, j, (double) Math.round(scores.getValue(i,j) * (int) 10000) / 10000); - } + if (!Double.isNaN(scores.getValue(i, j))) + { + scores.setValue(i, j, + (double) Math.round(scores.getValue(i, j) * (int) 10000) + / 10000); + } } } this.scoresOld = scores; this.dim = dim; } - /** - * Initialise a distrust-score for each hypothesis (h) of hSigns - * distrust = conHypNum - proHypNum - * - * @param hSigns ~ hypothesis signs (+/-) for each sequence - * @param scores ~ input score matrix - * - * @return distrustScores - */ + /** + * Initialise a distrust-score for each hypothesis (h) of hSigns distrust = + * conHypNum - proHypNum + * + * @param hSigns + * ~ hypothesis signs (+/-) for each sequence + * @param scores + * ~ input score matrix + * + * @return distrustScores + */ private int[] initialiseDistrusts(byte[] hSigns, MatrixI scores) { int[] distrustScores = new int[scores.width()]; - + // loop over symmetric matrix for (int i = 0; i < scores.width(); i++) { @@ -100,34 +104,43 @@ public class ccAnalysis for (int j = 0; j < scores.width(); j++) { - double cell = scores.getRow(i)[j]; // value at [i][j] in scores - byte hBSign = hSigns[j]; - if (!Double.isNaN(cell)) - { - byte cellSign = (byte) Math.signum(cell); //check if sign of matrix value fits hyptohesis - if (cellSign == hASign * hBSign) - { - proHypNum++; - } else { - conHypNum++; - } - } + double cell = scores.getRow(i)[j]; // value at [i][j] in scores + byte hBSign = hSigns[j]; + if (!Double.isNaN(cell)) + { + byte cellSign = (byte) Math.signum(cell); // check if sign of matrix + // value fits hyptohesis + if (cellSign == hASign * hBSign) + { + proHypNum++; + } + else + { + conHypNum++; + } + } } - distrustScores[i] = conHypNum - proHypNum; //create distrust score for each sequence + distrustScores[i] = conHypNum - proHypNum; // create distrust score for + // each sequence } return distrustScores; } /** - * Optemise hypothesis concerning the sign of the hypothetical value for each hSigns by interpreting the pairwise correlation coefficients as scalar products - * - * @param hSigns ~ hypothesis signs (+/-) - * @param distrustScores - * @param scores ~ input score matrix - * - * @return hSigns - */ - private byte[] optimiseHypothesis(byte[] hSigns, int[] distrustScores, MatrixI scores) + * Optemise hypothesis concerning the sign of the hypothetical value for each + * hSigns by interpreting the pairwise correlation coefficients as scalar + * products + * + * @param hSigns + * ~ hypothesis signs (+/-) + * @param distrustScores + * @param scores + * ~ input score matrix + * + * @return hSigns + */ + private byte[] optimiseHypothesis(byte[] hSigns, int[] distrustScores, + MatrixI scores) { // get maximum distrust score int[] maxes = MiscMath.findMax(distrustScores); @@ -137,7 +150,7 @@ public class ccAnalysis // if hypothesis is not optimal yet if (maxDistrust > 0) { - //toggle sign for hI with maximum distrust + // toggle sign for hI with maximum distrust hSigns[maxDistrustIndex] *= -1; // update distrust at same position distrustScores[maxDistrustIndex] *= -1; @@ -146,299 +159,325 @@ public class ccAnalysis byte hASign = hSigns[maxDistrustIndex]; for (int NOTmaxDistrustIndex = 0; NOTmaxDistrustIndex < distrustScores.length; NOTmaxDistrustIndex++) { - if (NOTmaxDistrustIndex != maxDistrustIndex) - { - byte hBSign = hSigns[NOTmaxDistrustIndex]; - double cell = scores.getValue(maxDistrustIndex, NOTmaxDistrustIndex); - - // distrust only changed if not NaN - if (!Double.isNaN(cell)) - { - byte cellSign = (byte) Math.signum(cell); - // if sign of cell matches hypothesis decrease distrust by 2 because 1 more value supporting and 1 less contradicting - // else increase by 2 - if (cellSign == hASign * hBSign) - { - distrustScores[NOTmaxDistrustIndex] -= 2; - } else { - distrustScores[NOTmaxDistrustIndex] += 2; - } - } - } + if (NOTmaxDistrustIndex != maxDistrustIndex) + { + byte hBSign = hSigns[NOTmaxDistrustIndex]; + double cell = scores.getValue(maxDistrustIndex, + NOTmaxDistrustIndex); + + // distrust only changed if not NaN + if (!Double.isNaN(cell)) + { + byte cellSign = (byte) Math.signum(cell); + // if sign of cell matches hypothesis decrease distrust by 2 because + // 1 more value supporting and 1 less contradicting + // else increase by 2 + if (cellSign == hASign * hBSign) + { + distrustScores[NOTmaxDistrustIndex] -= 2; + } + else + { + distrustScores[NOTmaxDistrustIndex] += 2; + } + } + } } - //further optimisation necessary + // further optimisation necessary return optimiseHypothesis(hSigns, distrustScores, scores); - } else { + } + else + { return hSigns; } } - /** - * takes the a symmetric MatrixI as input scores which may contain Double.NaN - * approximate the missing values using hypothesis optimisation - * - * runs analysis - * - * @param scores ~ score matrix - * - * @return - */ - public MatrixI run () throws Exception + /** + * takes the a symmetric MatrixI as input scores which may contain Double.NaN + * approximate the missing values using hypothesis optimisation + * + * runs analysis + * + * @param scores + * ~ score matrix + * + * @return + */ + public MatrixI run() throws Exception { - //initialse eigenMatrix and repMatrix + // initialse eigenMatrix and repMatrix MatrixI eigenMatrix = scoresOld.copy(); MatrixI repMatrix = scoresOld.copy(); try { - /* - * Calculate correction factor for 2nd and higher eigenvalue(s). - * This correction is NOT needed for the 1st eigenvalue, because the - * unknown (=NaN) values of the matrix are approximated by presuming - * 1-dimensional vectors as the basis of the matrix interpretation as dot - * products. - */ - - System.out.println("Input correlation matrix:"); - eigenMatrix.print(System.out, "%1.4f "); - - int matrixWidth = eigenMatrix.width(); // square matrix, so width == height - int matrixElementsTotal = (int) Math.pow(matrixWidth, 2); //total number of elemts - - float correctionFactor = (float) (matrixElementsTotal - eigenMatrix.countNaN()) / (float) matrixElementsTotal; - - /* - * Calculate hypothetical value (1-dimensional vector) h_i for each - * dataset by interpreting the given correlation coefficients as scalar - * products. - */ - - /* - * Memory for current hypothesis concerning sign of each h_i. - * List of signs for all h_i in the encoding: + /* + * Calculate correction factor for 2nd and higher eigenvalue(s). + * This correction is NOT needed for the 1st eigenvalue, because the + * unknown (=NaN) values of the matrix are approximated by presuming + * 1-dimensional vectors as the basis of the matrix interpretation as dot + * products. + */ + + System.out.println("Input correlation matrix:"); + eigenMatrix.print(System.out, "%1.4f "); + + int matrixWidth = eigenMatrix.width(); // square matrix, so width == + // height + int matrixElementsTotal = (int) Math.pow(matrixWidth, 2); // total number + // of elemts + + float correctionFactor = (float) (matrixElementsTotal + - eigenMatrix.countNaN()) / (float) matrixElementsTotal; + + /* + * Calculate hypothetical value (1-dimensional vector) h_i for each + * dataset by interpreting the given correlation coefficients as scalar + * products. + */ + + /* + * Memory for current hypothesis concerning sign of each h_i. + * List of signs for all h_i in the encoding: * * 1: positive * * 0: zero * * -1: negative - * Initial hypothesis: all signs are positive. - */ - byte[] hSigns = new byte[matrixWidth]; - Arrays.fill(hSigns, (byte) 1); - - //Estimate signs for each h_i by refining hypothesis on signs. - hSigns = optimiseHypothesis(hSigns, initialiseDistrusts(hSigns, eigenMatrix), eigenMatrix); - - - //Estimate absolute values for each h_i by determining sqrt of mean of - //non-NaN absolute values for every row. - double[] hAbs = MiscMath.sqrt(eigenMatrix.absolute().meanRow()); - - //Combine estimated signs with absolute values in obtain total value for - //each h_i. - double[] hValues = MiscMath.elementwiseMultiply(hSigns, hAbs); - - /*Complement symmetric matrix by using the scalar products of estimated - *values of h_i to replace NaN-cells. - *Matrix positions that have estimated values - *(only for diagonal and upper off-diagonal values, due to the symmetry - *the positions of the lower-diagonal values can be inferred). - List of tuples (row_idx, column_idx).*/ - - ArrayList estimatedPositions = new ArrayList(); - - // for off-diagonal cells - for (int rowIndex = 0; rowIndex < matrixWidth - 1; rowIndex++) - { - for (int columnIndex = rowIndex + 1; columnIndex < matrixWidth; columnIndex++) + * Initial hypothesis: all signs are positive. + */ + byte[] hSigns = new byte[matrixWidth]; + Arrays.fill(hSigns, (byte) 1); + + // Estimate signs for each h_i by refining hypothesis on signs. + hSigns = optimiseHypothesis(hSigns, + initialiseDistrusts(hSigns, eigenMatrix), eigenMatrix); + + // Estimate absolute values for each h_i by determining sqrt of mean of + // non-NaN absolute values for every row. + double[] hAbs = MiscMath.sqrt(eigenMatrix.absolute().meanRow()); + + // Combine estimated signs with absolute values in obtain total value for + // each h_i. + double[] hValues = MiscMath.elementwiseMultiply(hSigns, hAbs); + + /*Complement symmetric matrix by using the scalar products of estimated + *values of h_i to replace NaN-cells. + *Matrix positions that have estimated values + *(only for diagonal and upper off-diagonal values, due to the symmetry + *the positions of the lower-diagonal values can be inferred). + List of tuples (row_idx, column_idx).*/ + + ArrayList estimatedPositions = new ArrayList(); + + // for off-diagonal cells + for (int rowIndex = 0; rowIndex < matrixWidth - 1; rowIndex++) { - double cell = eigenMatrix.getValue(rowIndex, columnIndex); - if (Double.isNaN(cell)) - { - //calculate scalar product as new cell value - cell = hValues[rowIndex] * hValues[columnIndex]; - //fill in new value in cell and symmetric partner - eigenMatrix.setValue(rowIndex, columnIndex, cell); - eigenMatrix.setValue(columnIndex, rowIndex, cell); - //save positions of estimated values - estimatedPositions.add(new int[]{rowIndex, columnIndex}); - } + for (int columnIndex = rowIndex + + 1; columnIndex < matrixWidth; columnIndex++) + { + double cell = eigenMatrix.getValue(rowIndex, columnIndex); + if (Double.isNaN(cell)) + { + // calculate scalar product as new cell value + cell = hValues[rowIndex] * hValues[columnIndex]; + // fill in new value in cell and symmetric partner + eigenMatrix.setValue(rowIndex, columnIndex, cell); + eigenMatrix.setValue(columnIndex, rowIndex, cell); + // save positions of estimated values + estimatedPositions.add(new int[] { rowIndex, columnIndex }); + } + } } - } - // for diagonal cells - for (int diagonalIndex = 0; diagonalIndex < matrixWidth; diagonalIndex++) + // for diagonal cells + for (int diagonalIndex = 0; diagonalIndex < matrixWidth; diagonalIndex++) { double cell = Math.pow(hValues[diagonalIndex], 2); - eigenMatrix.setValue(diagonalIndex, diagonalIndex, cell); - estimatedPositions.add(new int[]{diagonalIndex, diagonalIndex}); + eigenMatrix.setValue(diagonalIndex, diagonalIndex, cell); + estimatedPositions.add(new int[] { diagonalIndex, diagonalIndex }); } - /*Refine total values of each h_i: - *Initialise h_values of the hypothetical non-existant previous iteration - *with the correct format but with impossible values. - Needed for exit condition of otherwise endless loop.*/ - System.out.print("initial values: [ "); - for (double h : hValues) - { - System.out.print(String.format("%1.4f, ", h)); - } - System.out.println(" ]"); - - - double[] hValuesOld = new double[matrixWidth]; - - int iterationCount = 0; - - // repeat unitl values of h do not significantly change anymore - while (true) - { - for (int hIndex = 0; hIndex < matrixWidth; hIndex++) - { - double newH = Arrays.stream(MiscMath.elementwiseMultiply(hValues, eigenMatrix.getRow(hIndex))).sum() / Arrays.stream(MiscMath.elementwiseMultiply(hValues, hValues)).sum(); - hValues[hIndex] = newH; - } - - System.out.print(String.format("iteration %d: [ ", iterationCount)); + /*Refine total values of each h_i: + *Initialise h_values of the hypothetical non-existant previous iteration + *with the correct format but with impossible values. + Needed for exit condition of otherwise endless loop.*/ + System.out.print("initial values: [ "); for (double h : hValues) { - System.out.print(String.format("%1.4f, ", h)); + System.out.print(String.format("%1.4f, ", h)); } System.out.println(" ]"); - //update values of estimated positions - for (int[] pair : estimatedPositions) // pair ~ row, col - { - double newVal = hValues[pair[0]] * hValues[pair[1]]; - eigenMatrix.setValue(pair[0], pair[1], newVal); - eigenMatrix.setValue(pair[1], pair[0], newVal); - } + double[] hValuesOld = new double[matrixWidth]; - iterationCount++; + int iterationCount = 0; - //exit loop as soon as new values are similar to the last iteration - if (MiscMath.allClose(hValues, hValuesOld, 0d, 1e-05d, false)) + // repeat unitl values of h do not significantly change anymore + while (true) { - break; + for (int hIndex = 0; hIndex < matrixWidth; hIndex++) + { + double newH = Arrays + .stream(MiscMath.elementwiseMultiply(hValues, + eigenMatrix.getRow(hIndex))) + .sum() + / Arrays.stream( + MiscMath.elementwiseMultiply(hValues, hValues)) + .sum(); + hValues[hIndex] = newH; + } + + System.out.print(String.format("iteration %d: [ ", iterationCount)); + for (double h : hValues) + { + System.out.print(String.format("%1.4f, ", h)); + } + System.out.println(" ]"); + + // update values of estimated positions + for (int[] pair : estimatedPositions) // pair ~ row, col + { + double newVal = hValues[pair[0]] * hValues[pair[1]]; + eigenMatrix.setValue(pair[0], pair[1], newVal); + eigenMatrix.setValue(pair[1], pair[0], newVal); + } + + iterationCount++; + + // exit loop as soon as new values are similar to the last iteration + if (MiscMath.allClose(hValues, hValuesOld, 0d, 1e-05d, false)) + { + break; + } + + // save hValues for comparison in the next iteration + System.arraycopy(hValues, 0, hValuesOld, 0, hValues.length); } - //save hValues for comparison in the next iteration - System.arraycopy(hValues, 0, hValuesOld, 0, hValues.length); - } - - //----------------------------- - //Use complemented symmetric matrix to calculate final representative - //vectors. - - //Eigendecomposition. - eigenMatrix.tred(); - eigenMatrix.tqli(); + // ----------------------------- + // Use complemented symmetric matrix to calculate final representative + // vectors. - System.out.println("eigenmatrix"); - eigenMatrix.print(System.out, "%8.2f"); - System.out.println(); - System.out.println("uncorrected eigenvalues"); - eigenMatrix.printD(System.out, "%2.4f "); - System.out.println(); + // Eigendecomposition. + eigenMatrix.tred(); + eigenMatrix.tqli(); - double[] eigenVals = eigenMatrix.getD(); + System.out.println("eigenmatrix"); + eigenMatrix.print(System.out, "%8.2f"); + System.out.println(); + System.out.println("uncorrected eigenvalues"); + eigenMatrix.printD(System.out, "%2.4f "); + System.out.println(); - TreeMap eigenPairs = new TreeMap<>(Comparator.reverseOrder()); - for (int i = 0; i < eigenVals.length; i++) - { - eigenPairs.put(eigenVals[i], i); - } + double[] eigenVals = eigenMatrix.getD(); - // matrix of representative eigenvectors (each row is a vector) - double[][] _repMatrix = new double[eigenVals.length][dim]; - double[][] _oldMatrix = new double[eigenVals.length][dim]; - double[] correctedEigenValues = new double[dim]; - - int l = 0; - for (Entry pair : eigenPairs.entrySet()) - { - double eigenValue = pair.getKey(); - int column = pair.getValue(); - double[] eigenVector = eigenMatrix.getColumn(column); - //for 2nd and higher eigenvalues - if (l >= 1) + TreeMap eigenPairs = new TreeMap<>( + Comparator.reverseOrder()); + for (int i = 0; i < eigenVals.length; i++) { - eigenValue /= correctionFactor; + eigenPairs.put(eigenVals[i], i); } - correctedEigenValues[l] = eigenValue; - for (int j = 0; j < eigenVector.length; j++) - { - _repMatrix[j][l] = (eigenValue < 0) ? 0.0 : - Math.sqrt(eigenValue) * eigenVector[j]; - double tmpOldScore = scoresOld.getColumn(column)[j]; - _oldMatrix[j][dim - l - 1] = (Double.isNaN(tmpOldScore)) ? 0.0 : tmpOldScore; - } - l++; - if (l >= dim) - { - break; - } - } - System.out.println("correctedEigenValues"); - MiscMath.print(correctedEigenValues, "%2.4f "); - - repMatrix = new Matrix(_repMatrix); - repMatrix.setD(correctedEigenValues); - MatrixI oldMatrix = new Matrix(_oldMatrix); - - MatrixI dotMatrix = repMatrix.postMultiply(repMatrix.transpose()); - - double rmsd = scoresOld.rmsd(dotMatrix); - - System.out.println("iteration, rmsd, maxDiff, rmsdDiff"); - System.out.println(String.format("0, %8.5f, -, -", rmsd)); - // Refine representative vectors by minimising sum-of-squared deviates between dotMatrix and original score matrix - for (int iteration = 1; iteration < 21; iteration++) // arbitrarily set to 20 - { - MatrixI repMatrixOLD = repMatrix.copy(); - MatrixI dotMatrixOLD = dotMatrix.copy(); + // matrix of representative eigenvectors (each row is a vector) + double[][] _repMatrix = new double[eigenVals.length][dim]; + double[][] _oldMatrix = new double[eigenVals.length][dim]; + double[] correctedEigenValues = new double[dim]; - // for all rows/hA in the original matrix - for (int hAIndex = 0; hAIndex < oldMatrix.height(); hAIndex++) + int l = 0; + for (Entry pair : eigenPairs.entrySet()) { - double[] row = oldMatrix.getRow(hAIndex); - double[] hA = repMatrix.getRow(hAIndex); - hAIndex = hAIndex; - //find least-squares-solution fo rdifferences between original scores and representative vectors - double[] hAlsm = leastSquaresOptimisation(repMatrix, scoresOld, hAIndex); - // update repMatrix with new hAlsm - for (int j = 0; j < repMatrix.width(); j++) - { - repMatrix.setValue(hAIndex, j, hAlsm[j]); - } - } - - // dot product of representative vecotrs yields a matrix with values approximating the correlation matrix - dotMatrix = repMatrix.postMultiply(repMatrix.transpose()); - // calculate rmsd between approximation and correlation matrix - rmsd = scoresOld.rmsd(dotMatrix); - - // calculate maximum change of representative vectors of current iteration - MatrixI diff = repMatrix.subtract(repMatrixOLD).absolute(); - double maxDiff = 0.0; - for (int i = 0; i < diff.height(); i++) - { - for (int j = 0; j < diff.width(); j++) - { - maxDiff = (diff.getValue(i, j) > maxDiff) ? diff.getValue(i, j) : maxDiff; - } + double eigenValue = pair.getKey(); + int column = pair.getValue(); + double[] eigenVector = eigenMatrix.getColumn(column); + // for 2nd and higher eigenvalues + if (l >= 1) + { + eigenValue /= correctionFactor; + } + correctedEigenValues[l] = eigenValue; + for (int j = 0; j < eigenVector.length; j++) + { + _repMatrix[j][l] = (eigenValue < 0) ? 0.0 + : -Math.sqrt(eigenValue) * eigenVector[j]; + double tmpOldScore = scoresOld.getColumn(column)[j]; + _oldMatrix[j][dim - l - 1] = (Double.isNaN(tmpOldScore)) ? 0.0 + : tmpOldScore; + } + l++; + if (l >= dim) + { + break; + } } - // calculate rmsd between current and previous estimation - double rmsdDiff = dotMatrix.rmsd(dotMatrixOLD); + System.out.println("correctedEigenValues"); + MiscMath.print(correctedEigenValues, "%2.4f "); + + repMatrix = new Matrix(_repMatrix); + repMatrix.setD(correctedEigenValues); + MatrixI oldMatrix = new Matrix(_oldMatrix); - System.out.println(String.format("%d, %8.5f, %8.5f, %8.5f", iteration, rmsd, maxDiff, rmsdDiff)); + MatrixI dotMatrix = repMatrix.postMultiply(repMatrix.transpose()); - if (!(Math.abs(maxDiff) > 1e-06)) + double rmsd = scoresOld.rmsd(dotMatrix); + + System.out.println("iteration, rmsd, maxDiff, rmsdDiff"); + System.out.println(String.format("0, %8.5f, -, -", rmsd)); + // Refine representative vectors by minimising sum-of-squared deviates + // between dotMatrix and original score matrix + for (int iteration = 1; iteration < 21; iteration++) // arbitrarily set to + // 20 { - repMatrix = repMatrixOLD.copy(); - break; + MatrixI repMatrixOLD = repMatrix.copy(); + MatrixI dotMatrixOLD = dotMatrix.copy(); + + // for all rows/hA in the original matrix + for (int hAIndex = 0; hAIndex < oldMatrix.height(); hAIndex++) + { + double[] row = oldMatrix.getRow(hAIndex); + double[] hA = repMatrix.getRow(hAIndex); + hAIndex = hAIndex; + // find least-squares-solution fo rdifferences between original scores + // and representative vectors + double[] hAlsm = leastSquaresOptimisation(repMatrix, scoresOld, + hAIndex); + // update repMatrix with new hAlsm + for (int j = 0; j < repMatrix.width(); j++) + { + repMatrix.setValue(hAIndex, j, hAlsm[j]); + } + } + + // dot product of representative vecotrs yields a matrix with values + // approximating the correlation matrix + dotMatrix = repMatrix.postMultiply(repMatrix.transpose()); + // calculate rmsd between approximation and correlation matrix + rmsd = scoresOld.rmsd(dotMatrix); + + // calculate maximum change of representative vectors of current + // iteration + MatrixI diff = repMatrix.subtract(repMatrixOLD).absolute(); + double maxDiff = 0.0; + for (int i = 0; i < diff.height(); i++) + { + for (int j = 0; j < diff.width(); j++) + { + maxDiff = (diff.getValue(i, j) > maxDiff) ? diff.getValue(i, j) + : maxDiff; + } + } + + // calculate rmsd between current and previous estimation + double rmsdDiff = dotMatrix.rmsd(dotMatrixOLD); + + System.out.println(String.format("%d, %8.5f, %8.5f, %8.5f", + iteration, rmsd, maxDiff, rmsdDiff)); + + if (!(Math.abs(maxDiff) > 1e-06)) + { + repMatrix = repMatrixOLD.copy(); + break; + } } - } - } catch (Exception q) { @@ -451,35 +490,38 @@ public class ccAnalysis } /** - * Create equations system using information on originally known - * pairwise correlation coefficients (parsed from infile) and the - * representative result vectors - * - * Each equation has the format: - * hA * hA - pairwiseCC = 0 - * with: - * hA: unknown variable - * hB: known representative vector - * pairwiseCC: known pairwise correlation coefficien - * - * The resulting equations system is overdetermined, if there are more - * equations than unknown elements - * - * @param x ~ unknown n-dimensional column-vector - * (needed for generating equations system, NOT to be specified by user). - * @param hAIndex ~ index of currently optimised representative result vector. - * @param h ~ matrix with row-wise listing of representative result vectors. - * @param originalRow ~ matrix-row of originally parsed pairwise correlation coefficients. - * - * @return - */ - private double[] originalToEquasionSystem(double[] hA, MatrixI repMatrix, MatrixI scoresOld, int hAIndex) + * Create equations system using information on originally known pairwise + * correlation coefficients (parsed from infile) and the representative result + * vectors + * + * Each equation has the format: hA * hA - pairwiseCC = 0 with: hA: unknown + * variable hB: known representative vector pairwiseCC: known pairwise + * correlation coefficien + * + * The resulting equations system is overdetermined, if there are more + * equations than unknown elements + * + * @param x + * ~ unknown n-dimensional column-vector (needed for generating + * equations system, NOT to be specified by user). + * @param hAIndex + * ~ index of currently optimised representative result vector. + * @param h + * ~ matrix with row-wise listing of representative result vectors. + * @param originalRow + * ~ matrix-row of originally parsed pairwise correlation + * coefficients. + * + * @return + */ + private double[] originalToEquasionSystem(double[] hA, MatrixI repMatrix, + MatrixI scoresOld, int hAIndex) { double[] originalRow = scoresOld.getRow(hAIndex); int nans = MiscMath.countNaN(originalRow); double[] result = new double[originalRow.length - nans]; - //for all pairwiseCC in originalRow + // for all pairwiseCC in originalRow int resultIndex = 0; for (int hBIndex = 0; hBIndex < originalRow.length; hBIndex++) { @@ -488,40 +530,48 @@ public class ccAnalysis if (!Double.isNaN(pairwiseCC)) { double[] hB = repMatrix.getRow(hBIndex); - result[resultIndex++] = MiscMath.sum(MiscMath.elementwiseMultiply(hA, hB)) - pairwiseCC; - } else { + result[resultIndex++] = MiscMath + .sum(MiscMath.elementwiseMultiply(hA, hB)) - pairwiseCC; + } + else + { } } return result; } /** - * returns the jacobian matrix - * @param repMatrix ~ matrix of representative vectors - * @param hAIndex ~ current row index - * - * @return - */ - private MatrixI approximateDerivative(MatrixI repMatrix, MatrixI scoresOld, int hAIndex) + * returns the jacobian matrix + * + * @param repMatrix + * ~ matrix of representative vectors + * @param hAIndex + * ~ current row index + * + * @return + */ + private MatrixI approximateDerivative(MatrixI repMatrix, + MatrixI scoresOld, int hAIndex) { - //hA = x0 + // hA = x0 double[] hA = repMatrix.getRow(hAIndex); - double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, hAIndex); + double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, + hAIndex); double[] signX0 = new double[hA.length]; double[] xAbs = new double[hA.length]; for (int i = 0; i < hA.length; i++) { signX0[i] = (hA[i] >= 0) ? 1 : -1; xAbs[i] = (Math.abs(hA[i]) >= 1.0) ? Math.abs(hA[i]) : 1.0; - } + } double rstep = Math.pow(Math.ulp(1.0), 0.5); - double[] h = new double [hA.length]; + double[] h = new double[hA.length]; for (int i = 0; i < hA.length; i++) { h[i] = rstep * signX0[i] * xAbs[i]; } - + int m = f0.length; int n = hA.length; double[][] jTransposed = new double[n][m]; @@ -531,11 +581,12 @@ public class ccAnalysis System.arraycopy(hA, 0, x, 0, h.length); x[i] += h[i]; double dx = x[i] - hA[i]; - double[] df = originalToEquasionSystem(x, repMatrix, scoresOld, hAIndex); + double[] df = originalToEquasionSystem(x, repMatrix, scoresOld, + hAIndex); for (int j = 0; j < df.length; j++) { - df[j] -= f0[j]; - jTransposed[i][j] = df[j] / dx; + df[j] -= f0[j]; + jTransposed[i][j] = df[j] / dx; } } MatrixI J = new Matrix(jTransposed).transpose(); @@ -543,31 +594,40 @@ public class ccAnalysis } /** - * norm of regularized (by alpha) least-squares solution minus Delta - * @param alpha - * @param suf - * @param s - * @param Delta - * - * @return - */ - private double[] phiAndDerivative(double alpha, double[] suf, double[] s, double Delta) + * norm of regularized (by alpha) least-squares solution minus Delta + * + * @param alpha + * @param suf + * @param s + * @param Delta + * + * @return + */ + private double[] phiAndDerivative(double alpha, double[] suf, double[] s, + double Delta) { - double[] denom = MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha); + double[] denom = MiscMath + .elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha); double pNorm = MiscMath.norm(MiscMath.elementwiseDivide(suf, denom)); double phi = pNorm - Delta; // - sum ( suf**2 / denom**3) / pNorm - double phiPrime = - MiscMath.sum(MiscMath.elementwiseDivide(MiscMath.elementwiseMultiply(suf, suf), MiscMath.elementwiseMultiply(MiscMath.elementwiseMultiply(denom, denom), denom))) / pNorm; - return new double[]{phi, phiPrime}; + double phiPrime = -MiscMath.sum(MiscMath.elementwiseDivide( + MiscMath.elementwiseMultiply(suf, suf), + MiscMath.elementwiseMultiply( + MiscMath.elementwiseMultiply(denom, denom), denom))) + / pNorm; + return new double[] { phi, phiPrime }; } /** - * class holding the result of solveLsqTrustRegion - */ + * class holding the result of solveLsqTrustRegion + */ private class TrustRegion { private double[] step; + private double alpha; + private int iteration; public TrustRegion(double[] step, double alpha, int iteration) @@ -586,7 +646,7 @@ public class ccAnalysis { return this.alpha; } - + public int getIteration() { return this.iteration; @@ -594,22 +654,30 @@ public class ccAnalysis } /** - * solve a trust-region problem arising in least-squares optimisation - * @param n ~ number of variables - * @param m ~ number of residuals - * @param uf - * @param s ~ singular values of J - * @param V ~ transpose of VT - * @param Delta ~ radius of a trust region - * @param alpha ~ initial guess for alpha - * - * @return - */ - private TrustRegion solveLsqTrustRegion(int n, int m, double[] uf, double[] s, MatrixI V, double Delta, double alpha) + * solve a trust-region problem arising in least-squares optimisation + * + * @param n + * ~ number of variables + * @param m + * ~ number of residuals + * @param uf + * @param s + * ~ singular values of J + * @param V + * ~ transpose of VT + * @param Delta + * ~ radius of a trust region + * @param alpha + * ~ initial guess for alpha + * + * @return + */ + private TrustRegion solveLsqTrustRegion(int n, int m, double[] uf, + double[] s, MatrixI V, double Delta, double alpha) { double[] suf = MiscMath.elementwiseMultiply(s, uf); - //check if J has full rank and tr Gauss-Newton step + // check if J has full rank and tr Gauss-Newton step boolean fullRank = false; if (m >= n) { @@ -618,7 +686,8 @@ public class ccAnalysis } if (fullRank) { - double[] p = MiscMath.elementwiseMultiply(V.sumProduct(MiscMath.elementwiseDivide(uf, s)), -1); + double[] p = MiscMath.elementwiseMultiply( + V.sumProduct(MiscMath.elementwiseDivide(uf, s)), -1); if (MiscMath.norm(p) <= Delta) { TrustRegion result = new TrustRegion(p, 0.0, 0); @@ -631,15 +700,21 @@ public class ccAnalysis if (fullRank) { double[] phiAndPrime = phiAndDerivative(0.0, suf, s, Delta); - alphaLower = - phiAndPrime[0] / phiAndPrime[1]; + alphaLower = -phiAndPrime[0] / phiAndPrime[1]; } - alpha = (!fullRank && alpha == 0.0) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha; + alpha = (!fullRank && alpha == 0.0) + ? alpha = Math.max(0.001 * alphaUpper, + Math.pow(alphaLower * alphaUpper, 0.5)) + : alpha; int iteration = 0; - while (iteration < 10) // 10 is default max_iter + while (iteration < 10) // 10 is default max_iter { - alpha = (alpha < alphaLower || alpha > alphaUpper) ? alpha = Math.max(0.001 * alphaUpper, Math.pow(alphaLower * alphaUpper, 0.5)) : alpha; + alpha = (alpha < alphaLower || alpha > alphaUpper) + ? alpha = Math.max(0.001 * alphaUpper, + Math.pow(alphaLower * alphaUpper, 0.5)) + : alpha; double[] phiAndPrime = phiAndDerivative(alpha, suf, s, Delta); double phi = phiAndPrime[0]; double phiPrime = phiAndPrime[1]; @@ -649,18 +724,20 @@ public class ccAnalysis alphaLower = Math.max(alphaLower, alpha - ratio); alpha -= (phi + Delta) * ratio / Delta; - if (Math.abs(phi) < 0.01 * Delta) // default rtol set to 0.01 + if (Math.abs(phi) < 0.01 * Delta) // default rtol set to 0.01 { - break; + break; } iteration++; } // p = - V.dot( suf / (s**2 + alpha)) - double[] tmp = MiscMath.elementwiseDivide(suf, MiscMath.elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha)); + double[] tmp = MiscMath.elementwiseDivide(suf, MiscMath + .elementwiseAdd(MiscMath.elementwiseMultiply(s, s), alpha)); double[] p = MiscMath.elementwiseMultiply(V.sumProduct(tmp), -1); - // Make the norm of p equal to Delta, p is changed only slightly during this. + // Make the norm of p equal to Delta, p is changed only slightly during + // this. // It is done to prevent p lie outside of the trust region p = MiscMath.elementwiseMultiply(p, Delta / MiscMath.norm(p)); @@ -669,15 +746,18 @@ public class ccAnalysis } /** - * compute values of a quadratic function arising in least squares - * function: 0.5 * s.T * (J.T * J + diag) * s + g.T * s - * - * @param J ~ jacobian matrix - * @param g ~ gradient - * @param s ~ steps and rows - * - * @return - */ + * compute values of a quadratic function arising in least squares function: + * 0.5 * s.T * (J.T * J + diag) * s + g.T * s + * + * @param J + * ~ jacobian matrix + * @param g + * ~ gradient + * @param s + * ~ steps and rows + * + * @return + */ private double evaluateQuadratic(MatrixI J, double[] g, double[] s) { @@ -689,50 +769,64 @@ public class ccAnalysis } /** - * update the radius of a trust region based on the cost reduction - * - * @param Delta - * @param actualReduction - * @param predictedReduction - * @param stepNorm - * @param boundHit - * - * @return - */ - private double[] updateTrustRegionRadius(double Delta, double actualReduction, double predictedReduction, double stepNorm, boolean boundHit) + * update the radius of a trust region based on the cost reduction + * + * @param Delta + * @param actualReduction + * @param predictedReduction + * @param stepNorm + * @param boundHit + * + * @return + */ + private double[] updateTrustRegionRadius(double Delta, + double actualReduction, double predictedReduction, + double stepNorm, boolean boundHit) { double ratio = 0; if (predictedReduction > 0) { ratio = actualReduction / predictedReduction; - } else if (predictedReduction == 0 && actualReduction == 0) { + } + else if (predictedReduction == 0 && actualReduction == 0) + { ratio = 1; - } else { + } + else + { ratio = 0; } if (ratio < 0.25) { Delta = 0.25 * stepNorm; - } else if (ratio > 0.75 && boundHit) { + } + else if (ratio > 0.75 && boundHit) + { Delta *= 2.0; } - return new double[]{Delta, ratio}; + return new double[] { Delta, ratio }; } /** - * trust region reflective algorithm - * @param repMatrix ~ Matrix containing representative vectors - * @param scoresOld ~ Matrix containing initial observations - * @param index ~ current row index - * @param J ~ jacobian matrix - * - * @return - */ - private double[] trf(MatrixI repMatrix, MatrixI scoresOld, int index, MatrixI J) + * trust region reflective algorithm + * + * @param repMatrix + * ~ Matrix containing representative vectors + * @param scoresOld + * ~ Matrix containing initial observations + * @param index + * ~ current row index + * @param J + * ~ jacobian matrix + * + * @return + */ + private double[] trf(MatrixI repMatrix, MatrixI scoresOld, int index, + MatrixI J) { - //hA = x0 + // hA = x0 double[] hA = repMatrix.getRow(index); double[] f0 = originalToEquasionSystem(hA, repMatrix, scoresOld, index); int nfev = 1; @@ -742,7 +836,7 @@ public class ccAnalysis double[] g = J.transpose().sumProduct(f0); double Delta = MiscMath.norm(hA); int maxNfev = hA.length * 100; - double alpha = 0.0; // "Levenberg-Marquardt" parameter + double alpha = 0.0; // "Levenberg-Marquardt" parameter double gNorm = 0; boolean terminationStatus = false; @@ -753,11 +847,12 @@ public class ccAnalysis gNorm = MiscMath.norm(g); if (terminationStatus || nfev == maxNfev) { - break; + break; } - SingularValueDecomposition svd = new SingularValueDecomposition(new Array2DRowRealMatrix(J.asArray())); + SingularValueDecomposition svd = new SingularValueDecomposition( + new Array2DRowRealMatrix(J.asArray())); MatrixI U = new Matrix(svd.getU().getData()); - double[] s = svd.getSingularValues(); + double[] s = svd.getSingularValues(); MatrixI V = new Matrix(svd.getV().getData()).transpose(); double[] uf = U.transpose().sumProduct(f0); @@ -766,60 +861,67 @@ public class ccAnalysis double[] fNew = new double[f0.length]; double costNew = 0; double stepHnorm = 0; - + while (actualReduction <= 0 && nfev < maxNfev) { - TrustRegion trustRegion = solveLsqTrustRegion(n, m, uf, s, V, Delta, alpha); - double[] stepH = trustRegion.getStep(); - alpha = trustRegion.getAlpha(); - int nIterations = trustRegion.getIteration(); - double predictedReduction = - (evaluateQuadratic(J, g, stepH)); + TrustRegion trustRegion = solveLsqTrustRegion(n, m, uf, s, V, Delta, + alpha); + double[] stepH = trustRegion.getStep(); + alpha = trustRegion.getAlpha(); + int nIterations = trustRegion.getIteration(); + double predictedReduction = -(evaluateQuadratic(J, g, stepH)); xNew = MiscMath.elementwiseAdd(hA, stepH); - fNew = originalToEquasionSystem(xNew, repMatrix, scoresOld, index); - nfev++; - - stepHnorm = MiscMath.norm(stepH); + fNew = originalToEquasionSystem(xNew, repMatrix, scoresOld, index); + nfev++; - if (MiscMath.countNaN(fNew) > 0) - { - Delta = 0.25 * stepHnorm; - continue; - } + stepHnorm = MiscMath.norm(stepH); - // usual trust-region step quality estimation - costNew = 0.5 * MiscMath.dot(fNew, fNew); - actualReduction = cost - costNew; + if (MiscMath.countNaN(fNew) > 0) + { + Delta = 0.25 * stepHnorm; + continue; + } - double[] updatedTrustRegion = updateTrustRegionRadius(Delta, actualReduction, predictedReduction, stepHnorm, stepHnorm > (0.95 * Delta)); - double DeltaNew = updatedTrustRegion[0]; - double ratio = updatedTrustRegion[1]; + // usual trust-region step quality estimation + costNew = 0.5 * MiscMath.dot(fNew, fNew); + actualReduction = cost - costNew; - // default ftol and xtol = 1e-8 - boolean ftolSatisfied = actualReduction < (1e-8 * cost) && ratio > 0.25; - boolean xtolSatisfied = stepHnorm < (1e-8 * (1e-8 + MiscMath.norm(hA))); - terminationStatus = ftolSatisfied || xtolSatisfied; - if (terminationStatus) - { - break; - } + double[] updatedTrustRegion = updateTrustRegionRadius(Delta, + actualReduction, predictedReduction, stepHnorm, + stepHnorm > (0.95 * Delta)); + double DeltaNew = updatedTrustRegion[0]; + double ratio = updatedTrustRegion[1]; - alpha *= Delta / DeltaNew; - Delta = DeltaNew; + // default ftol and xtol = 1e-8 + boolean ftolSatisfied = actualReduction < (1e-8 * cost) + && ratio > 0.25; + boolean xtolSatisfied = stepHnorm < (1e-8 + * (1e-8 + MiscMath.norm(hA))); + terminationStatus = ftolSatisfied || xtolSatisfied; + if (terminationStatus) + { + break; + } + + alpha *= Delta / DeltaNew; + Delta = DeltaNew; } if (actualReduction > 0) { - hA = xNew; - f0 = fNew; - cost = costNew; + hA = xNew; + f0 = fNew; + cost = costNew; - J = approximateDerivative(repMatrix, scoresOld, index); + J = approximateDerivative(repMatrix, scoresOld, index); g = J.transpose().sumProduct(f0); - } else { + } + else + { stepHnorm = 0; - actualReduction = 0; + actualReduction = 0; } iteration++; } @@ -828,16 +930,20 @@ public class ccAnalysis } /** - * performs the least squares optimisation - * adapted from https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.least_squares.html#scipy.optimize.least_squares - * - * @param repMatrix ~ Matrix containing representative vectors - * @param scoresOld ~ Matrix containing initial observations - * @param index ~ current row index - * - * @return - */ - private double[] leastSquaresOptimisation(MatrixI repMatrix, MatrixI scoresOld, int index) + * performs the least squares optimisation adapted from + * https://docs.scipy.org/doc/scipy/reference/generated/scipy.optimize.least_squares.html#scipy.optimize.least_squares + * + * @param repMatrix + * ~ Matrix containing representative vectors + * @param scoresOld + * ~ Matrix containing initial observations + * @param index + * ~ current row index + * + * @return + */ + private double[] leastSquaresOptimisation(MatrixI repMatrix, + MatrixI scoresOld, int index) { MatrixI J = approximateDerivative(repMatrix, scoresOld, index); double[] result = trf(repMatrix, scoresOld, index, J); diff --git a/src/jalview/analysis/scoremodels/DistanceScoreModel.java b/src/jalview/analysis/scoremodels/DistanceScoreModel.java index 55510bd..1bdaad6 100644 --- a/src/jalview/analysis/scoremodels/DistanceScoreModel.java +++ b/src/jalview/analysis/scoremodels/DistanceScoreModel.java @@ -57,5 +57,5 @@ public abstract class DistanceScoreModel implements ScoreModelI return similarities; } - + } diff --git a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java index df45a72..bcc0855 100644 --- a/src/jalview/analysis/scoremodels/FeatureDistanceModel.java +++ b/src/jalview/analysis/scoremodels/FeatureDistanceModel.java @@ -235,7 +235,7 @@ public class FeatureDistanceModel extends DistanceScoreModel public boolean isProtein() { return true; - } + } @Override public String toString() diff --git a/src/jalview/analysis/scoremodels/ScoreModels.java b/src/jalview/analysis/scoremodels/ScoreModels.java index f591c8e..490ec00 100644 --- a/src/jalview/analysis/scoremodels/ScoreModels.java +++ b/src/jalview/analysis/scoremodels/ScoreModels.java @@ -40,7 +40,7 @@ public class ScoreModels private final ScoreMatrix PAM250; private final ScoreMatrix DNA; - + private final ScoreMatrix SECONDARYSTRUCTURE; private static ScoreModels instance; @@ -70,7 +70,7 @@ public class ScoreModels *
  • PAM250
    • *
  • PID
    • *
  • DNA
    • - *
  • Sequence Feature Similarity
    • * + *
  • Sequence Feature Similarity
    • * *
  • Secondary Structure Similarity
    • * */ @@ -85,8 +85,9 @@ public class ScoreModels DNA = loadScoreMatrix("scoreModel/dna.scm"); registerScoreModel(new PIDModel()); registerScoreModel(new FeatureDistanceModel()); - SECONDARYSTRUCTURE = loadScoreMatrix("scoreModel/secondarystructure.scm"); - registerScoreModel(new SecondaryStructureDistanceModel()); + SECONDARYSTRUCTURE = loadScoreMatrix( + "scoreModel/secondarystructure.scm"); + registerScoreModel(new SecondaryStructureDistanceModel()); } @@ -146,7 +147,8 @@ public class ScoreModels public void registerScoreModel(ScoreModelI sm) { - if(sm.getName().equals("SECONDARYSTRUCTURE")) { + if (sm.getName().equals("SECONDARYSTRUCTURE")) + { return; } ScoreModelI sm2 = models.get(sm.getName()); @@ -187,7 +189,7 @@ public class ScoreModels { return PAM250; } - + public ScoreMatrix getSecondaryStructureMatrix() { return SECONDARYSTRUCTURE; diff --git a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java index ceccec0..6ed94b2 100644 --- a/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java +++ b/src/jalview/analysis/scoremodels/SecondaryStructureDistanceModel.java @@ -49,20 +49,19 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel private static final String NAME = "Secondary Structure Similarity"; private ScoreMatrix ssRateMatrix; - - private String description; - + + private String description; + FeatureRenderer fr; - - + /** * Constructor */ public SecondaryStructureDistanceModel() { - + } - + @Override public ScoreModelI getInstance(AlignmentViewPanel view) { @@ -89,51 +88,56 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel fr = view.cloneFeatureRenderer(); return true; } - + ArrayList ssForSeqs = null; @Override public SequenceI[] expandSeqData(SequenceI[] sequences, - AlignmentView seqData, SimilarityParamsI scoreParams,List labels) + AlignmentView seqData, SimilarityParamsI scoreParams, + List labels) { ssForSeqs = new ArrayList(); List newSequences = new ArrayList(); List newCigs = new ArrayList(); int sq = 0; - - AlignmentAnnotation[] alignAnnotList = fr.getViewport().getAlignment() - .getAlignmentAnnotation(); - - String ssSource = scoreParams.getSecondaryStructureSource(); - if(ssSource == null || ssSource == "") { + .getAlignmentAnnotation(); + + String ssSource = scoreParams.getSecondaryStructureSource(); + if (ssSource == null || ssSource == "") + { ssSource = Constants.SS_ALL_PROVIDERS; } - + /* * Add secondary structure annotations that are added to the annotation track * to the map */ - Map> ssAlignmentAnnotationForSequences - = AlignmentUtils.getSequenceAssociatedAlignmentAnnotations(alignAnnotList, ssSource); - + Map> ssAlignmentAnnotationForSequences = AlignmentUtils + .getSequenceAssociatedAlignmentAnnotations(alignAnnotList, + ssSource); + for (SeqCigar scig : seqData.getSequences()) { // get the next sequence that should be bound to this scig: may be null SequenceI alSeq = sequences[sq++]; - List ssec = ssAlignmentAnnotationForSequences.get(scig.getRefSeq()); + List ssec = ssAlignmentAnnotationForSequences + .get(scig.getRefSeq()); if (ssec == null) { // not defined newSequences.add(alSeq); - if (alSeq!=null) { + if (alSeq != null) + { labels.add("No Secondary Structure"); } - SeqCigar newSeqCigar = scig; //new SeqCigar(scig); + SeqCigar newSeqCigar = scig; // new SeqCigar(scig); newCigs.add(newSeqCigar); ssForSeqs.add(null); - } else { + } + else + { for (int i = 0; i < ssec.size(); i++) { if (alSeq != null) @@ -141,7 +145,7 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel labels.add(AlignmentUtils .extractSSSourceFromAnnotationDescription(ssec.get(i))); } - //newSequences.add(seq); + // newSequences.add(seq); newSequences.add(alSeq); SeqCigar newSeqCigar = scig; // new SeqCigar(scig); newCigs.add(newSeqCigar); @@ -156,25 +160,30 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel } /** - * Calculates distance score [i][j] between each pair of protein sequences - * based on their secondary structure annotations (H, E, C). - * The final score is normalised by the number of - * alignment columns processed, providing an average similarity score. + * Calculates distance score [i][j] between each pair of protein sequences + * based on their secondary structure annotations (H, E, C). The final score + * is normalised by the number of alignment columns processed, providing an + * average similarity score. *

    - * The parameters argument can include settings for handling gap-residue aligned - * positions and may determine if the score calculation is based on the longer or shorter - * sequence in each pair. This can be important for handling partial alignments or - * sequences of significantly different lengths. + * The parameters argument can include settings for handling gap-residue + * aligned positions and may determine if the score calculation is based on + * the longer or shorter sequence in each pair. This can be important for + * handling partial alignments or sequences of significantly different + * lengths. * - * @param seqData The aligned sequence data including secondary structure annotations. - * @param params Additional parameters for customising the scoring process, such as gap - * handling and sequence length consideration. + * @param seqData + * The aligned sequence data including secondary structure + * annotations. + * @param params + * Additional parameters for customising the scoring process, such as + * gap handling and sequence length consideration. */ @Override public MatrixI findDistances(AlignmentView seqData, SimilarityParamsI params) - { - if (ssForSeqs==null || ssForSeqs.size()!=seqData.getSequences().length) + { + if (ssForSeqs == null + || ssForSeqs.size() != seqData.getSequences().length) { // expandSeqData needs to be called to initialise the hash SequenceI[] sequences = new SequenceI[seqData.getSequences().length]; @@ -182,20 +191,21 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel expandSeqData(sequences, seqData, params, new ArrayList()); } SeqCigar[] seqs = seqData.getSequences(); - int noseqs = seqs.length; //no of sequences - int cpwidth = 0; - double[][] similarities = new double[noseqs][noseqs]; //matrix to store similarity score - //secondary structure source parameter selected by the user from the drop down. - String ssSource = params.getSecondaryStructureSource(); - if(ssSource == null || ssSource == "") { + int noseqs = seqs.length; // no of sequences + int cpwidth = 0; + double[][] similarities = new double[noseqs][noseqs]; // matrix to store + // similarity score + // secondary structure source parameter selected by the user from the drop + // down. + String ssSource = params.getSecondaryStructureSource(); + if (ssSource == null || ssSource == "") + { ssSource = Constants.SS_ALL_PROVIDERS; } ssRateMatrix = ScoreModels.getInstance().getSecondaryStructureMatrix(); - + // need to get real position for view position int[] viscont = seqData.getVisibleContigs(); - - /* * scan each column, compute and add to each similarity[i, j] @@ -204,15 +214,16 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel */ for (int vc = 0; vc < viscont.length; vc += 2) { - //Iterates for each column position - for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++) + // Iterates for each column position + for (int cpos = viscont[vc]; cpos <= viscont[vc + 1]; cpos++) { - cpwidth++; //used to normalise the similarity score + cpwidth++; // used to normalise the similarity score /* * get set of sequences without gap in the current column */ - Set seqsWithoutGapAtCol = findSeqsWithoutGapAtColumn(seqs, cpos); + Set seqsWithoutGapAtCol = findSeqsWithoutGapAtColumn(seqs, + cpos); /* * calculate similarity score for each secondary structure annotation on i'th and j'th @@ -292,30 +303,31 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel * and fill in the bottom half of the matrix */ // TODO JAL-2424 cpwidth may be out by 1 - affects scores but not tree shape - + for (int i = 0; i < noseqs; i++) { for (int j = i + 1; j < noseqs; j++) - { + { similarities[i][j] /= cpwidth; similarities[j][i] = similarities[i][j]; } } - return SimilarityScoreModel.similarityToDistance(new Matrix(similarities)); - + return SimilarityScoreModel + .similarityToDistance(new Matrix(similarities)); + } /** - * Builds and returns a set containing sequences (SeqCigar) which do not - * have a gap at the given column position. + * Builds and returns a set containing sequences (SeqCigar) which do not have + * a gap at the given column position. * * @param seqs * @param columnPosition * (0..) * @return */ - private Set findSeqsWithoutGapAtColumn( - SeqCigar[] seqs, int columnPosition) + private Set findSeqsWithoutGapAtColumn(SeqCigar[] seqs, + int columnPosition) { Set seqsWithoutGapAtCol = new HashSet<>(); for (SeqCigar seq : seqs) @@ -325,14 +337,13 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel { /* * position is not a gap - */ + */ seqsWithoutGapAtCol.add(seq); } } return seqsWithoutGapAtCol; } - @Override public String getName() { @@ -348,7 +359,7 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel @Override public boolean isDNA() { - return false; + return false; } @Override @@ -356,7 +367,7 @@ public class SecondaryStructureDistanceModel extends DistanceScoreModel { return false; } - + @Override public boolean isSecondaryStructure() { diff --git a/src/jalview/analysis/scoremodels/SimilarityParams.java b/src/jalview/analysis/scoremodels/SimilarityParams.java index 2a25fa8..40a4636 100644 --- a/src/jalview/analysis/scoremodels/SimilarityParams.java +++ b/src/jalview/analysis/scoremodels/SimilarityParams.java @@ -103,7 +103,7 @@ public class SimilarityParams implements SimilarityParamsI private boolean includeGaps; private boolean denominateByShortestLength; - + private String secondaryStructureSource; /** diff --git a/src/jalview/api/AlignViewControllerI.java b/src/jalview/api/AlignViewControllerI.java index 25e4873..098024c 100644 --- a/src/jalview/api/AlignViewControllerI.java +++ b/src/jalview/api/AlignViewControllerI.java @@ -121,7 +121,9 @@ public interface AlignViewControllerI /** * Justify alignment or currently selected region left or right - * @param left - true - means justify left + * + * @param left + * - true - means justify left * @return */ boolean justify_Region(boolean left); diff --git a/src/jalview/api/AlignViewportI.java b/src/jalview/api/AlignViewportI.java index 2cdb251..5e1b812 100644 --- a/src/jalview/api/AlignViewportI.java +++ b/src/jalview/api/AlignViewportI.java @@ -85,9 +85,9 @@ public interface AlignViewportI extends ViewStyleI boolean isValidCharWidth(); boolean isShowConsensusHistogram(); - + boolean isShowSequenceLogo(); - + boolean isNormaliseSequenceLogo(); ColourSchemeI getGlobalColourScheme(); @@ -129,9 +129,8 @@ public interface AlignViewportI extends ViewStyleI * @return */ AlignmentAnnotation getAlignmentConsensusAnnotation(); - - List getAlignmentSecondaryStructureConsensusAnnotation(); + List getAlignmentSecondaryStructureConsensusAnnotation(); /** * get the container for alignment gap annotation @@ -178,9 +177,9 @@ public interface AlignViewportI extends ViewStyleI * @param hconsensus */ void setSequenceConsensusHash(ProfilesI hconsensus); - - void setSequenceSSConsensusHash(Map hSSConsesnusProfileMap); - + + void setSequenceSSConsensusHash( + Map hSSConsesnusProfileMap); /** * Set the cDNA complement consensus for the viewport @@ -571,6 +570,7 @@ public interface AlignViewportI extends ViewStyleI * @return */ Iterator getViewAsVisibleContigs(boolean selectedRegionOnly); + /** * notify all concerned that the alignment data has changed and derived data * needs to be recalculated @@ -578,7 +578,8 @@ public interface AlignViewportI extends ViewStyleI public void notifyAlignmentChanged(); /** - * retrieve a matrix associated with the view's alignment's annotation + * retrieve a matrix associated with the view's alignment's annotation + * * @param alignmentAnnotation * @return contact matrix or NULL */ diff --git a/src/jalview/api/ViewStyleI.java b/src/jalview/api/ViewStyleI.java index bed31c4..78bd2c9 100644 --- a/src/jalview/api/ViewStyleI.java +++ b/src/jalview/api/ViewStyleI.java @@ -38,7 +38,7 @@ public interface ViewStyleI boolean getColourAppliesToAllGroups(); boolean getAbovePIDThreshold(); - + boolean getByConsensusSecondaryStructureSelected(); void setIncrement(int inc); @@ -66,9 +66,9 @@ public interface ViewStyleI boolean getScaleRightWrapped(); void setAbovePIDThreshold(boolean b); - + void setByConsensusSecondaryStructureSelected(boolean b); - + void setShowStructureProvider(boolean b); boolean isShowStructureProvider(); diff --git a/src/jalview/api/analysis/ScoreModelI.java b/src/jalview/api/analysis/ScoreModelI.java index 3613afd..d6ab555 100644 --- a/src/jalview/api/analysis/ScoreModelI.java +++ b/src/jalview/api/analysis/ScoreModelI.java @@ -65,21 +65,18 @@ public interface ScoreModelI // TODO getName, isDNA, isProtein can be static methods in Java 8 - default public boolean isSecondaryStructure() { return false; } /** - * Answers false by default - * Answers true if the data has secondary structure (so should be - * shown in menus in that context) + * Answers false by default Answers true if the data has secondary structure + * (so should be shown in menus in that context) * * @return */ - - + /** * Returns a distance score for the given sequence regions, that is, a matrix * whose value [i][j] is the distance of sequence i from sequence j by some @@ -117,13 +114,22 @@ public interface ScoreModelI ScoreModelI getInstance(AlignmentViewPanel avp); /** - * Score models may create multiple leaves for a single sequence - implement this method if you do - * @param sequences - sequences to be filtered/expanded set of leaves - * @param seqData - origin - * @param labels - strings to show instead of the SequenceI.getName() for each element of sequences attached to leaves + * Score models may create multiple leaves for a single sequence - implement + * this method if you do + * + * @param sequences + * - sequences to be filtered/expanded set of leaves + * @param seqData + * - origin + * @param labels + * - strings to show instead of the SequenceI.getName() for each + * element of sequences attached to leaves * @return filtered/expanded set of leaves to be analysed */ - default SequenceI[] expandSeqData(SequenceI[] sequences, AlignmentView seqData, SimilarityParamsI scoreParams, List labels) { - return sequences; + default SequenceI[] expandSeqData(SequenceI[] sequences, + AlignmentView seqData, SimilarityParamsI scoreParams, + List labels) + { + return sequences; }; } diff --git a/src/jalview/api/analysis/SimilarityParamsI.java b/src/jalview/api/analysis/SimilarityParamsI.java index 43f2866..2558515 100644 --- a/src/jalview/api/analysis/SimilarityParamsI.java +++ b/src/jalview/api/analysis/SimilarityParamsI.java @@ -60,7 +60,7 @@ public interface SimilarityParamsI * @return */ boolean denominateByShortestLength(); - + String getSecondaryStructureSource(); void setSecondaryStructureSource(String secondaryStructureSource); diff --git a/src/jalview/appletgui/AlignFrame.java b/src/jalview/appletgui/AlignFrame.java index 55a5364..b77ee85 100644 --- a/src/jalview/appletgui/AlignFrame.java +++ b/src/jalview/appletgui/AlignFrame.java @@ -3432,8 +3432,8 @@ public class AlignFrame extends EmbmenuFrame implements ActionListener, Menu autoAnnMenu = new Menu( MessageManager.getString("label.autocalculated_annotation")); - Menu selectSS = new Menu( - MessageManager.getString("label.select_secondary_structure_source")); + Menu selectSS = new Menu(MessageManager + .getString("label.select_secondary_structure_source")); showGroupConsensus.addItemListener(this); showGroupConservation.addItemListener(this); showConsensusHistogram.addItemListener(this); diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index a45fc42..8c3c5dd 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1489,11 +1489,10 @@ 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/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index 7e1296e..2e2dd49 100644 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -2251,8 +2251,8 @@ public class JalviewLite extends Applet PDBEntry[] pdb = new PDBEntry[pdbs.size()]; String[][] chains = new String[pdbs.size()][]; String[] protocols = new String[pdbs.size()]; - for (int pdbsi = 0, - pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++) + for (int pdbsi = 0, pdbsiSize = pdbs + .size(); pdbsi < pdbsiSize; pdbsi++) { Object[] o = (Object[]) pdbs.elementAt(pdbsi); pdb[pdbsi] = (PDBEntry) o[0]; diff --git a/src/jalview/commands/JustifyLeftOrRightCommand.java b/src/jalview/commands/JustifyLeftOrRightCommand.java index 2559662..c1eb655 100644 --- a/src/jalview/commands/JustifyLeftOrRightCommand.java +++ b/src/jalview/commands/JustifyLeftOrRightCommand.java @@ -58,8 +58,8 @@ public class JustifyLeftOrRightCommand extends EditCommand { continue; } - char[] range = seq.getSequence(from, to+1); - if (range==null || range.length==0) + char[] range = seq.getSequence(from, to + 1); + if (range == null || range.length == 0) { continue; } @@ -78,7 +78,7 @@ public class JustifyLeftOrRightCommand extends EditCommand alseq[gapstart + gp] = gc; } - for (int sqp = 0,insp=0; sqp codonFrameList; - + private void initAlignment(SequenceI[] seqs) { groups = Collections.synchronizedList(new ArrayList()); @@ -82,13 +82,12 @@ public class Alignment implements AlignmentI, AutoCloseable nucleotide = Comparison.isNucleotide(seqs); sequences = Collections.synchronizedList(new ArrayList()); - for (int i = 0; i < seqs.length; i++) { sequences.add(seqs[i]); } - + } /** diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index d660f8f..12c7225 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -57,7 +57,7 @@ public class AlignmentAnnotation public static final int CDNA_PROFILE = 2; private static long counter = 0; - + private long noOfSequencesIncluded = -1; /** diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java index 2b5894a..ef543db 100755 --- a/src/jalview/datamodel/BinaryNode.java +++ b/src/jalview/datamodel/BinaryNode.java @@ -34,7 +34,7 @@ public class BinaryNode String name; - String label=null; + String label = null; BinaryNode left; @@ -366,14 +366,17 @@ public class BinaryNode return oldstate; } + /** * check if there's a label to show + * * @return true if non-empty/null string */ public boolean hasLabel() { - return label!=null && !label.isEmpty(); + return label != null && !label.isEmpty(); } + public String getLabel() { return label; @@ -402,14 +405,15 @@ public class BinaryNode public String getDisplayName() { - if (name!=null && !name.isBlank()) + if (name != null && !name.isBlank()) { - - if (hasLabel()) { - return getName()+"|"+label; + + if (hasLabel()) + { + return getName() + "|" + label; } return name; } - return hasLabel() ? label:""; + return hasLabel() ? label : ""; } } diff --git a/src/jalview/datamodel/PDBEntry.java b/src/jalview/datamodel/PDBEntry.java index fb9e96a..08f3eff 100755 --- a/src/jalview/datamodel/PDBEntry.java +++ b/src/jalview/datamodel/PDBEntry.java @@ -516,7 +516,8 @@ public class PDBEntry if (_hasProperty(AUTHORITATIVE_ID)) { Object authId = getProperty(AUTHORITATIVE_ID); - return (authId instanceof Boolean) ? (Boolean) authId : Boolean.valueOf(authId.toString()); + return (authId instanceof Boolean) ? (Boolean) authId + : Boolean.valueOf(authId.toString()); } return false; } @@ -650,9 +651,9 @@ public class PDBEntry public void setProviderCategory(String providerCategory) { - setProperty(PROVIDERCATEGORY, providerCategory); + setProperty(PROVIDERCATEGORY, providerCategory); } - + public String getProviderCategory() { return (String) getProperty(PROVIDERCATEGORY); @@ -662,5 +663,5 @@ public class PDBEntry { return _hasProperty(PROVIDERCATEGORY); } - + } diff --git a/src/jalview/datamodel/Profile.java b/src/jalview/datamodel/Profile.java index bc87204..cd892e4 100644 --- a/src/jalview/datamodel/Profile.java +++ b/src/jalview/datamodel/Profile.java @@ -32,9 +32,9 @@ public class Profile implements ProfileI * an object holding counts of symbols in the profile */ private ResidueCount counts; - + private SecondaryStructureCount ssCounts; - + private int seqWithSSCount = -1; /* @@ -51,15 +51,15 @@ public class Profile implements ProfileI * the highest count for any residue in the profile */ private int maxCount; + private int maxSSCount; - /* * the residue (e.g. K) or residues (e.g. KQW) with the * highest count in the profile */ private String modalResidue; - + private String modalSS; /** @@ -82,8 +82,9 @@ public class Profile implements ProfileI this.maxCount = max; this.modalResidue = modalRes; } - - public Profile(String modalSS, int ssCount, int gaps, int maxSSCount, int seqWithSSCount) + + public Profile(String modalSS, int ssCount, int gaps, int maxSSCount, + int seqWithSSCount) { this.height = ssCount; this.gapped = gaps; @@ -100,7 +101,7 @@ public class Profile implements ProfileI { this.counts = residueCounts; } - + @Override public void setSSCounts(SecondaryStructureCount secondaryStructureCount) { @@ -128,7 +129,7 @@ public class Profile implements ProfileI } return pid; } - + @Override public float getSSPercentageIdentity(boolean ignoreGaps) { @@ -156,7 +157,7 @@ public class Profile implements ProfileI { return counts; } - + @Override public SecondaryStructureCount getSSCounts() { @@ -189,7 +190,7 @@ public class Profile implements ProfileI { return maxCount; } - + @Override public int getMaxSSCount() { @@ -204,7 +205,7 @@ public class Profile implements ProfileI { return modalResidue; } - + @Override public String getModalSS() { diff --git a/src/jalview/datamodel/ProfileI.java b/src/jalview/datamodel/ProfileI.java index 9046f23..3e01507 100644 --- a/src/jalview/datamodel/ProfileI.java +++ b/src/jalview/datamodel/ProfileI.java @@ -29,8 +29,9 @@ public interface ProfileI * @param residueCounts */ public abstract void setCounts(ResidueCount residueCounts); - public abstract void setSSCounts(SecondaryStructureCount secondaryStructureCount); - + + public abstract void setSSCounts( + SecondaryStructureCount secondaryStructureCount); /** * Returns the percentage identity of the profile, i.e. the highest proportion @@ -41,7 +42,7 @@ public interface ProfileI * @return */ public abstract float getPercentageIdentity(boolean ignoreGaps); - + public abstract float getSSPercentageIdentity(boolean ignoreGaps); /** @@ -57,7 +58,7 @@ public interface ProfileI * @return */ public abstract int getHeight(); - + public abstract int getSeqWithSSCount(); /** @@ -74,6 +75,7 @@ public interface ProfileI * @return */ public abstract int getMaxCount(); + public abstract int getMaxSSCount(); /** @@ -83,6 +85,7 @@ public interface ProfileI * @return */ public abstract String getModalResidue(); + public abstract String getModalSS(); /** @@ -91,6 +94,7 @@ public interface ProfileI * @return */ public abstract int getNonGapped(); + SecondaryStructureCount getSSCounts(); } \ No newline at end of file diff --git a/src/jalview/datamodel/SecondaryStructureCount.java b/src/jalview/datamodel/SecondaryStructureCount.java index 52e9746..7d1b43c 100644 --- a/src/jalview/datamodel/SecondaryStructureCount.java +++ b/src/jalview/datamodel/SecondaryStructureCount.java @@ -63,7 +63,6 @@ public class SecondaryStructureCount */ private static final String SS_SYMBOLS = "HEC"; - static final int GAP_COUNT = 0; /* @@ -116,7 +115,7 @@ public class SecondaryStructureCount */ public SecondaryStructureCount() { - //isSS = true; + // isSS = true; int charsToCount = SS_SYMBOLS.length(); counts = new short[charsToCount + 1]; } @@ -419,8 +418,7 @@ public class SecondaryStructureCount { if (intCounts[i] == count) { - modal.append( - SS_SYMBOLS.charAt(i - 1)); + modal.append(SS_SYMBOLS.charAt(i - 1)); } } } @@ -430,8 +428,7 @@ public class SecondaryStructureCount { if (counts[i] == count) { - modal.append( - SS_SYMBOLS.charAt(i - 1)); + modal.append(SS_SYMBOLS.charAt(i - 1)); } } } diff --git a/src/jalview/datamodel/SequenceGroup.java b/src/jalview/datamodel/SequenceGroup.java index 38104e5..a2eaf1d 100755 --- a/src/jalview/datamodel/SequenceGroup.java +++ b/src/jalview/datamodel/SequenceGroup.java @@ -136,7 +136,6 @@ public class SequenceGroup implements AnnotatedCollectionI * consensus calculation property */ private boolean showSequenceLogo = false; - /** * flag indicating if logo should be rendered normalised @@ -154,18 +153,17 @@ public class SequenceGroup implements AnnotatedCollectionI private boolean hidecols = false; AlignmentAnnotation consensus = null; - List ssConsensus = null; - + List secondaryStructureSources = null; AlignmentAnnotation conservation = null; private boolean showConsensusHistogram; - + private AnnotatedCollectionI context; - + public Map hSSConsensusProfileMap; /** @@ -418,7 +416,7 @@ public class SequenceGroup implements AnnotatedCollectionI } return tmp.toArray(new SequenceI[tmp.size()]); } - + public List getSecondaryStructureSources() { return secondaryStructureSources; @@ -633,38 +631,39 @@ public class SequenceGroup implements AnnotatedCollectionI cs.setConsensus(cnsns); upd = true; } - + hSSConsensusProfileMap = new HashMap(); - List ssSources = new ArrayList(); + List ssSources = new ArrayList(); AnnotatedCollectionI aa = this.getContext(); - - if(aa !=null ) + + if (aa != null) { - ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa.getAlignmentAnnotation()); + ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation( + aa.getAlignmentAnnotation()); } - if(ssSources != null) { + if (ssSources != null) + { ssSources.add(Constants.SS_ALL_PROVIDERS); - for(String ssSource : ssSources) { - ProfilesI hSSConsensus = AAFrequency.calculateSS(sequences, startRes, endRes + 1, showSequenceLogo, - ssSource); + for (String ssSource : ssSources) + { + ProfilesI hSSConsensus = AAFrequency.calculateSS(sequences, + startRes, endRes + 1, showSequenceLogo, ssSource); hSSConsensusProfileMap.put(ssSource, hSSConsensus); } } - if (ssConsensus != null) { _updateSSConsensusRow(hSSConsensusProfileMap, sequences.size()); upd = true; } - + if (cs != null) { cs.setSSConsensusProfileMap(hSSConsensusProfileMap); upd = true; } - if ((conservation != null) || (cs != null && cs.conservationApplied())) @@ -754,68 +753,82 @@ public class SequenceGroup implements AnnotatedCollectionI // for // ignoreGapsInConsensusCalculation); } - - + /** - * Updates the secondary structure consensus row based on the provided profiles map and the number of sequences. + * Updates the secondary structure consensus row based on the provided + * profiles map and the number of sequences. * - * @param hSSConsensusProfileMap A map containing secondary structure consensus profiles for each providers. - * @param nseq The number of sequences. + * @param hSSConsensusProfileMap + * A map containing secondary structure consensus profiles for each + * providers. + * @param nseq + * The number of sequences. */ - private void _updateSSConsensusRow(Map hSSConsensusProfileMap, long nseq) + private void _updateSSConsensusRow( + Map hSSConsensusProfileMap, long nseq) { // Get a list of secondary structure sources from the profile map keys - List ssSources = new ArrayList<>(hSSConsensusProfileMap.keySet()); + List ssSources = new ArrayList<>( + hSSConsensusProfileMap.keySet()); secondaryStructureSources = new ArrayList(); // Sort the secondary structure sources alphabetically Collections.sort(ssSources); - + // Initialize ssConsensus if it is null if (ssConsensus == null) { getSSConsensus(ssSources); } - + // Iterate through each alignment annotation in the ssConsensus list - for (AlignmentAnnotation aa : ssConsensus) { + for (AlignmentAnnotation aa : ssConsensus) + { ProfilesI profile = null; String ssSource = null; - - // Find the matching profile for the current annotation based on its description - for(String source : ssSources) { - if(aa.description.startsWith(source)) { + + // Find the matching profile for the current annotation based on its + // description + for (String source : ssSources) + { + if (aa.description.startsWith(source)) + { profile = hSSConsensusProfileMap.get(source); ssSource = source; } } - + // If no matching profile is found, continue to the next annotation - if(profile == null) { + if (profile == null) + { continue; } - // Update the label and description of the annotation with the source/provider - aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " " + ssSource + " " + getName(); - aa.description = ssSource + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL +" for " + getName(); - + // Update the label and description of the annotation with the + // source/provider + aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " " + + ssSource + " " + getName(); + aa.description = ssSource + + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " for " + + getName(); + // Get the width of the annotations array int aWidth = (aa.annotations != null) - ? (endRes < aa.annotations.length - ? aa.annotations.length + ? (endRes < aa.annotations.length ? aa.annotations.length : endRes + 1) : endRes + 1; - aa.annotations = new Annotation[aWidth]; - + aa.annotations = new Annotation[aWidth]; + // Complete the secondary structure consensus AAFrequency.completeSSConsensus(aa, profile, startRes, endRes + 1, - ignoreGapsInConsensus, showSequenceLogo, nseq); - - //Add the provider to the list if the no of sequences - //contributed to the secondary structure consensus is - //more than 0. - if(aa.getNoOfSequencesIncluded()>0 && !Constants.SS_ALL_PROVIDERS.equals(ssSource)) - { + ignoreGapsInConsensus, showSequenceLogo, nseq); + + // Add the provider to the list if the no of sequences + // contributed to the secondary structure consensus is + // more than 0. + if (aa.getNoOfSequencesIncluded() > 0 + && !Constants.SS_ALL_PROVIDERS.equals(ssSource)) + { // Remove "All" from the hidden types list{ secondaryStructureSources.add(ssSource); } @@ -1247,7 +1260,7 @@ public class SequenceGroup implements AnnotatedCollectionI consensus = aan; } } - + public void setSSConsensusRow(AlignmentAnnotation aan) { @@ -1256,10 +1269,12 @@ public class SequenceGroup implements AnnotatedCollectionI ssConsensus = new ArrayList(); ssConsensus.add(aan); } - else { + else + { boolean annotExists = ssConsensus.stream() .anyMatch(ssa -> ssa.label.equals(aan.label)); - if(!annotExists) { + if (!annotExists) + { ssConsensus.add(aan); } } @@ -1293,7 +1308,7 @@ public class SequenceGroup implements AnnotatedCollectionI } return consensus; } - + public List getSSConsensus(List ssSources) { // TODO get or calculate and get consensus annotation row for this group @@ -1305,25 +1320,29 @@ public class SequenceGroup implements AnnotatedCollectionI { return null; } - if (ssConsensus == null && ssSources!=null) + if (ssConsensus == null && ssSources != null) { ssConsensus = new ArrayList(); - - for(String ssSource : ssSources) { - AlignmentAnnotation aa = new AlignmentAnnotation("", "", new Annotation[1], 0f, - 100f, AlignmentAnnotation.BAR_GRAPH); - // Setting the annotation visibility to true of the provider is "All" + + for (String ssSource : ssSources) + { + AlignmentAnnotation aa = new AlignmentAnnotation("", "", + new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + // Setting the annotation visibility to true of the provider is "All" // and false otherwise. aa.visible = Constants.SS_ALL_PROVIDERS.equals(ssSource); aa.hasText = true; aa.autoCalculated = true; aa.groupRef = this; - aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " " + ssSource + " " + getName(); - aa.description = ssSource + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL +" for " + getName(); + aa.label = Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " " + + ssSource + " " + getName(); + aa.description = ssSource + + Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL + " for " + + getName(); ssConsensus.add(aa); } - + } return ssConsensus; } @@ -1429,7 +1448,7 @@ public class SequenceGroup implements AnnotatedCollectionI } this.showSequenceLogo = showSequenceLogo; } - + /** * * @param showConsHist diff --git a/src/jalview/ext/jmol/JalviewJmolBinding.java b/src/jalview/ext/jmol/JalviewJmolBinding.java index 1c19854..36b2546 100644 --- a/src/jalview/ext/jmol/JalviewJmolBinding.java +++ b/src/jalview/ext/jmol/JalviewJmolBinding.java @@ -785,15 +785,21 @@ public abstract class JalviewJmolBinding extends AAStructureBindingModel } else { - PDBEntry ppe=getPdbEntry(pe); - if (ppe==null) { - Console.warn("Please report under JAL-4440: Unexpected null entry for PDBEntry for a structure (for structure "+fileName+")"); - + PDBEntry ppe = getPdbEntry(pe); + if (ppe == null) + { + Console.warn( + "Please report under JAL-4440: Unexpected null entry for PDBEntry for a structure (for structure " + + fileName + ")"); + continue; } - if (ppe.getFile()==null) + if (ppe.getFile() == null) { - Console.warn("Please report under JAL-4440: Unexpected null entry for file that we just tried to load into Jmol: pdbEntry: "+ppe.toString()+"(for structure "+fileName+")"); + Console.warn( + "Please report under JAL-4440: Unexpected null entry for file that we just tried to load into Jmol: pdbEntry: " + + ppe.toString() + "(for structure " + fileName + + ")"); continue; } File fl = new File(getPdbEntry(pe).getFile()); diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index 3885d4f..6affe38 100644 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -4255,7 +4255,7 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, //// *************************************************** //// TODO REFACTOR TREE I/O TO CONTROLLER/SEPARATE CLASS //// *************************************************** - + /** * DOCUMENT ME! * @@ -4362,8 +4362,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - public TreePanel showNewickTreeForAnnotation(NewickFile nf, String treeTitle, - AlignmentView input, int w, int h, int x, int y) + + public TreePanel showNewickTreeForAnnotation(NewickFile nf, + String treeTitle, AlignmentView input, int w, int h, int x, int y) { TreePanel tp = null; @@ -4373,7 +4374,8 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, if (nf.getTree() != null) { - tp = TreePanel.newTreeForAnnotations(alignPanel, nf, treeTitle, input); + tp = TreePanel.newTreeForAnnotations(alignPanel, nf, treeTitle, + input); // TODO - refactor layout code to one place for tree view methods tp.setSize(w, h); @@ -4392,7 +4394,6 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, return tp; } - public void showContactMapTree(AlignmentAnnotation aa, ContactMatrixI cm) { int x = 4, y = 5; @@ -5780,8 +5781,9 @@ public class AlignFrame extends GAlignFrame implements DropTargetListener, { viewport.setShowStructureProvider(showStrucProvider.getState()); alignPanel.paintAlignment(false, false); - + } + @Override protected void updateShowSecondaryStructureMenu(JMenu showSS, ButtonGroup ssButtonGroup) diff --git a/src/jalview/gui/AlignViewport.java b/src/jalview/gui/AlignViewport.java index 9430a8b..c2b77c7 100644 --- a/src/jalview/gui/AlignViewport.java +++ b/src/jalview/gui/AlignViewport.java @@ -242,7 +242,8 @@ public class AlignViewport extends AlignmentViewport .getDefault(Preferences.SHOW_AUTOCALC_ABOVE, false); viewStyle.setScaleProteinAsCdna( Cache.getDefault(Preferences.SCALE_PROTEIN_TO_CDNA, true)); - viewStyle.setShowStructureProvider(Cache.getDefault(Preferences.SHOW_STRUC_PROVIDER, false)); + viewStyle.setShowStructureProvider( + Cache.getDefault(Preferences.SHOW_STRUC_PROVIDER, false)); } void init() @@ -287,7 +288,7 @@ public class AlignViewport extends AlignmentViewport false); showGroupConsensus = Cache.getDefault("SHOW_GROUP_CONSENSUS", false); showConsensus = Cache.getDefault("SHOW_IDENTITY", true); - + showSSConsensus = Cache.getDefault("SHOW_SS_CONSENSUS", false); showOccupancy = Cache.getDefault(Preferences.SHOW_OCCUPANCY, true); diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 9478c6f..3b968a4 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -249,13 +249,15 @@ public class AnnotationLabels extends JPanel { ap.av.getAlignment().deleteAnnotation(aa[selectedRow]); ap.av.getCalcManager().removeWorkerForAnnotation(aa[selectedRow]); - - + List workers = ap.av.getCalcManager() - .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class); - if (!workers.isEmpty()) { - - ap.alignFrame.getViewport().getCalcManager().startWorker(workers.remove(0)); + .getRegisteredWorkersOfClass( + SecondaryStructureConsensusThread.class); + if (!workers.isEmpty()) + { + + ap.alignFrame.getViewport().getCalcManager() + .startWorker(workers.remove(0)); } } @@ -882,11 +884,11 @@ public class AnnotationLabels extends JPanel { msg.append(aa.sequenceRef.getName()).append(" : "); } - + if (aa.graphGroup == -1) { msg.append(aa.label); - if(aa.getNoOfSequencesIncluded()>=0) + if (aa.getNoOfSequencesIncluded() >= 0) { msg.append(" ("); msg.append(MessageManager.getString("label.sequence_count")); @@ -894,7 +896,7 @@ public class AnnotationLabels extends JPanel msg.append(")"); } } - + else if (anns != null) { boolean first = true; @@ -937,10 +939,10 @@ public class AnnotationLabels extends JPanel // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature // tooltips String desc = aa.getDescription(true).trim(); - if(aa.getNoOfSequencesIncluded()>=0) { + if (aa.getNoOfSequencesIncluded() >= 0) + { desc += " (" + MessageManager.getString("label.sequence_count") - + aa.getNoOfSequencesIncluded() - + ")"; + + aa.getNoOfSequencesIncluded() + ")"; } if (!desc.toLowerCase(Locale.ROOT).startsWith(HTML_START_TAG)) { @@ -1494,11 +1496,15 @@ public class AnnotationLabels extends JPanel vertBar = true; } } - - if(isShowStructureProvider && aa[i].hasIcons && Constants.SECONDARY_STRUCTURE_LABELS.keySet().contains(aa[i].label)) { - String ssSource = AlignmentUtils.extractSSSourceFromAnnotationDescription(aa[i]); - if(ssSource != null && ssSource.length()>0) - label += " (" + ssSource + ")"; + + if (isShowStructureProvider && aa[i].hasIcons + && Constants.SECONDARY_STRUCTURE_LABELS.keySet() + .contains(aa[i].label)) + { + String ssSource = AlignmentUtils + .extractSSSourceFromAnnotationDescription(aa[i]); + if (ssSource != null && ssSource.length() > 0) + label += " (" + ssSource + ")"; } int labelWidth = fm.stringWidth(label) + 3; diff --git a/src/jalview/gui/AppJmol.java b/src/jalview/gui/AppJmol.java index 4d0de1b..d37c9c0 100644 --- a/src/jalview/gui/AppJmol.java +++ b/src/jalview/gui/AppJmol.java @@ -423,12 +423,13 @@ public class AppJmol extends StructureViewerBase public boolean isRepainting() { - if (renderPanel!=null && renderPanel.isVisible()) + if (renderPanel != null && renderPanel.isVisible()) { return renderPanel.repainting; } return false; } + /** * Outputs the Jmol viewer image as an image file, after prompting the user to * choose a file and (for EPS) choice of Text or Lineart character rendering @@ -441,10 +442,12 @@ public class AppJmol extends StructureViewerBase { while (!isRepainting()) { - try { + try + { Thread.sleep(2); } catch (Exception q) - {} + { + } } try { @@ -642,17 +645,18 @@ public class AppJmol extends StructureViewerBase } else { - repainting=true; + repainting = true; synchronized (jmb) { jmb.jmolViewer.renderScreenImage(g, currentSize.width, currentSize.height); - + } - repainting=false; + repainting = false; } } - volatile boolean repainting=false; + + volatile boolean repainting = false; } @Override diff --git a/src/jalview/gui/CalculationChooser.java b/src/jalview/gui/CalculationChooser.java index 2e4e99d..fd8745d 100644 --- a/src/jalview/gui/CalculationChooser.java +++ b/src/jalview/gui/CalculationChooser.java @@ -541,13 +541,14 @@ public class CalculationChooser extends JPanel final JComboBox comboBox = new JComboBox<>(); Object curSel = comboBox.getSelectedItem(); DefaultComboBoxModel sourcesModel = new DefaultComboBoxModel<>(); - + List ssSources = getApplicableSecondaryStructureSources(); - - if(ssSources == null) { + + if (ssSources == null) + { return comboBox; } - ssSources.add(0, MessageManager.getString("option.ss_providers_all")); + ssSources.add(0, MessageManager.getString("option.ss_providers_all")); boolean selectedIsPresent = false; for (String source : ssSources) @@ -639,8 +640,10 @@ public class CalculationChooser extends JPanel * * @param nucleotide * @param forPca - * @param ssPresent - include secondary structure similarity model - * @param forPasimap - limit to ScoreMatrix based models - allows use of AlignSeq + * @param ssPresent + * - include secondary structure similarity model + * @param forPasimap + * - limit to ScoreMatrix based models - allows use of AlignSeq * @return */ protected static List getApplicableScoreModels( @@ -652,7 +655,7 @@ public class CalculationChooser extends JPanel ScoreModels scoreModels = ScoreModels.getInstance(); for (ScoreModelI sm : scoreModels.getModels()) { - if ((!forPasimap || sm instanceof ScoreMatrix) + if ((!forPasimap || sm instanceof ScoreMatrix) && (!nucleotide && sm.isProtein() || nucleotide && sm.isDNA() || sm.isSecondaryStructure() && ssPresent)) @@ -676,9 +679,11 @@ public class CalculationChooser extends JPanel protected List getApplicableSecondaryStructureSources() { - AlignmentAnnotation[] annotations = af.getViewport().getAlignment().getAlignmentAnnotation(); - - List ssSources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations); + AlignmentAnnotation[] annotations = af.getViewport().getAlignment() + .getAlignmentAnnotation(); + + List ssSources = AlignmentUtils + .extractSSSourceInAlignmentAnnotation(annotations); return ssSources; } @@ -694,16 +699,18 @@ public class CalculationChooser extends JPanel : modelNames.getSelectedItem().toString(); String ssSource = null; - - if (modelName.equals(secondaryStructureModelName)) { + + if (modelName.equals(secondaryStructureModelName)) + { Object selectedItem = ssSourceDropdown.getSelectedItem(); - if (selectedItem != null) { - ssSource = selectedItem.toString(); + if (selectedItem != null) + { + ssSource = selectedItem.toString(); } } SimilarityParams params = getSimilarityParameters(doPCA); params.setSecondaryStructureSource(ssSource); - + if (doPCA) { openPcaPanel(modelName, params); diff --git a/src/jalview/gui/CutAndPasteTransfer.java b/src/jalview/gui/CutAndPasteTransfer.java index 299af6b..10aa229 100644 --- a/src/jalview/gui/CutAndPasteTransfer.java +++ b/src/jalview/gui/CutAndPasteTransfer.java @@ -94,13 +94,14 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer /** * set font size of the textarea + * * @param size */ public void setFont(Font font) { textarea.setFont(font); } - + /** * DOCUMENT ME! */ @@ -217,11 +218,12 @@ public class CutAndPasteTransfer extends GCutAndPasteTransfer { } } - + /** - * show menu for changing the font - * @param e - */ + * show menu for changing the font + * + * @param e + */ @Override public void fontSizeMenu_actionPerformed(ActionEvent e) { diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index c144268..9c542a3 100644 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -2945,11 +2945,11 @@ public class Desktop extends jalview.jbgui.GDesktop if (progressBars.get(Long.valueOf(id)) == null) return null; - + for (Component c : progressBars.get(Long.valueOf(id)).getComponents()) { if (c.getClass() == JProgressBar.class) - return (JProgressBar) c; + return (JProgressBar) c; } return null; } diff --git a/src/jalview/gui/FontChooser.java b/src/jalview/gui/FontChooser.java index 853d4aa..1ec4881 100755 --- a/src/jalview/gui/FontChooser.java +++ b/src/jalview/gui/FontChooser.java @@ -113,8 +113,9 @@ public class FontChooser extends GFontChooser /** * Creates a new FontChooser for a CutAndPasteTransfer + * * @param cap - */ + */ public FontChooser(CutAndPasteTransfer cap) { oldFont = new Font("Monospaced", Font.PLAIN, 12); @@ -131,7 +132,7 @@ public class FontChooser extends GFontChooser if (!isCapFont()) { smoothFont.setSelected(ap.av.antiAlias); - + /* * Enable 'scale protein as cDNA' in a SplitFrame view. The selection is * stored in the ViewStyle of both dna and protein Viewport. Also enable @@ -289,6 +290,7 @@ public class FontChooser extends GFontChooser { return cap != null; } + /** * DOCUMENT ME! */ diff --git a/src/jalview/gui/PCAPanel.java b/src/jalview/gui/PCAPanel.java index 1bf1e76..42e2e40 100644 --- a/src/jalview/gui/PCAPanel.java +++ b/src/jalview/gui/PCAPanel.java @@ -133,12 +133,15 @@ public class PCAPanel extends GPCAPanel setRotatableCanvas(new RotatableCanvas(alignPanel)); - if(params.getSecondaryStructureSource()!=null ) { + if (params.getSecondaryStructureSource() != null) + { // Initialize and set subtitle text - JLabel subtitleLabel = new JLabel(" Secondary Structure Provider : " - + params.getSecondaryStructureSource(), SwingConstants.LEFT); - this.getContentPane().add(subtitleLabel, BorderLayout.NORTH); - + JLabel subtitleLabel = new JLabel( + " Secondary Structure Provider : " + + params.getSecondaryStructureSource(), + SwingConstants.LEFT); + this.getContentPane().add(subtitleLabel, BorderLayout.NORTH); + } this.getContentPane().add(getRotatableCanvas(), BorderLayout.CENTER); diff --git a/src/jalview/gui/PaSiMapPanel.java b/src/jalview/gui/PaSiMapPanel.java index 702c4f4..7926efc 100644 --- a/src/jalview/gui/PaSiMapPanel.java +++ b/src/jalview/gui/PaSiMapPanel.java @@ -101,12 +101,12 @@ public class PaSiMapPanel extends GPaSiMapPanel */ public PaSiMapPanel(AlignmentPanel alignPanel, String modelName) { - super(8); // dim = 8 + super(8); // dim = 8 this.av = alignPanel.av; this.ap = alignPanel; boolean nucleotide = av.getAlignment().isNucleotide(); - //progressBar = new ProgressBar(statusPanel, statusBar); + // progressBar = new ProgressBar(statusPanel, statusBar); addInternalFrameListener(new InternalFrameAdapter() { @@ -131,8 +131,7 @@ public class PaSiMapPanel extends GPaSiMapPanel ScoreModelI scoreModel = ScoreModels.getInstance() .getScoreModel(modelName, ap); - setPasimapModel( - new PaSiMapModel(av, seqs, nucleotide, scoreModel)); + setPasimapModel(new PaSiMapModel(av, seqs, nucleotide, scoreModel)); PaintRefresher.Register(this, av.getSequenceSetId()); setRotatableCanvas(new RotatableCanvas(alignPanel)); @@ -143,8 +142,8 @@ public class PaSiMapPanel extends GPaSiMapPanel } /** - * Ensure references to potentially very large objects (the PaSiMap matrices) are - * nulled when the frame is closed + * Ensure references to potentially very large objects (the PaSiMap matrices) + * are nulled when the frame is closed */ protected void close_actionPerformed() { @@ -193,29 +192,31 @@ public class PaSiMapPanel extends GPaSiMapPanel progressBar.setProgressBar(message, progId); try { - SequenceGroup selGroup=av.getSelectionGroup(); - - if (selGroup==null) + SequenceGroup selGroup = av.getSelectionGroup(); + + if (selGroup == null) { selGroup = new SequenceGroup(av.getAlignment().getSequences()); selGroup.setStartRes(0); - selGroup.setEndRes(av.getAlignment().getWidth()-1); + selGroup.setEndRes(av.getAlignment().getWidth() - 1); } - - if (selGroup.getSize()>MAX_PASIMAP_SEQ) + + if (selGroup.getSize() > MAX_PASIMAP_SEQ) { - int start = selGroup.getStartRes(),end=selGroup.getEndRes(); - selGroup = new SequenceGroup(selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ)); - selGroup.setStartRes(start); - selGroup.setEndRes(end); - Console.warn("Truncated input sequences for PASIMAP analysis to "+MAX_PASIMAP_SEQ); + int start = selGroup.getStartRes(), end = selGroup.getEndRes(); + selGroup = new SequenceGroup( + selGroup.getSequences().subList(0, MAX_PASIMAP_SEQ)); + selGroup.setStartRes(start); + selGroup.setEndRes(end); + Console.warn("Truncated input sequences for PASIMAP analysis to " + + MAX_PASIMAP_SEQ); } - + PairwiseAlignPanel pap = new PairwiseAlignPanel(av, selGroup, true, GAP_OPEN_COST, GAP_EXTEND_COST, false, null); pap.setDiscardAlignments(true); pap.setQuiet(true); - + System.out.println(pap != null); setPairwiseAlignPanel(pap); getPasimapModel().calculate(pap); @@ -241,9 +242,9 @@ public class PaSiMapPanel extends GPaSiMapPanel repaint(); if (getParent() == null) { - Desktop.addInternalFrame( - this, MessageManager.formatMessage("label.calc_title", - "PaSiMap", ap.alignFrame.getTitle()), + Desktop.addInternalFrame(this, + MessageManager.formatMessage("label.calc_title", "PaSiMap", + ap.alignFrame.getTitle()), 475, 450); this.setMinimumSize(new Dimension(MIN_WIDTH, MIN_HEIGHT)); } @@ -251,8 +252,8 @@ public class PaSiMapPanel extends GPaSiMapPanel } /** - * Updates the PaSiMap display after a change of component to use for x, y or z - * axis + * Updates the PaSiMap display after a change of component to use for x, y or + * z axis */ @Override protected void doDimensionChange() @@ -270,8 +271,8 @@ public class PaSiMapPanel extends GPaSiMapPanel } /** - * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...) for - * the given axis (X/Y/Z) + * Sets the selected checkbox item index for PaSiMap dimension (1, 2, 3...) + * for the given axis (X/Y/Z) * * @param index * @param axis @@ -323,8 +324,8 @@ public class PaSiMapPanel extends GPaSiMapPanel } /** - * If available, shows the data which formed the inputs for the PaSiMap as a new - * alignment + * If available, shows the data which formed the inputs for the PaSiMap as a + * new alignment */ @Override public void originalSeqData_actionPerformed() @@ -452,7 +453,7 @@ public class PaSiMapPanel extends GPaSiMapPanel } } - public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception + public void makePaSiMapImage(ImageMaker.TYPE type) throws Exception { int width = getRotatableCanvas().getWidth(); int height = getRotatableCanvas().getHeight(); @@ -612,7 +613,8 @@ public class PaSiMapPanel extends GPaSiMapPanel { cap.setText(getPasimapModel().getAlignmentOutput()); Desktop.addInternalFrame(cap, MessageManager.formatMessage( - "label.pairwise_alignment_for_params", new String[] { this.getTitle() }), 500, 500); + "label.pairwise_alignment_for_params", new String[] + { this.getTitle() }), 500, 500); } catch (OutOfMemoryError oom) { new OOMWarning("exporting pairwise alignments", oom); @@ -680,7 +682,7 @@ public class PaSiMapPanel extends GPaSiMapPanel public void updateProgressBar(int lengthOfTask, int progress) { JProgressBar pBar = progressBar.getProgressBar(progId); - if (pBar==null) + if (pBar == null) { return; } @@ -692,22 +694,24 @@ public class PaSiMapPanel extends GPaSiMapPanel } updateProgressBar(progress); } + public void updateProgressBar(int progress) { JProgressBar pBar = progressBar.getProgressBar(progId); - - if (pBar==null) + + if (pBar == null) { return; } - + pBar.setValue(progress); pBar.repaint(); } /** - * adds a listener for a pairwise alignment panel's progress - * TODO: generalise for anything that can report progress ? + * adds a listener for a pairwise alignment panel's progress TODO: generalise + * for anything that can report progress ? + * * @param pap */ public void setPairwiseAlignPanel(PairwiseAlignPanel pap) @@ -794,8 +798,8 @@ public class PaSiMapPanel extends GPaSiMapPanel } /** - * Answers the selected checkbox item index for PaSiMap dimension for the X, Y or - * Z axis of the display + * Answers the selected checkbox item index for PaSiMap dimension for the X, Y + * or Z axis of the display * * @param axis * @return diff --git a/src/jalview/gui/PairwiseAlignPanel.java b/src/jalview/gui/PairwiseAlignPanel.java index 3e8fb02..77ec0f5 100755 --- a/src/jalview/gui/PairwiseAlignPanel.java +++ b/src/jalview/gui/PairwiseAlignPanel.java @@ -47,7 +47,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel private float[][] scores; - private float[][] alignmentScores; // scores used by PaSiMap + private float[][] alignmentScores; // scores used by PaSiMap private int GAP_OPEN_COST; @@ -60,7 +60,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel private String alignmentOutput; private boolean quiet; - + private boolean discardAlignments; private boolean endGaps; @@ -73,12 +73,13 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel private int total; private int progress; - + private SequenceGroup selection; + /** * input sequences */ - private SequenceI[] seqs=null; + private SequenceI[] seqs = null; private ScoreMatrix scoreMatrix; @@ -87,23 +88,31 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel * * @param viewport * contains selected sequences to align - * @param endGaps ~ toggle gaps and the beginning and end of sequences + * @param endGaps + * ~ toggle gaps and the beginning and end of sequences */ public PairwiseAlignPanel(AlignmentViewport viewport) { - this(viewport, null, false, 120, 20, true, null); // default penalties used in AlignSeq + this(viewport, null, false, 120, 20, true, null); // default penalties used + // in AlignSeq } + public PairwiseAlignPanel(AlignmentViewport viewport, ScoreMatrix params) { - this(viewport, null, false, 120, 20, true,params); // default penalties used in AlignSeq + this(viewport, null, false, 120, 20, true, params); // default penalties + // used in AlignSeq } - public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, int gapOpenCost, int gapExtendCost) + + public PairwiseAlignPanel(AlignmentViewport viewport, boolean endGaps, + int gapOpenCost, int gapExtendCost) { this(viewport, null, endGaps, gapOpenCost, gapExtendCost, true, null); } /** - * Create a new pairwise alignpanel with specified parameters and score model, and optionally start the calculation + * Create a new pairwise alignpanel with specified parameters and score model, + * and optionally start the calculation + * * @param viewport * @param selection * @param endGaps @@ -112,8 +121,9 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel * @param run * @param scoreMatrix */ - public PairwiseAlignPanel(AlignmentViewport viewport, SequenceGroup selection, boolean endGaps, - int gapOpenCost, int gapExtendCost, boolean run, ScoreMatrix scoreMatrix) + public PairwiseAlignPanel(AlignmentViewport viewport, + SequenceGroup selection, boolean endGaps, int gapOpenCost, + int gapExtendCost, boolean run, ScoreMatrix scoreMatrix) { super(); this.av = viewport; @@ -123,23 +133,25 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel this.selection = selection; this.total = MiscMath.combinations(av.getAlignment().getHeight(), 2); this.scoreMatrix = scoreMatrix; - if (run) { + if (run) + { calculate(); } } - + public void calculate() { calculate(scoreMatrix); } - public void calculate (ScoreMatrix sm) + + public void calculate(ScoreMatrix sm) { StringBuilder sb = new StringBuilder(1024); sequences = new Vector(); String[] seqStrings; - seqs=null; + seqs = null; if (selection != null) { @@ -169,7 +181,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel seqs = av.getAlignment().getSequencesArray(); } } - + String type = (av.getAlignment().isNucleotide()) ? AlignSeq.DNA : AlignSeq.PEP; @@ -177,7 +189,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel float[][] alignmentScores = new float[seqs.length][seqs.length]; double totscore = 0D; int count = seqs.length; - + boolean first = true; progress = 0; @@ -192,11 +204,12 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel AlignSeq as = new AlignSeq(seqs[i], seqStrings[i], seqs[j], seqStrings[j], type, GAP_OPEN_COST, GAP_EXTEND_COST); - if (sm != null) { - as.setScoreMatrix(sm); - } + if (sm != null) + { + as.setScoreMatrix(sm); + } - if (as.s1str.length() == 0 || as.s2str.length() == 0) + if (as.s1str.length() == 0 || as.s2str.length() == 0) { continue; } @@ -219,7 +232,8 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel sb.append(DASHES); } first = false; - if (!discardAlignments) { + if (!discardAlignments) + { as.printAlignment(System.out); } scores[i][j] = as.getMaxScore() / as.getASeq1().length; @@ -243,7 +257,7 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel this.scores = scores; this.alignmentScores = alignmentScores; - if (count > 2 && !quiet) + if (count > 2 && !quiet) { printScoreMatrix(seqs, scores, totscore); } @@ -344,24 +358,29 @@ public class PairwiseAlignPanel extends GPairwiseAlignPanel { return progress; } + public SequenceI[] getInputSequences() { return seqs; } + /** - * Set to true to suppress output of progress to Console.stdout or GUI - * @param quiet + * Set to true to suppress output of progress to Console.stdout or GUI + * + * @param quiet */ public void setQuiet(boolean quiet) { - this.quiet=quiet; + this.quiet = quiet; } + /** * set this if you are only interested in final alignment scores + * * @param discard */ public void setDiscardAlignments(boolean discard) { - discardAlignments=discard; + discardAlignments = discard; } } diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index a47a0a1..c03a300 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -176,9 +176,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener JMenuItem textColour = new JMenuItem(); - JMenu editGroupMenu = new JMenu(); + JMenu editGroupMenu = new JMenu(); - JMenu groupShowAutoCalculatedAnnotations = new JMenu(); + JMenu groupShowAutoCalculatedAnnotations = new JMenu(); JMenu groupHideAutoCalculatedAnnotations = new JMenu(); @@ -455,16 +455,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener final List selectedGroup = (alignPanel.av .getSelectionGroup() == null ? Collections. emptyList() - : alignPanel.av.getSelectionGroup().getSequences()); + : alignPanel.av.getSelectionGroup().getSequences()); buildAnnotationTypesMenus(groupShowAnnotationsMenu, groupHideAnnotationsMenu, selectedGroup); configureReferenceAnnotationsMenu(groupAddReferenceAnnotations, selectedGroup); - - //If a sequence group is selected, build show/hide auto calculated annotations menu + + // If a sequence group is selected, build show/hide auto calculated + // annotations menu SequenceGroup selectedSequenceGroup = alignPanel.av.getSelectionGroup(); - if(selectedSequenceGroup != null) { - buildAutoCalculatedAnnotationsMenu(groupShowAutoCalculatedAnnotations, + if (selectedSequenceGroup != null) + { + buildAutoCalculatedAnnotationsMenu(groupShowAutoCalculatedAnnotations, groupHideAutoCalculatedAnnotations, selectedSequenceGroup); } @@ -664,7 +666,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme()); conservationMenuItem.setEnabled(!sg.isNucleotide()); - + byConsensusSecondaryStructureMenuItem.setEnabled(!sg.isNucleotide()); if (sg.cs != null) @@ -677,7 +679,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { abovePIDColour.setSelected(true); } - if(sg.cs.isConsensusSecondaryStructureColouring()) + if (sg.cs.isConsensusSecondaryStructureColouring()) { byConsensusSecondaryStructureMenuItem.setSelected(true); } @@ -736,9 +738,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener unGroupMenuItem.setVisible(false); editGroupMenu .setText(MessageManager.getString("action.edit_new_group")); - - // Hide show/hide auto calculated annotations menus for group if a sequence - // group is not defined. + + // Hide show/hide auto calculated annotations menus for group if a + // sequence + // group is not defined. groupShowAutoCalculatedAnnotations.setVisible(false); groupHideAutoCalculatedAnnotations.setVisible(false); } @@ -747,14 +750,18 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener createGroupMenuItem.setVisible(false); unGroupMenuItem.setVisible(true); editGroupMenu.setText(MessageManager.getString("action.edit_group")); - - // Show show/hide auto calculated annotations menus for group if a sequence - // group is defined and showGroupSSConsensus is true. Hide the menus otherwise. - if(alignPanel.av.isShowGroupSSConsensus()) { + + // Show show/hide auto calculated annotations menus for group if a + // sequence + // group is defined and showGroupSSConsensus is true. Hide the menus + // otherwise. + if (alignPanel.av.isShowGroupSSConsensus()) + { groupShowAutoCalculatedAnnotations.setVisible(true); groupHideAutoCalculatedAnnotations.setVisible(true); } - else { + else + { groupShowAutoCalculatedAnnotations.setVisible(false); groupHideAutoCalculatedAnnotations.setVisible(false); } @@ -1074,7 +1081,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener // grey out 'hide annotations' if none are shown hideMenu.setEnabled(!shownTypes.isEmpty()); } - + /** * Builds the menu for showing and hiding auto calculated annotations for a * selected sequence group. It clears existing menu items and adds menu items @@ -1127,7 +1134,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener AlignmentAnnotationUtils.asList(annotations), selectedSequenceGroup); - // Add code if additional auto calculated annotation types (like residue consensus, + // Add code if additional auto calculated annotation types (like residue + // consensus, // conservation, etc.) are needed for a selected group // Add currently hidden types to the show menu @@ -1151,8 +1159,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener groupShowAutoCalculatedAnnotations.setEnabled(!hiddenTypes.isEmpty()); groupHideAutoCalculatedAnnotations.setEnabled(!shownTypes.isEmpty()); } - - + /** * Adds a menu item to the provided menu for showing or hiding a specific type * of auto calculated annotation @@ -1165,8 +1172,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * @param type * The type of annotation to show or hide. * @param allTypes - * Indicates if the action should apply to all annotation types. - * True if user selects "All". + * Indicates if the action should apply to all annotation types. True + * if user selects "All". * @param actionIsShow * Indicates if the item is for showing (true) or hiding (false) the * annotation type. @@ -1199,8 +1206,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener showOrHideAutoCalculatedAnnotationsMenu.add(item); } - - /** * Returns a list of sequences - either the current selection group (if there * is one), else the specified single sequence. @@ -1622,10 +1627,10 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener .setText(MessageManager.getString("label.show_annotations")); groupHideAnnotationsMenu .setText(MessageManager.getString("label.hide_annotations")); - groupShowAutoCalculatedAnnotations - .setText(MessageManager.getString("label.group_show_auto_calculated_annotations")); - groupHideAutoCalculatedAnnotations - .setText(MessageManager.getString("label.group_hide_auto_calculated_annotations")); + groupShowAutoCalculatedAnnotations.setText(MessageManager + .getString("label.group_show_auto_calculated_annotations")); + groupHideAutoCalculatedAnnotations.setText(MessageManager + .getString("label.group_hide_auto_calculated_annotations")); JMenuItem sequenceFeature = new JMenuItem( MessageManager.getString("label.create_sequence_feature")); sequenceFeature.addActionListener(new ActionListener() @@ -1794,18 +1799,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener conservationMenuItem.isSelected()); } }); - - byConsensusSecondaryStructureMenuItem.setText( - MessageManager.getString("action.by_secondary_structure_conservation")); - byConsensusSecondaryStructureMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - colourByConsensusSecondaryStructureMenuItem_actionPerformed( - byConsensusSecondaryStructureMenuItem.isSelected()); - } - }); + + byConsensusSecondaryStructureMenuItem.setText(MessageManager + .getString("action.by_secondary_structure_conservation")); + byConsensusSecondaryStructureMenuItem + .addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + colourByConsensusSecondaryStructureMenuItem_actionPerformed( + byConsensusSecondaryStructureMenuItem.isSelected()); + } + }); annotationColour = new JRadioButtonMenuItem( MessageManager.getString("action.by_annotation")); @@ -1824,17 +1830,19 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener modifyConservation_actionPerformed(); } }); - - modifyConsensusSecondaryStructureThreshold.setText(MessageManager - .getString("label.modify_secondary_structure_conservation_threshold")); - modifyConsensusSecondaryStructureThreshold.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - modifyConsensusSecondaryStructureThreshold_actionPerformed(); - } - }); + + modifyConsensusSecondaryStructureThreshold + .setText(MessageManager.getString( + "label.modify_secondary_structure_conservation_threshold")); + modifyConsensusSecondaryStructureThreshold + .addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyConsensusSecondaryStructureThreshold_actionPerformed(); + } + }); } /** @@ -1878,17 +1886,17 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener SliderPanel.showConservationSlider(); } } - + protected void modifyConsensusSecondaryStructureThreshold_actionPerformed() { SequenceGroup sg = getGroup(); if (sg.cs != null) { - SliderPanel.setConsensusSecondaryStructureSlider(ap, sg.cs, sg.getName()); + SliderPanel.setConsensusSecondaryStructureSlider(ap, sg.cs, + sg.getName()); SliderPanel.showConsensusSecondaryStructureSlider(); } } - protected void modifyPID_actionPerformed() { @@ -1971,34 +1979,36 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener { final AlignmentI alignment = this.ap.getAlignment(); AlignmentUtils.addReferenceAnnotations(candidates, alignment, null); - - if(AlignmentUtils.isSSAnnotationPresent(candidates)) { - + + if (AlignmentUtils.isSSAnnotationPresent(candidates)) + { + restartSSConsensusWorker(); ap.validateAnnotationDimensions(true); ap.fontChanged(); ap.av.alignmentChanged(ap); ap.adjustAnnotationHeight(); restartSSConsensusWorker(); - //ap.alignFrame.getViewport().getCalcManager().restartWorkers(); + // ap.alignFrame.getViewport().getCalcManager().restartWorkers(); } - + } - - - private void restartSSConsensusWorker() { - - List workers = ap.alignFrame.getViewport().getCalcManager() - .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class); - if (!workers.isEmpty()) { - - ap.alignFrame.getViewport().getCalcManager().startWorker(workers.remove(0)); - - } - + + private void restartSSConsensusWorker() + { + + List workers = ap.alignFrame.getViewport() + .getCalcManager().getRegisteredWorkersOfClass( + SecondaryStructureConsensusThread.class); + if (!workers.isEmpty()) + { + + ap.alignFrame.getViewport().getCalcManager() + .startWorker(workers.remove(0)); + + } + } - - protected void makeReferenceSeq_actionPerformed(ActionEvent actionEvent) { @@ -2233,8 +2243,9 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } - - public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(boolean selected) + + public void colourByConsensusSecondaryStructureMenuItem_actionPerformed( + boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -2244,11 +2255,11 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener if (selected) { - + sg.cs.setConsensusSecondaryStructureColouring(selected); - SliderPanel.setConsensusSecondaryStructureSlider(ap, sg.getGroupColourScheme(), - sg.getName()); + SliderPanel.setConsensusSecondaryStructureSlider(ap, + sg.getGroupColourScheme(), sg.getName()); SliderPanel.showConsensusSecondaryStructureSlider(); } else diff --git a/src/jalview/gui/ProgressBar.java b/src/jalview/gui/ProgressBar.java index 73cd496..9d2cb2c 100644 --- a/src/jalview/gui/ProgressBar.java +++ b/src/jalview/gui/ProgressBar.java @@ -274,7 +274,7 @@ public class ProgressBar implements IProgressIndicator public JProgressBar getProgressBar(long id) { Container progBar = progressBars.get(id); - if (progBar==null || progBar.getComponentCount()==0) + if (progBar == null || progBar.getComponentCount() == 0) { return null; } diff --git a/src/jalview/gui/RotatableCanvas.java b/src/jalview/gui/RotatableCanvas.java index 5261b23..03d8d87 100755 --- a/src/jalview/gui/RotatableCanvas.java +++ b/src/jalview/gui/RotatableCanvas.java @@ -119,10 +119,13 @@ public class RotatableCanvas extends JPanel private Point[] axisEndPoints; // fields for 'select rectangle' (JAL-1124) - int rectx1; - int recty1; - int rectx2; - int recty2; + int rectx1; + + int recty1; + + int rectx2; + + int recty2; AlignmentViewport av; @@ -405,11 +408,12 @@ public class RotatableCanvas extends JPanel } } // //Now the rectangle - if (rectx2 != -1 && recty2 != -1) { - g.setColor(Color.white); - - g.drawRect(rectx1,recty1,rectx2-rectx1,recty2-recty1); - } + if (rectx2 != -1 && recty2 != -1) + { + g.setColor(Color.white); + + g.drawRect(rectx1, recty1, rectx2 - rectx1, recty2 - recty1); + } } /** @@ -566,10 +570,10 @@ public class RotatableCanvas extends JPanel mouseX = x; mouseY = y; - rectx1 = x; - recty1 = y; - rectx2 = -1; - recty2 = -1; + rectx1 = x; + recty1 = y; + rectx2 = -1; + recty2 = -1; SequenceI found = findSequenceAtPoint(x, y); @@ -634,12 +638,12 @@ public class RotatableCanvas extends JPanel // Check if this is a rectangle drawing drag if ((evt.getModifiersEx() & InputEvent.BUTTON3_DOWN_MASK) != 0) { - rectx2 = evt.getX(); - recty2 = evt.getY(); - if ((rectx2 != -1) && (recty2 != -1)) - { - rectSelect(rectx1, recty1, rectx2, recty2); - } + rectx2 = evt.getX(); + recty2 = evt.getY(); + if ((rectx2 != -1) && (recty2 != -1)) + { + rectSelect(rectx1, recty1, rectx2, recty2); + } } else { @@ -649,7 +653,7 @@ public class RotatableCanvas extends JPanel mouseY = yPos; // findWidths(); } - repaint(); + repaint(); } @Override @@ -753,12 +757,10 @@ public class RotatableCanvas extends JPanel { SequencePoint sp = sequencePoints.get(i); int tmp1 = (int) (((sp.coord.x - centre[0]) * getScaleFactor()) - * (getWidth() / 3.15) - + (getWidth() / 2.0)); + * (getWidth() / 3.15) + (getWidth() / 2.0)); float pre1 = ((sp.coord.x - centre[0]) * getScaleFactor()); int tmp2 = (int) (((sp.coord.y - centre[1]) * getScaleFactor()) - * (getHeight() / 1.70) - + (getHeight() / 2.0)); + * (getHeight() / 1.70) + (getHeight() / 2.0)); float pre2 = ((sp.coord.y - centre[1]) * getScaleFactor()); if ((tmp1 > x1) && (tmp1 < x2) && (tmp2 > y1) && (tmp2 < y2)) diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 6f3fb2d..80ab32c 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -2489,7 +2489,8 @@ public class SeqPanel extends JPanel } if (stretchGroup.cs.isConsensusSecondaryStructureColouring()) { - SliderPanel.setConsensusSecondaryStructureSlider(ap, groupColourScheme, name); + SliderPanel.setConsensusSecondaryStructureSlider(ap, + groupColourScheme, name); } } PaintRefresher.Refresh(this, av.getSequenceSetId()); diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index 5e1935d..a8d1386 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -49,7 +49,7 @@ public class SliderPanel extends GSliderPanel private static final String BACKGROUND = "Background"; static JInternalFrame conservationSlider; - + static JInternalFrame consensusSecondaryStructureSlider; static JInternalFrame PIDSlider; @@ -57,7 +57,7 @@ public class SliderPanel extends GSliderPanel AlignmentPanel ap; boolean forConservation = true; - + boolean forConsensusSecondaryStructure = false; ResidueShaderI cs; @@ -77,9 +77,11 @@ public class SliderPanel extends GSliderPanel { return (SliderPanel) PIDSlider.getContentPane(); } - if (consensusSecondaryStructureSlider != null && consensusSecondaryStructureSlider.isVisible()) + if (consensusSecondaryStructureSlider != null + && consensusSecondaryStructureSlider.isVisible()) { - return (SliderPanel) consensusSecondaryStructureSlider.getContentPane(); + return (SliderPanel) consensusSecondaryStructureSlider + .getContentPane(); } return null; } @@ -97,13 +99,14 @@ public class SliderPanel extends GSliderPanel * DOCUMENT ME! */ public SliderPanel(final AlignmentPanel ap, int value, - boolean forConserve, boolean forConsensusSS, ResidueShaderI scheme) + boolean forConserve, boolean forConsensusSS, + ResidueShaderI scheme) { this.ap = ap; this.cs = scheme; forConservation = forConserve; forConsensusSecondaryStructure = forConsensusSS; - + undoButton.setVisible(false); applyButton.setVisible(false); @@ -114,7 +117,8 @@ public class SliderPanel extends GSliderPanel slider.setMinimum(0); slider.setMaximum(100); } - if(forConsensusSS) { + if (forConsensusSS) + { label.setText(MessageManager.getString( "label.enter_value_increase_conservation_visibility")); slider.setMinimum(0); @@ -170,7 +174,8 @@ public class SliderPanel extends GSliderPanel if (conservationSlider == null) { - sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, false, rs); + sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, + false, rs); conservationSlider = new JInternalFrame(); conservationSlider.setFrameIcon(null); conservationSlider.setContentPane(sliderPanel); @@ -262,7 +267,7 @@ public class SliderPanel extends GSliderPanel conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); } } - + public static int setConsensusSecondaryStructureSlider(AlignmentPanel ap, ResidueShaderI rs, String source) { @@ -270,20 +275,25 @@ public class SliderPanel extends GSliderPanel if (consensusSecondaryStructureSlider == null) { - sliderPanel = new SliderPanel(ap, rs.getConsensusSecondaryStructureThreshold(), false, true, rs); + sliderPanel = new SliderPanel(ap, + rs.getConsensusSecondaryStructureThreshold(), false, true, + rs); consensusSecondaryStructureSlider = new JInternalFrame(); consensusSecondaryStructureSlider.setFrameIcon(null); consensusSecondaryStructureSlider.setContentPane(sliderPanel); - consensusSecondaryStructureSlider.setLayer(JLayeredPane.PALETTE_LAYER); + consensusSecondaryStructureSlider + .setLayer(JLayeredPane.PALETTE_LAYER); } else { - sliderPanel = (SliderPanel) consensusSecondaryStructureSlider.getContentPane(); - sliderPanel.valueField - .setText(String.valueOf(rs.getConsensusSecondaryStructureThreshold())); + sliderPanel = (SliderPanel) consensusSecondaryStructureSlider + .getContentPane(); + sliderPanel.valueField.setText( + String.valueOf(rs.getConsensusSecondaryStructureThreshold())); sliderPanel.cs = rs; sliderPanel.ap = ap; - sliderPanel.slider.setValue(rs.getConsensusSecondaryStructureThreshold()); + sliderPanel.slider + .setValue(rs.getConsensusSecondaryStructureThreshold()); } consensusSecondaryStructureSlider.setTitle(MessageManager.formatMessage( @@ -304,8 +314,7 @@ public class SliderPanel extends GSliderPanel return sliderPanel.getValue(); } - - + public static void hideConsensusSecondaryStructureSlider() { if (consensusSecondaryStructureSlider != null) @@ -319,8 +328,7 @@ public class SliderPanel extends GSliderPanel } } } - - + public static void showConsensusSecondaryStructureSlider() { hidePIDSlider(); @@ -329,17 +337,19 @@ public class SliderPanel extends GSliderPanel if (!consensusSecondaryStructureSlider.isVisible()) { Desktop.addInternalFrame(consensusSecondaryStructureSlider, - consensusSecondaryStructureSlider.getTitle(), true, FRAME_WIDTH, - FRAME_HEIGHT, false, true); - consensusSecondaryStructureSlider.addInternalFrameListener(new InternalFrameAdapter() - { - @Override - public void internalFrameClosed(InternalFrameEvent e) - { - consensusSecondaryStructureSlider = null; - } - }); - consensusSecondaryStructureSlider.setLayer(JLayeredPane.PALETTE_LAYER); + consensusSecondaryStructureSlider.getTitle(), true, + FRAME_WIDTH, FRAME_HEIGHT, false, true); + consensusSecondaryStructureSlider + .addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent e) + { + consensusSecondaryStructureSlider = null; + } + }); + consensusSecondaryStructureSlider + .setLayer(JLayeredPane.PALETTE_LAYER); } } @@ -486,7 +496,7 @@ public class SliderPanel extends GSliderPanel { scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus()); } - if(forConsensusSecondaryStructure) + if (forConsensusSecondaryStructure) { scheme.setConsensusSecondaryStructureColouring(true); scheme.setConsensusSecondaryStructureThreshold(percent); @@ -568,7 +578,7 @@ public class SliderPanel extends GSliderPanel { return getValue(PIDSlider); } - + public static int getConsensusSecondaryStructureSliderValue() { return getValue(consensusSecondaryStructureSlider); @@ -605,7 +615,7 @@ public class SliderPanel extends GSliderPanel { title = PIDSlider.getTitle(); } - else if(consensusSecondaryStructureSlider != null) + else if (consensusSecondaryStructureSlider != null) { title = consensusSecondaryStructureSlider.getTitle(); } diff --git a/src/jalview/gui/StructureChooser.java b/src/jalview/gui/StructureChooser.java index 9658a92..ce043fe 100644 --- a/src/jalview/gui/StructureChooser.java +++ b/src/jalview/gui/StructureChooser.java @@ -1347,8 +1347,9 @@ public class StructureChooser extends GStructureChooser String pdbFilename = selectedPdbFileName; // TODO - tidy up this ugly hack so we call launchStructureViewer too StructureChooser.openStructureFileForSequence(ssm, sc, ap, - selectedSequence, true, pdbFilename, tft, paeFilename,false, - true,false,getTargetedStructureViewer(ssm).getViewerType()); + selectedSequence, true, pdbFilename, tft, paeFilename, + false, true, false, + getTargetedStructureViewer(ssm).getViewerType()); } SwingUtilities.invokeLater(new Runnable() { @@ -1820,7 +1821,9 @@ public class StructureChooser extends GStructureChooser * @param forceHeadless * @param showRefAnnotations * @param doXferSettings - * @param viewerType - when not null means the viewer will be opened, providing forceHeadless/headless is not true + * @param viewerType + * - when not null means the viewer will be opened, providing + * forceHeadless/headless is not true * @return */ public static StructureViewer openStructureFileForSequence( @@ -1845,7 +1848,7 @@ public class StructureChooser extends GStructureChooser ssm = ap.getStructureSelectionManager(); StructureSelectionManager.doConfigureStructurePrefs(ssm); } - + PDBEntry fileEntry = new AssociatePdbFileWithSeq().associatePdbWithSeq( sFilename, DataSourceType.FILE, seq, prompt, Desktop.instance, tft, paeFilename, doXferSettings); @@ -1863,7 +1866,8 @@ public class StructureChooser extends GStructureChooser sc.mainFrame.dispose(); - // TODO should honor preferences - only show reference annotation that is requested - JAL-4415 JAL-3124 + // TODO should honor preferences - only show reference annotation that is + // requested - JAL-4415 JAL-3124 if (showRefAnnotations) { showReferenceAnnotationsForSequence(ap.alignFrame, seq); diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java index 588a4f9..08ecba6 100755 --- a/src/jalview/gui/TreeCanvas.java +++ b/src/jalview/gui/TreeCanvas.java @@ -244,11 +244,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, has_placeholders = true; } - if (longestName.length() < lf.getDisplayName() - .length()) + if (longestName.length() < lf.getDisplayName().length()) { - longestName = TreeCanvas.PLACEHOLDER - + lf.getDisplayName(); + longestName = TreeCanvas.PLACEHOLDER + lf.getDisplayName(); } if (tp.isColumnWise() && cm != null) { @@ -443,7 +441,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } if (node.hasLabel()) { - nodeLabel = node.getLabel()+" "+nodeLabel; + nodeLabel = node.getLabel() + " " + nodeLabel; } if (!nodeLabel.equals("")) @@ -1074,10 +1072,10 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); - gatherLabelsTo(groups.get(i),l); + gatherLabelsTo(groups.get(i), l); if (!tp.isColumnWise()) { - createSeqGroupFor(aps, l, col); + createSeqGroupFor(aps, l, col); } else { @@ -1123,7 +1121,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, private void gatherLabelsTo(BinaryNode binaryNode, Vector l) { LinkedHashSet labelsForNode = new LinkedHashSet(); - for (BinaryNode leaf:l) + for (BinaryNode leaf : l) { if (leaf.hasLabel()) { @@ -1131,13 +1129,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, } } StringBuilder sb = new StringBuilder(); - boolean first=true; - for (String label:labelsForNode) + boolean first = true; + for (String label : labelsForNode) { - if (!first) { + if (!first) + { sb.append(" | "); } - first=false; + first = false; sb.append(label); } binaryNode.setLabel(sb.toString()); @@ -1344,11 +1343,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, c.verdict(false, viewport.getConsPercGaps()); sg.cs.setConservation(c); } - if(viewport.getResidueShading().isConsensusSecondaryStructureColouring()) + if (viewport.getResidueShading() + .isConsensusSecondaryStructureColouring()) { sg.getGroupColourScheme().setConsensusSecondaryStructureThreshold( viewport.getResidueShading().getThreshold()); - sg.getGroupColourScheme().setConsensusSecondaryStructureColouring(true); + sg.getGroupColourScheme() + .setConsensusSecondaryStructureColouring(true); } } // indicate that associated structure views will need an update diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index c80bf3a..bfdc119 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -100,7 +100,6 @@ public class TreePanel extends GTreePanel TreeModel tree; private AlignViewport av; - // New JLabel for subtitle private JLabel subtitleLabel; @@ -129,7 +128,7 @@ public class TreePanel extends GTreePanel public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, String theTitle, AlignmentView inputData) { - this(alignPanel, newtree, theTitle, inputData, null,null); + this(alignPanel, newtree, theTitle, inputData, null, null); } /** @@ -138,10 +137,12 @@ public class TreePanel extends GTreePanel boolean forAnnotation = false; public TreePanel(AlignmentPanel alignPanel, NewickFile newtree, - String theTitle, AlignmentView inputData, AlignmentAnnotation[] leafAnnotations, String subTitle) + String theTitle, AlignmentView inputData, + AlignmentAnnotation[] leafAnnotations, String subTitle) { super(); - this.forAnnotation=leafAnnotations!=null && leafAnnotations.length>0; + this.forAnnotation = leafAnnotations != null + && leafAnnotations.length > 0; this.setFrameIcon(null); this.treeTitle = theTitle; initTreePanel(alignPanel, null, null, newtree, inputData, null); @@ -203,7 +204,8 @@ public class TreePanel extends GTreePanel } void initTreePanel(AlignmentPanel ap, String type, String modelName, - NewickFile newTree, AlignmentView inputData, AlignmentAnnotation[] leafAnnotations) + NewickFile newTree, AlignmentView inputData, + AlignmentAnnotation[] leafAnnotations) { av = ap.av; @@ -212,7 +214,7 @@ public class TreePanel extends GTreePanel treeCanvas = new TreeCanvas(this, ap, scrollPane); scrollPane.setViewportView(treeCanvas); - + if (similarityParams != null && similarityParams.getSecondaryStructureSource() != null) { @@ -220,9 +222,9 @@ public class TreePanel extends GTreePanel addSubtitlePanel(" Secondary Structure Provider : " + similarityParams.getSecondaryStructureSource()); } - if (leafAnnotations!=null) + if (leafAnnotations != null) { - forAnnotation=true; + forAnnotation = true; } if (columnWise) { @@ -399,12 +401,14 @@ public class TreePanel extends GTreePanel private AlignmentView odata = null; private AlignmentAnnotation[] leafAnnotations; - public TreeLoader(NewickFile newickFile, AlignmentView inputData, AlignmentAnnotation[] leafAnnotations) + + public TreeLoader(NewickFile newickFile, AlignmentView inputData, + AlignmentAnnotation[] leafAnnotations) { this.newtree = newickFile; this.odata = inputData; this.leafAnnotations = leafAnnotations; - + if (newickFile != null) { // Must be outside run(), as Jalview2XML tries to @@ -967,7 +971,8 @@ public class TreePanel extends GTreePanel NewickFile nf, String treeTitle2, AlignmentView input) { // TODO - recover subpanel name - TreePanel tp = new TreePanel(alignPanel, nf, treeTitle2, input, null, "Annotation Tree"); + TreePanel tp = new TreePanel(alignPanel, nf, treeTitle2, input, null, + "Annotation Tree"); return tp; } } diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java index 333f995..2bd5a91 100644 --- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java +++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java @@ -426,8 +426,9 @@ public class ThreeDBStructureChooserQuerySource String modelPage = humanUrl < 1 ? null : (String) restable.getValueAt(row, humanUrl); - String modelCategory = idx_mcat < 1 ? null :(String) restable.getValueAt(row,idx_mcat); - + String modelCategory = idx_mcat < 1 ? null + : (String) restable.getValueAt(row, idx_mcat); + String strucFormat = restable.getValueAt(row, modelformat).toString(); SequenceI selectedSeq = (SequenceI) restable.getValueAt(row, diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java index 66c620b..f8783b7 100755 --- a/src/jalview/io/AnnotationFile.java +++ b/src/jalview/io/AnnotationFile.java @@ -1607,11 +1607,13 @@ public class AnnotationFile sg.cs.setThreshold(Integer.parseInt(value), true); } - else if(key.equalsIgnoreCase("secondaryStructureConservationThreshold")) + else if (key + .equalsIgnoreCase("secondaryStructureConservationThreshold")) { - sg.cs.setConsensusSecondaryStructureThreshold(Integer.parseInt(value)); + sg.cs.setConsensusSecondaryStructureThreshold( + Integer.parseInt(value)); sg.cs.setConsensusSecondaryStructureColouring(true); - + } else if (key.equalsIgnoreCase("consThreshold")) { diff --git a/src/jalview/jbgui/GAlignFrame.java b/src/jalview/jbgui/GAlignFrame.java index fa9626b..69ebd56 100755 --- a/src/jalview/jbgui/GAlignFrame.java +++ b/src/jalview/jbgui/GAlignFrame.java @@ -132,10 +132,10 @@ public class GAlignFrame extends JInternalFrame protected JCheckBoxMenuItem abovePIDThreshold; - protected JMenuItem modifyPID; + protected JMenuItem modifyPID; protected JCheckBoxMenuItem byConsensusSecondaryStructureMenuItem; - + protected JMenuItem modifyConsensusSecondaryStructureThreshold; protected JRadioButtonMenuItem annotationColour; @@ -199,18 +199,18 @@ public class GAlignFrame extends JInternalFrame protected JMenuItem gatherViews = new JMenuItem(); protected JMenuItem expandViews = new JMenuItem(); - - protected JCheckBoxMenuItem showStrucProvider = new JCheckBoxMenuItem(); - - protected JCheckBoxMenuItem showSSConsensus = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showStrucProvider = new JCheckBoxMenuItem(); + + protected JCheckBoxMenuItem showSSConsensus = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showGroupSSConsensus = new JCheckBoxMenuItem(); - + protected JCheckBoxMenuItem showGroupConsensus = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showGroupConservation = new JCheckBoxMenuItem(); - protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); + protected JCheckBoxMenuItem showConsensusHistogram = new JCheckBoxMenuItem(); protected JCheckBoxMenuItem showSequenceLogo = new JCheckBoxMenuItem(); @@ -684,13 +684,14 @@ public class GAlignFrame extends JInternalFrame }); showStrucProvider = new JCheckBoxMenuItem( MessageManager.getString("label.show_structure_provider")); - showStrucProvider.addActionListener(new ActionListener() { + showStrucProvider.addActionListener(new ActionListener() + { @Override public void actionPerformed(ActionEvent e) { showStructureProvider_actionPerformed(e); } - + }); colourTextMenuItem = new JCheckBoxMenuItem( MessageManager.getString("label.colour_text")); @@ -877,30 +878,30 @@ public class GAlignFrame extends JInternalFrame }); - showSSConsensus - .setText(MessageManager.getString("label.show_secondary_structure_consensus")); + showSSConsensus.setText(MessageManager + .getString("label.show_secondary_structure_consensus")); showSSConsensus.addActionListener(new ActionListener() { - - @Override - public void actionPerformed(ActionEvent e) - { - showSSConsensus_actionPerformed(e); - } - + + @Override + public void actionPerformed(ActionEvent e) + { + showSSConsensus_actionPerformed(e); + } + }); - + showGroupSSConsensus .setText(MessageManager.getString("label.group_ss_consensus")); showGroupSSConsensus.addActionListener(new ActionListener() { - + @Override public void actionPerformed(ActionEvent e) { showGroupSSConsensus_actionPerformed(e); } - + }); showGroupConsensus @@ -926,7 +927,7 @@ public class GAlignFrame extends JInternalFrame showConsensusHistogram_actionPerformed(e); } - }); + }); showSequenceLogo .setText(MessageManager.getString("label.show_consensus_logo")); showSequenceLogo.addActionListener(new ActionListener() @@ -1833,7 +1834,7 @@ public class GAlignFrame extends JInternalFrame addMenuActionAndAccelerator(keyStroke, copyHighlighted, al); copyHighlighted.addActionListener(al); - ButtonGroup ssButtonGroup = new ButtonGroup(); + ButtonGroup ssButtonGroup = new ButtonGroup(); JMenu tooltipSettingsMenu = new JMenu( MessageManager.getString("label.sequence_id_tooltip")); @@ -1841,53 +1842,72 @@ public class GAlignFrame extends JInternalFrame MessageManager.getString("label.autocalculated_annotation")); JMenu showSS = new JMenu( - MessageManager.getString("label.show_secondary_structure")); - - JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem(MessageManager.getString("option.ss_providers_all")); - radioButtonAllSS.addActionListener(new ActionListener() { - @Override - public void actionPerformed(ActionEvent e) { - showOrHideSecondaryStructureForSource(MessageManager.getString("option.ss_providers_all"), true); - // Select all checkboxes if "All" is selected - Component[] components = showSS.getMenuComponents(); - for (Component component : components) { - if (component instanceof JCheckBoxMenuItem) { - ((JCheckBoxMenuItem) component).setSelected(true); - } + MessageManager.getString("label.show_secondary_structure")); + + JRadioButtonMenuItem radioButtonAllSS = new JRadioButtonMenuItem( + MessageManager.getString("option.ss_providers_all")); + radioButtonAllSS.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showOrHideSecondaryStructureForSource( + MessageManager.getString("option.ss_providers_all"), true); + // Select all checkboxes if "All" is selected + Component[] components = showSS.getMenuComponents(); + for (Component component : components) + { + if (component instanceof JCheckBoxMenuItem) + { + ((JCheckBoxMenuItem) component).setSelected(true); } + } } }); ssButtonGroup.add(radioButtonAllSS); showSS.add(radioButtonAllSS); - - JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem(MessageManager.getString("option.ss_providers_none")); - radioButtonNoneSS.addActionListener(new ActionListener() { - @Override - public void actionPerformed(ActionEvent e) { - showOrHideSecondaryStructureForSource(MessageManager.getString("option.ss_providers_none"), false); - // Remove selection of all checkboxes if "None" is selected - Component[] components = showSS.getMenuComponents(); - for (Component component : components) { - if (component instanceof JCheckBoxMenuItem) { - ((JCheckBoxMenuItem) component).setSelected(false); - } + + JRadioButtonMenuItem radioButtonNoneSS = new JRadioButtonMenuItem( + MessageManager.getString("option.ss_providers_none")); + radioButtonNoneSS.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + showOrHideSecondaryStructureForSource( + MessageManager.getString("option.ss_providers_none"), + false); + // Remove selection of all checkboxes if "None" is selected + Component[] components = showSS.getMenuComponents(); + for (Component component : components) + { + if (component instanceof JCheckBoxMenuItem) + { + ((JCheckBoxMenuItem) component).setSelected(false); } + } } }); ssButtonGroup.add(radioButtonNoneSS); showSS.add(radioButtonNoneSS); showSS.addSeparator(); - - annotationsMenu.addMouseListener(new MouseAdapter() { - + + annotationsMenu.addMouseListener(new MouseAdapter() + { + @Override - public void mouseEntered(MouseEvent e) { + public void mouseEntered(MouseEvent e) + { + + updateShowSecondaryStructureMenu(showSS, ssButtonGroup); // Update radio + // buttons + // every time + // the menu is + // clicked - updateShowSecondaryStructureMenu(showSS, ssButtonGroup); // Update radio buttons every time the menu is clicked - } }); - + JMenu exportImageMenu = new JMenu( MessageManager.getString("label.export_image")); JMenu fileMenu = new JMenu(MessageManager.getString("action.file")); @@ -1998,7 +2018,7 @@ public class GAlignFrame extends JInternalFrame autoAnnMenu.add(showConsensusHistogram); autoAnnMenu.add(showSequenceLogo); autoAnnMenu.add(normaliseSequenceLogo); - //autoAnnMenu.add(showSSConsensus); + // autoAnnMenu.add(showSSConsensus); autoAnnMenu.addSeparator(); autoAnnMenu.add(showGroupConservation); autoAnnMenu.add(showGroupConsensus); @@ -2087,13 +2107,13 @@ public class GAlignFrame extends JInternalFrame protected void showStructureProvider_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void showSSConsensus_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub - + } protected void createPNG_actionPerformed(ActionEvent object) @@ -2163,19 +2183,20 @@ public class GAlignFrame extends JInternalFrame conservationMenuItem.isSelected()); } }); - byConsensusSecondaryStructureMenuItem = new JCheckBoxMenuItem( - MessageManager.getString("action.by_secondary_structure_conservation")); - byConsensusSecondaryStructureMenuItem.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - colourByConsensusSecondaryStructureMenuItem_actionPerformed( - byConsensusSecondaryStructureMenuItem.isSelected()); - } - }); + MessageManager.getString( + "action.by_secondary_structure_conservation")); + byConsensusSecondaryStructureMenuItem + .addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + colourByConsensusSecondaryStructureMenuItem_actionPerformed( + byConsensusSecondaryStructureMenuItem.isSelected()); + } + }); abovePIDThreshold = new JCheckBoxMenuItem( MessageManager.getString("label.above_identity_threshold")); @@ -2207,18 +2228,19 @@ public class GAlignFrame extends JInternalFrame modifyConservation_actionPerformed(); } }); - - modifyConsensusSecondaryStructureThreshold = new JMenuItem(MessageManager - .getString("label.modify_secondary_structure_conservation_threshold")); - modifyConsensusSecondaryStructureThreshold.addActionListener(new ActionListener() - { - @Override - public void actionPerformed(ActionEvent e) - { - modifyConsensusSecondaryStructureThreshold_actionPerformed(); - } - }); - + + modifyConsensusSecondaryStructureThreshold = new JMenuItem( + MessageManager.getString( + "label.modify_secondary_structure_conservation_threshold")); + modifyConsensusSecondaryStructureThreshold + .addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + modifyConsensusSecondaryStructureThreshold_actionPerformed(); + } + }); annotationColour = new JRadioButtonMenuItem( MessageManager.getString("action.by_annotation")); @@ -2387,7 +2409,7 @@ public class GAlignFrame extends JInternalFrame // TODO Auto-generated method stub } - + protected void showGroupSSConsensus_actionPerformed(ActionEvent e) { // TODO Auto-generated method stub @@ -2581,8 +2603,9 @@ public class GAlignFrame extends JInternalFrame protected void conservationMenuItem_actionPerformed(boolean selected) { } - - public void colourByConsensusSecondaryStructureMenuItem_actionPerformed(boolean selected) + + public void colourByConsensusSecondaryStructureMenuItem_actionPerformed( + boolean selected) { } @@ -2692,7 +2715,7 @@ public class GAlignFrame extends JInternalFrame protected void modifyConservation_actionPerformed() { } - + protected void modifyConsensusSecondaryStructureThreshold_actionPerformed() { } @@ -2947,16 +2970,17 @@ public class GAlignFrame extends JInternalFrame return null; } - protected void showOrHideSecondaryStructureForSource(String ssSourceSelection, boolean visible) + protected void showOrHideSecondaryStructureForSource( + String ssSourceSelection, boolean visible) { // TODO Auto-generated method stub - + } protected void updateShowSecondaryStructureMenu(JMenu showSS, ButtonGroup ssButtonGroup) { // TODO Auto-generated method stub - + } } diff --git a/src/jalview/jbgui/GCutAndPasteTransfer.java b/src/jalview/jbgui/GCutAndPasteTransfer.java index 5daea78..106ad7c 100755 --- a/src/jalview/jbgui/GCutAndPasteTransfer.java +++ b/src/jalview/jbgui/GCutAndPasteTransfer.java @@ -198,7 +198,7 @@ public class GCutAndPasteTransfer extends JInternalFrame @Override public void actionPerformed(ActionEvent e) { - fontSizeMenu_actionPerformed(e); + fontSizeMenu_actionPerformed(e); } }); copyItem.setText(MessageManager.getString("action.copy")); @@ -256,6 +256,7 @@ public class GCutAndPasteTransfer extends JInternalFrame /** * shows a menu for changing the font + * * @param e */ public void fontSizeMenu_actionPerformed(ActionEvent e) diff --git a/src/jalview/jbgui/GPCAPanel.java b/src/jalview/jbgui/GPCAPanel.java index ec5b209..65394ed 100755 --- a/src/jalview/jbgui/GPCAPanel.java +++ b/src/jalview/jbgui/GPCAPanel.java @@ -85,6 +85,7 @@ public class GPCAPanel extends JInternalFrame zCombobox.addItem("dim " + i); } } + public GPCAPanel(int dim) { try diff --git a/src/jalview/jbgui/GPaSiMapPanel.java b/src/jalview/jbgui/GPaSiMapPanel.java index 369a005..3c7fb5a 100755 --- a/src/jalview/jbgui/GPaSiMapPanel.java +++ b/src/jalview/jbgui/GPaSiMapPanel.java @@ -85,6 +85,7 @@ public class GPaSiMapPanel extends JInternalFrame zCombobox.addItem("dim " + i); } } + public GPaSiMapPanel(int dim) { try @@ -223,8 +224,8 @@ public class GPaSiMapPanel extends JInternalFrame } }); JMenuItem outputAlignment = new JMenuItem(); - outputAlignment.setText( - MessageManager.getString("label.output_alignment")); + outputAlignment + .setText(MessageManager.getString("label.output_alignment")); outputAlignment.addActionListener(new ActionListener() { @Override diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java index e574327..c644e3c 100755 --- a/src/jalview/jbgui/GPreferences.java +++ b/src/jalview/jbgui/GPreferences.java @@ -160,7 +160,7 @@ public class GPreferences extends JPanel protected JCheckBox conservation = new JCheckBox(); - protected JCheckBox identity = new JCheckBox(); + protected JCheckBox identity = new JCheckBox(); protected JCheckBox ssConsensus = new JCheckBox(); diff --git a/src/jalview/math/Matrix.java b/src/jalview/math/Matrix.java index 7ae4b94..f767444 100755 --- a/src/jalview/math/Matrix.java +++ b/src/jalview/math/Matrix.java @@ -123,12 +123,12 @@ public class Matrix implements MatrixI if (row != null) { value[i] = new double[row.length]; - int j = 0; - for (float oldValue : row) - { - value[i][j] = oldValue; - j++; - } + int j = 0; + for (float oldValue : row) + { + value[i][j] = oldValue; + j++; + } } i++; } @@ -191,10 +191,11 @@ public class Matrix implements MatrixI */ for (int k = 0; k < in.width(); k++) { - if (!Double.isNaN(in.getValue(i,k)) && !Double.isNaN(this.value[k][j])) - { + if (!Double.isNaN(in.getValue(i, k)) + && !Double.isNaN(this.value[k][j])) + { tmp[i][j] += (in.getValue(i, k) * this.value[k][j]); - } + } } } } @@ -833,10 +834,10 @@ public class Matrix implements MatrixI } /** - * returns the matrix as a double[][] array - * - * @return - */ + * returns the matrix as a double[][] array + * + * @return + */ @Override public double[][] asArray() { @@ -1018,7 +1019,8 @@ public class Matrix implements MatrixI /** * Add d to all entries of this matrix * - * @param d ~ value to add + * @param d + * ~ value to add */ @Override public void add(double d) @@ -1086,7 +1088,7 @@ public class Matrix implements MatrixI } /** - * Returns a copy in which every value in the matrix is its absolute + * Returns a copy in which every value in the matrix is its absolute * * @return */ @@ -1122,7 +1124,7 @@ public class Matrix implements MatrixI { if (row != null) { - mean[i++] = MiscMath.mean(row); + mean[i++] = MiscMath.mean(row); } } return mean; @@ -1142,17 +1144,17 @@ public class Matrix implements MatrixI double[] column = getColumn(j); if (column != null) { - mean[j] = MiscMath.mean(column); + mean[j] = MiscMath.mean(column); } } return mean; } /** - * return a flattened matrix containing the sum of each column - * - * @return - */ + * return a flattened matrix containing the sum of each column + * + * @return + */ @Override public double[] sumCol() { @@ -1162,17 +1164,17 @@ public class Matrix implements MatrixI double[] column = getColumn(j); if (column != null) { - sum[j] = MiscMath.sum(column); + sum[j] = MiscMath.sum(column); } - } + } return sum; } /** - * returns the mean value of the complete matrix - * - * @return - */ + * returns the mean value of the complete matrix + * + * @return + */ @Override public double mean() { @@ -1182,47 +1184,51 @@ public class Matrix implements MatrixI { for (double col : row) { - if (!Double.isNaN(col)) - { - sum += col; - } else { - nanCount++; - } + if (!Double.isNaN(col)) + { + sum += col; + } + else + { + nanCount++; + } } } return sum / (double) (this.rows * this.cols - nanCount); } /** - * fills up a diagonal matrix with its transposed copy - * !other side should be filled with 0 - * !keeps Double.NaN found in either side - * - * TODO check on which side it was diagonal and only do calculations for the other side - */ + * fills up a diagonal matrix with its transposed copy !other side should be + * filled with 0 !keeps Double.NaN found in either side + * + * TODO check on which side it was diagonal and only do calculations for the + * other side + */ @Override public void fillDiagonal() { int n = this.rows; int m = this.cols; - MatrixI copy = this.transpose(); // goes through each element in the matrix and - for (int i = 0; i < n; i++) // adds the value in the transposed copy to the original value + MatrixI copy = this.transpose(); // goes through each element in the matrix + // and + for (int i = 0; i < n; i++) // adds the value in the transposed copy to the + // original value { for (int j = 0; j < m; j++) { - if (i != j) - { - this.addValue(i, j, copy.getValue(i,j)); - } + if (i != j) + { + this.addValue(i, j, copy.getValue(i, j)); + } } } } /** - * counts the number of Double.NaN in the matrix - * - * @return - */ + * counts the number of Double.NaN in the matrix + * + * @return + */ @Override public int countNaN() { @@ -1231,117 +1237,139 @@ public class Matrix implements MatrixI { for (int j = 0; j < this.cols; j++) { - if (Double.isNaN(this.getValue(i,j))) - { - NaN++; - } + if (Double.isNaN(this.getValue(i, j))) + { + NaN++; + } } } return NaN; } /** - * performs an element-wise addition of this matrix by another matrix ~ this - m - * @param m ~ other matrix - * - * @return - */ + * performs an element-wise addition of this matrix by another matrix ~ this - + * m + * + * @param m + * ~ other matrix + * + * @return + */ @Override public MatrixI add(MatrixI m) { if (m.width() != cols || m.height() != rows) { - throw new IllegalArgumentException("Can't add a " + m.height() + "x" + m.width() + " to a " + this.rows + "x" + this.cols + " matrix"); + throw new IllegalArgumentException( + "Can't add a " + m.height() + "x" + m.width() + " to a " + + this.rows + "x" + this.cols + " matrix"); } double[][] tmp = new double[this.rows][this.cols]; for (int i = 0; i < this.rows; i++) { for (int j = 0; j < this.cols; j++) { - tmp[i][j] = this.getValue(i,j) + m.getValue(i,j); + tmp[i][j] = this.getValue(i, j) + m.getValue(i, j); } } return new Matrix(tmp); } /** - * performs an element-wise subtraction of this matrix by another matrix ~ this - m - * @param m ~ other matrix - * - * @return - */ + * performs an element-wise subtraction of this matrix by another matrix ~ + * this - m + * + * @param m + * ~ other matrix + * + * @return + */ @Override public MatrixI subtract(MatrixI m) { if (m.width() != cols || m.height() != rows) { - throw new IllegalArgumentException("Can't subtract a " + m.height() + "x" + m.width() + " from a " + this.rows + "x" + this.cols + " matrix"); + throw new IllegalArgumentException("Can't subtract a " + m.height() + + "x" + m.width() + " from a " + this.rows + "x" + this.cols + + " matrix"); } double[][] tmp = new double[this.rows][this.cols]; for (int i = 0; i < this.rows; i++) { for (int j = 0; j < this.cols; j++) { - tmp[i][j] = this.getValue(i,j) - m.getValue(i,j); + tmp[i][j] = this.getValue(i, j) - m.getValue(i, j); } } return new Matrix(tmp); } /** - * performs an element-wise multiplication of this matrix by another matrix ~ this * m - * @param m ~ other matrix - * - * @return - */ + * performs an element-wise multiplication of this matrix by another matrix ~ + * this * m + * + * @param m + * ~ other matrix + * + * @return + */ @Override public MatrixI elementwiseMultiply(MatrixI m) { if (m.width() != cols || m.height() != rows) { - throw new IllegalArgumentException("Can't multiply a " + this.rows + "x" + this.cols + " by a " + m.height() + "x" + m.width() + " matrix"); + throw new IllegalArgumentException( + "Can't multiply a " + this.rows + "x" + this.cols + " by a " + + m.height() + "x" + m.width() + " matrix"); } double[][] tmp = new double[this.rows][this.cols]; for (int i = 0; i < this.rows; i++) { for (int j = 0; j < this.cols; j++) { - tmp[i][j] = this.getValue(i, j) * m.getValue(i,j); + tmp[i][j] = this.getValue(i, j) * m.getValue(i, j); } } return new Matrix(tmp); } /** - * performs an element-wise division of this matrix by another matrix ~ this / m - * @param m ~ other matrix - * - * @return - */ + * performs an element-wise division of this matrix by another matrix ~ this / + * m + * + * @param m + * ~ other matrix + * + * @return + */ @Override public MatrixI elementwiseDivide(MatrixI m) { if (m.width() != cols || m.height() != rows) { - throw new IllegalArgumentException("Can't divide a " + this.rows + "x" + this.cols + " by a " + m.height() + "x" + m.width() + " matrix"); + throw new IllegalArgumentException( + "Can't divide a " + this.rows + "x" + this.cols + " by a " + + m.height() + "x" + m.width() + " matrix"); } double[][] tmp = new double[this.rows][this.cols]; for (int i = 0; i < this.rows; i++) { for (int j = 0; j < this.cols; j++) { - tmp[i][j] = this.getValue(i, j) / m.getValue(i,j); + tmp[i][j] = this.getValue(i, j) / m.getValue(i, j); } } return new Matrix(tmp); } /** - * calculate the root-mean-square for tow matrices - * @param m ~ other matrix - * - * @return - */ + * calculate the root-mean-square for tow matrices + * + * @param m + * ~ other matrix + * + * @return + */ @Override public double rmsd(MatrixI m) { @@ -1351,10 +1379,10 @@ public class Matrix implements MatrixI } /** - * calculates the Frobenius norm of this matrix - * - * @return - */ + * calculates the Frobenius norm of this matrix + * + * @return + */ @Override public double norm() { @@ -1363,17 +1391,17 @@ public class Matrix implements MatrixI { for (double val : row) { - result += Math.pow(val, 2); + result += Math.pow(val, 2); } } return Math.sqrt(result); } /** - * returns the sum of all values in this matrix - * - * @return - */ + * returns the sum of all values in this matrix + * + * @return + */ @Override public double sum() { @@ -1382,24 +1410,28 @@ public class Matrix implements MatrixI { for (double val : row) { - sum += (Double.isNaN(val)) ? 0.0 : val; + sum += (Double.isNaN(val)) ? 0.0 : val; } } return sum; } /** - * returns the sum-product of this matrix with vector v - * @param v ~ vector - * - * @return - */ + * returns the sum-product of this matrix with vector v + * + * @param v + * ~ vector + * + * @return + */ @Override public double[] sumProduct(double[] v) { if (v.length != cols) { - throw new IllegalArgumentException("Vector and matrix do not have the same dimension! (" + v.length + " != " + cols + ")"); + throw new IllegalArgumentException( + "Vector and matrix do not have the same dimension! (" + + v.length + " != " + cols + ")"); } double[] result = new double[rows]; for (int i = 0; i < rows; i++) @@ -1408,7 +1440,7 @@ public class Matrix implements MatrixI double sum = 0; for (int j = 0; j < row.length; j++) { - sum += row[j] * v[j]; + sum += row[j] * v[j]; } result[i] = sum; } @@ -1416,20 +1448,20 @@ public class Matrix implements MatrixI } /** - * mirrors columns of the matrix - * - * @return - */ + * mirrors columns of the matrix + * + * @return + */ @Override public MatrixI mirrorCol() { double[][] result = new double[rows][cols]; for (int i = 0; i < rows; i++) { - int k = cols - 1; // reverse col + int k = cols - 1; // reverse col for (int j = 0; j < cols; j++) { - result[i][k--] = this.getValue(i,j); + result[i][k--] = this.getValue(i, j); } } MatrixI resultMatrix = new Matrix(result); diff --git a/src/jalview/math/MatrixI.java b/src/jalview/math/MatrixI.java index 7faac73..b932b33 100644 --- a/src/jalview/math/MatrixI.java +++ b/src/jalview/math/MatrixI.java @@ -61,10 +61,10 @@ public interface MatrixI void setValue(int i, int j, double d); /** - * Returns the matrix as a double[][] array - * - * @return - */ + * Returns the matrix as a double[][] array + * + * @return + */ double[][] asArray(); /** @@ -175,10 +175,11 @@ public interface MatrixI void multiply(double d); /** - * Add d to all entries of this matrix - * - * @param d ~ value to add - */ + * Add d to all entries of this matrix + * + * @param d + * ~ value to add + */ void add(double d); /** @@ -193,7 +194,7 @@ public interface MatrixI boolean equals(MatrixI m2, double delta); /** - * Returns a copy in which every value in the matrix is its absolute + * Returns a copy in which every value in the matrix is its absolute */ MatrixI absolute(); @@ -208,110 +209,122 @@ public interface MatrixI double[] meanCol(); /** - * Returns a flattened matrix containing the sum of each column - * - * @return - */ + * Returns a flattened matrix containing the sum of each column + * + * @return + */ double[] sumCol(); /** - * returns the mean value of the complete matrix - */ + * returns the mean value of the complete matrix + */ double mean(); /** - * fills up a diagonal matrix with its transposed copy - * !other side should be filled with either 0 or Double.NaN - */ + * fills up a diagonal matrix with its transposed copy !other side should be + * filled with either 0 or Double.NaN + */ void fillDiagonal(); /** - * counts the number of Double.NaN in the matrix - * - * @return - */ + * counts the number of Double.NaN in the matrix + * + * @return + */ int countNaN(); /** - * performs an element-wise addition of this matrix by another matrix - * !matrices have to be the same size - * @param m ~ other matrix - * - * @return - * @throws IllegalArgumentException - * if this and m do not have the same dimensions - */ + * performs an element-wise addition of this matrix by another matrix + * !matrices have to be the same size + * + * @param m + * ~ other matrix + * + * @return + * @throws IllegalArgumentException + * if this and m do not have the same dimensions + */ MatrixI add(MatrixI m); /** - * performs an element-wise subtraction of this matrix by another matrix - * !matrices have to be the same size - * @param m ~ other matrix - * - * @return - * @throws IllegalArgumentException - * if this and m do not have the same dimensions - */ + * performs an element-wise subtraction of this matrix by another matrix + * !matrices have to be the same size + * + * @param m + * ~ other matrix + * + * @return + * @throws IllegalArgumentException + * if this and m do not have the same dimensions + */ MatrixI subtract(MatrixI m); - + /** - * performs an element-wise multiplication of this matrix by another matrix ~ this * m - * !matrices have to be the same size - * @param m ~ other matrix - * - * @return - * @throws IllegalArgumentException - * if this and m do not have the same dimensions - */ + * performs an element-wise multiplication of this matrix by another matrix ~ + * this * m !matrices have to be the same size + * + * @param m + * ~ other matrix + * + * @return + * @throws IllegalArgumentException + * if this and m do not have the same dimensions + */ MatrixI elementwiseMultiply(MatrixI m); /** - * performs an element-wise division of this matrix by another matrix ~ this / m - * !matrices have to be the same size - * @param m ~ other matrix - * - * @return - * @throws IllegalArgumentException - * if this and m do not have the same dimensions - */ + * performs an element-wise division of this matrix by another matrix ~ this / + * m !matrices have to be the same size + * + * @param m + * ~ other matrix + * + * @return + * @throws IllegalArgumentException + * if this and m do not have the same dimensions + */ MatrixI elementwiseDivide(MatrixI m); /** - * calculates the root-mean-square for two matrices - * @param m ~ other matrix - * - * @return - */ + * calculates the root-mean-square for two matrices + * + * @param m + * ~ other matrix + * + * @return + */ double rmsd(MatrixI m); /** - * calculates the Frobenius norm of this matrix - * - * @return - */ + * calculates the Frobenius norm of this matrix + * + * @return + */ double norm(); - + /** - * returns the sum of all values in this matrix - * - * @return - */ + * returns the sum of all values in this matrix + * + * @return + */ double sum(); /** - * returns the sum-product of this matrix with vector v - * @param v ~ vector - * - * @return - * @throws IllegalArgumentException - * if this.cols and v do not have the same length - */ + * returns the sum-product of this matrix with vector v + * + * @param v + * ~ vector + * + * @return + * @throws IllegalArgumentException + * if this.cols and v do not have the same length + */ double[] sumProduct(double[] v); /** - * mirrors the columns of this matrix - * - * @return - */ + * mirrors the columns of this matrix + * + * @return + */ MatrixI mirrorCol(); } diff --git a/src/jalview/math/MiscMath.java b/src/jalview/math/MiscMath.java index b5218d5..eee7ef8 100755 --- a/src/jalview/math/MiscMath.java +++ b/src/jalview/math/MiscMath.java @@ -27,14 +27,17 @@ import java.util.Arrays; /** * A collection of miscellaneous mathematical operations + * * @AUTHOR MorellThomas */ public class MiscMath { /** - * prints an array - * @param m ~ array - */ + * prints an array + * + * @param m + * ~ array + */ public static void print(double[] m, String format) { System.out.print("[ "); @@ -46,39 +49,43 @@ public class MiscMath } /** - * calculates the mean of an array - * - * @param m ~ array - * @return - */ + * calculates the mean of an array + * + * @param m + * ~ array + * @return + */ public static double mean(double[] m) { double sum = 0; int nanCount = 0; for (int i = 0; i < m.length; i++) { - if (!Double.isNaN(m[i])) // ignore NaN values in the array + if (!Double.isNaN(m[i])) // ignore NaN values in the array { sum += m[i]; - } else { - nanCount++; + } + else + { + nanCount++; } } return sum / (double) (m.length - nanCount); } /** - * calculates the sum of an array - * - * @param m ~ array - * @return - */ + * calculates the sum of an array + * + * @param m + * ~ array + * @return + */ public static double sum(double[] m) { double sum = 0; for (int i = 0; i < m.length; i++) { - if (!Double.isNaN(m[i])) // ignore NaN values in the array + if (!Double.isNaN(m[i])) // ignore NaN values in the array { sum += m[i]; } @@ -87,14 +94,14 @@ public class MiscMath } /** - * calculates the square root of each element in an array - * - * @param m ~ array - * - * @return - * TODO - * make general with function passed -> apply function to each element - */ + * calculates the square root of each element in an array + * + * @param m + * ~ array + * + * @return TODO make general with function passed -> apply function to each + * element + */ public static double[] sqrt(double[] m) { double[] sqrts = new double[m.length]; @@ -106,16 +113,20 @@ public class MiscMath } /** - * calculate element wise multiplication of two arrays with the same length - * - * @param a ~ array - * @param b ~ array - * - * @return - */ - public static double[] elementwiseMultiply(byte[] a, double[] b) throws RuntimeException + * calculate element wise multiplication of two arrays with the same length + * + * @param a + * ~ array + * @param b + * ~ array + * + * @return + */ + public static double[] elementwiseMultiply(byte[] a, double[] b) + throws RuntimeException { - if (a.length != b.length) // throw exception if the arrays do not have the same length + if (a.length != b.length) // throw exception if the arrays do not have the + // same length { throw new SameLengthException(a.length, b.length); } @@ -126,9 +137,12 @@ public class MiscMath } return result; } - public static double[] elementwiseMultiply(double[] a, double[] b) throws RuntimeException + + public static double[] elementwiseMultiply(double[] a, double[] b) + throws RuntimeException { - if (a.length != b.length) // throw exception if the arrays do not have the same length + if (a.length != b.length) // throw exception if the arrays do not have the + // same length { throw new SameLengthException(a.length, b.length); } @@ -139,9 +153,12 @@ public class MiscMath } return result; } - public static byte[] elementwiseMultiply(byte[] a, byte[] b) throws RuntimeException + + public static byte[] elementwiseMultiply(byte[] a, byte[] b) + throws RuntimeException { - if (a.length != b.length) // throw exception if the arrays do not have the same length + if (a.length != b.length) // throw exception if the arrays do not have the + // same length { throw new SameLengthException(a.length, b.length); } @@ -152,6 +169,7 @@ public class MiscMath } return result; } + public static double[] elementwiseMultiply(double[] a, double b) { double[] result = new double[a.length]; @@ -163,16 +181,20 @@ public class MiscMath } /** - * calculate element wise division of two arrays ~ a / b - * - * @param a ~ array - * @param b ~ array - * - * @return - */ - public static double[] elementwiseDivide(double[] a, double[] b) throws RuntimeException + * calculate element wise division of two arrays ~ a / b + * + * @param a + * ~ array + * @param b + * ~ array + * + * @return + */ + public static double[] elementwiseDivide(double[] a, double[] b) + throws RuntimeException { - if (a.length != b.length) // throw exception if the arrays do not have the same length + if (a.length != b.length) // throw exception if the arrays do not have the + // same length { throw new SameLengthException(a.length, b.length); } @@ -185,16 +207,20 @@ public class MiscMath } /** - * calculate element wise addition of two arrays - * - * @param a ~ array - * @param b ~ array - * - * @return - */ - public static double[] elementwiseAdd(double[] a, double[] b) throws RuntimeException + * calculate element wise addition of two arrays + * + * @param a + * ~ array + * @param b + * ~ array + * + * @return + */ + public static double[] elementwiseAdd(double[] a, double[] b) + throws RuntimeException { - if (a.length != b.length) // throw exception if the arrays do not have the same length + if (a.length != b.length) // throw exception if the arrays do not have the + // same length { throw new SameLengthException(a.length, b.length); } @@ -206,6 +232,7 @@ public class MiscMath } return result; } + public static double[] elementwiseAdd(double[] a, double b) { double[] result = new double[a.length]; @@ -217,41 +244,59 @@ public class MiscMath } /** - * returns true if two arrays are element wise within a tolerance - * - * @param a ~ array - * @param b ~ array - * @param rtol ~ relative tolerance - * @param atol ~ absolute tolerance - * @param equalNAN ~ whether NaN at the same position return true - * - * @return - */ - public static boolean allClose(double[] a, double[] b, double rtol, double atol, boolean equalNAN) + * returns true if two arrays are element wise within a tolerance + * + * @param a + * ~ array + * @param b + * ~ array + * @param rtol + * ~ relative tolerance + * @param atol + * ~ absolute tolerance + * @param equalNAN + * ~ whether NaN at the same position return true + * + * @return + */ + public static boolean allClose(double[] a, double[] b, double rtol, + double atol, boolean equalNAN) { boolean areEqual = true; for (int i = 0; i < a.length; i++) { - if (equalNAN && (Double.isNaN(a[i]) && Double.isNaN(b[i]))) // if equalNAN == true -> skip the NaN pair + if (equalNAN && (Double.isNaN(a[i]) && Double.isNaN(b[i]))) // if equalNAN + // == true -> + // skip the + // NaN pair { - continue; + continue; } - if (Math.abs(a[i] - b[i]) > (atol + rtol * Math.abs(b[i]))) // check for the similarity condition -> if not met -> break and return false + if (Math.abs(a[i] - b[i]) > (atol + rtol * Math.abs(b[i]))) // check for + // the + // similarity + // condition + // -> if not + // met -> + // break and + // return + // false { - areEqual = false; - break; + areEqual = false; + break; } } return areEqual; } /** - * returns the index of the maximum and the maximum value of an array - * - * @param a ~ array - * - * @return - */ + * returns the index of the maximum and the maximum value of an array + * + * @param a + * ~ array + * + * @return + */ public static int[] findMax(int[] a) { int max = 0; @@ -260,25 +305,30 @@ public class MiscMath { if (a[i] > max) { - max = a[i]; - maxIndex = i; + max = a[i]; + maxIndex = i; } } - return new int[]{maxIndex, max}; + return new int[] { maxIndex, max }; } /** - * returns the dot product of two arrays - * @param a ~ array a - * @param b ~ array b - * - * @return - */ + * returns the dot product of two arrays + * + * @param a + * ~ array a + * @param b + * ~ array b + * + * @return + */ public static double dot(double[] a, double[] b) { if (a.length != b.length) { - throw new IllegalArgumentException(String.format("Vectors do not have the same length (%d, %d)!", a.length, b.length)); + throw new IllegalArgumentException( + String.format("Vectors do not have the same length (%d, %d)!", + a.length, b.length)); } double aibi = 0; @@ -290,11 +340,13 @@ public class MiscMath } /** - * returns the euklidian norm of the vector - * @param v ~ vector - * - * @return - */ + * returns the euklidian norm of the vector + * + * @param v + * ~ vector + * + * @return + */ public static double norm(double[] v) { double result = 0; @@ -302,15 +354,17 @@ public class MiscMath { result += Math.pow(i, 2); } - return Math.sqrt(result); + return Math.sqrt(result); } /** - * returns the number of NaN in the vector - * @param v ~ vector - * - * @return - */ + * returns the number of NaN in the vector + * + * @param v + * ~ vector + * + * @return + */ public static int countNaN(double[] v) { int cnt = 0; @@ -318,20 +372,21 @@ public class MiscMath { if (Double.isNaN(i)) { - cnt++; + cnt++; } } return cnt; } /** - * recursively calculates the permutations of total n items with r items per combination - * according to n!/(n-r)! by only multiplying the relevant terms - * @param n - * @param r - * - * @return permutations - */ + * recursively calculates the permutations of total n items with r items per + * combination according to n!/(n-r)! by only multiplying the relevant terms + * + * @param n + * @param r + * + * @return permutations + */ public static long permutations(int n, int r) { if (n < r) @@ -340,13 +395,14 @@ public class MiscMath long result = 1l; for (int i = 0; i < r; i++) { - result *= (n-i); + result *= (n - i); } return result; } /** * calculate all unique combinations of n elements into r sized groups + * * @param n * @param r * @@ -357,13 +413,14 @@ public class MiscMath int result = 1; for (int i = 0; i < r; i++) { - result *= (n-1); + result *= (n - 1); } return (int) (result / MiscMath.factorial(r)); } /** * calculate the factorial of n (n >= 0) + * * @param n * * @return diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 7729e18..32dc558 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -1490,12 +1490,15 @@ public class Jalview2XML // group has references so set its ID field jGroup.setId(groupRefs.get(sg)); } - - List groupSecondaryStructureSources = sg.getSecondaryStructureSources(); - if(groupSecondaryStructureSources != null && groupSecondaryStructureSources.size()>0) { + + List groupSecondaryStructureSources = sg + .getSecondaryStructureSources(); + if (groupSecondaryStructureSources != null + && groupSecondaryStructureSources.size() > 0) + { jGroup.getSecStrProvider().addAll(groupSecondaryStructureSources); } - + ColourSchemeI colourScheme = sg.getColourScheme(); if (colourScheme != null) { @@ -1532,16 +1535,16 @@ public class Jalview2XML } jGroup.setPidThreshold(groupColourScheme.getThreshold()); - - if(groupColourScheme.isConsensusSecondaryStructureColouring()) + + if (groupColourScheme.isConsensusSecondaryStructureColouring()) { - jGroup.setSecstrSelected( - groupColourScheme.isConsensusSecondaryStructureColouring()); + jGroup.setSecstrSelected(groupColourScheme + .isConsensusSecondaryStructureColouring()); jGroup.setSecstrThreshold(groupColourScheme .getConsensusSecondaryStructureThreshold()); } } - + jGroup.setOutlineColour(sg.getOutlineColour().getRGB()); jGroup.setDisplayBoxes(sg.getDisplayBoxes()); jGroup.setDisplayText(sg.getDisplayText()); @@ -1560,7 +1563,7 @@ public class Jalview2XML jGroup.getSeq().add(seqHash(seq)); } } - + // jms.setJGroup(groups); Object group; for (JGroup grp : groups) @@ -1660,10 +1663,11 @@ public class Jalview2XML } } view.setPidThreshold(vcs.getThreshold()); - - if(vcs.isConsensusSecondaryStructureColouring()) + + if (vcs.isConsensusSecondaryStructureColouring()) { - view.setSecstrThreshold(vcs.getConsensusSecondaryStructureThreshold()); + view.setSecstrThreshold( + vcs.getConsensusSecondaryStructureThreshold()); } } @@ -2011,13 +2015,14 @@ public class Jalview2XML } /** - * Writes PaSiMap viewer attributes and computed values to an XML model object and - * adds it to the JalviewModel. Any exceptions are reported by logging. + * Writes PaSiMap viewer attributes and computed values to an XML model object + * and adds it to the JalviewModel. Any exceptions are reported by logging. * uses the functions from PCA */ protected void savePaSiMap(PaSiMapPanel panel, JalviewModel object) { - // TODO: this should be merged with above savePCAPanel - otherwise it is essentially redundant code + // TODO: this should be merged with above savePCAPanel - otherwise it is + // essentially redundant code try { PcaViewer viewer = new PcaViewer(); @@ -2107,6 +2112,7 @@ public class Jalview2XML Console.error("Error saving PaSiMap: " + t.getMessage()); } } + /** * Stores values from a matrix into an XML element, including (if present) the * D or E vectors @@ -4381,7 +4387,7 @@ public class Jalview2XML .setConservationInc(safeInt(jGroup.getConsThreshold())); sg.getGroupColourScheme().setConsensusSecondaryStructureThreshold( safeInt(jGroup.getSecstrThreshold())); - + sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour()))); sg.textColour = new Color(safeInt(jGroup.getTextCol1())); @@ -4814,20 +4820,23 @@ public class Jalview2XML } else { - if (false)//tree.isAnnotationAssociated()) + if (false)// tree.isAnnotationAssociated()) { // TODO - resolve annotation IDs against newick tree labels // then fix up labels so they are human readable - - tp = af.showNewickTreeForAnnotation(new NewickFile(tree.getNewick()), - tree.getTitle(), null, safeInt(tree.getWidth()), + + tp = af.showNewickTreeForAnnotation( + new NewickFile(tree.getNewick()), tree.getTitle(), + null, safeInt(tree.getWidth()), safeInt(tree.getHeight()), safeInt(tree.getXpos()), safeInt(tree.getYpos())); - } else { + } + else + { tp = af.showNewickTree(new NewickFile(tree.getNewick()), - tree.getTitle(), safeInt(tree.getWidth()), - safeInt(tree.getHeight()), safeInt(tree.getXpos()), - safeInt(tree.getYpos())); + tree.getTitle(), safeInt(tree.getWidth()), + safeInt(tree.getHeight()), safeInt(tree.getXpos()), + safeInt(tree.getYpos())); } } if (tree.getId() != null) @@ -5358,7 +5367,8 @@ public class Jalview2XML // recover view properties and display parameters viewport.setShowAnnotation(safeBoolean(view.isShowAnnotation())); - viewport.setShowStructureProvider(safeBoolean(view.isShowStructureProviders())); + viewport.setShowStructureProvider( + safeBoolean(view.isShowStructureProviders())); viewport.setAbovePIDThreshold(safeBoolean(view.isPidSelected())); final int pidThreshold = safeInt(view.getPidThreshold()); viewport.setThreshold(pidThreshold); @@ -5464,8 +5474,8 @@ public class Jalview2XML view.isIgnoreGapsinConsensus()); viewport.getResidueShading() .setConsensus(viewport.getSequenceConsensusHash()); - viewport.getResidueShading() - .setSSConsensusProfileMap(viewport.getSequenceSSConsensusHash()); + viewport.getResidueShading().setSSConsensusProfileMap( + viewport.getSequenceSSConsensusHash()); if (safeBoolean(view.isConservationSelected()) && cs != null) { viewport.getResidueShading() @@ -5473,9 +5483,8 @@ public class Jalview2XML } if (safeBoolean(view.isSecstrSelected()) && cs != null) { - viewport.getResidueShading() - .setConsensusSecondaryStructureThreshold( - safeInt(view.getSecstrThreshold())); + viewport.getResidueShading().setConsensusSecondaryStructureThreshold( + safeInt(view.getSecstrThreshold())); } af.changeColour(cs); viewport.setColourAppliesToAllGroups(true); @@ -6762,9 +6771,9 @@ public class Jalview2XML private boolean isPasimap(PcaViewer viewer) { - return viewer.getTitle().toLowerCase(Locale.ROOT) - .startsWith("pasimap"); + return viewer.getTitle().toLowerCase(Locale.ROOT).startsWith("pasimap"); } + /** * Loads any saved PaSiMAp viewers using the function from PCA * @@ -6788,7 +6797,7 @@ public class Jalview2XML viewer.isIncludeGappedColumns(), viewer.isMatchGaps(), viewer.isIncludeGaps(), viewer.isDenominateByShortestLength()); - */ + */ /* * create the panel (without computing the PaSiMAp) @@ -6815,7 +6824,8 @@ public class Jalview2XML PaSiMap pasimap = new PaSiMap(null, scoreModel, null); PcaDataType pasimapData = viewer.getPcaData(); - MatrixI pairwise = loadDoubleMatrix(pasimapData.getPairwiseMatrix()); + MatrixI pairwise = loadDoubleMatrix( + pasimapData.getPairwiseMatrix()); pasimap.setPairwiseScores(pairwise); MatrixI result = loadDoubleMatrix(pasimapData.getEigenMatrix()); diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java index 4b4ef8d..58c93a4 100644 --- a/src/jalview/renderer/AnnotationRenderer.java +++ b/src/jalview/renderer/AnnotationRenderer.java @@ -92,7 +92,7 @@ public class AnnotationRenderer private HiddenColumns hiddenColumns; private ProfilesI hconsensus; - + private Map hSSconsensus; private Hashtable[] complementConsensus; @@ -433,57 +433,65 @@ public class AnnotationRenderer } } } - - if(aa.autoCalculated && aa.label.startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL)) + + if (aa.autoCalculated && aa.label + .startsWith(Constants.SECONDARY_STRUCTURE_CONSENSUS_LABEL)) { - - if(aa.groupRef != null && aa.groupRef.hSSConsensusProfileMap != null - && aa.groupRef.isShowSequenceLogo()) { - for (String source : aa.groupRef.hSSConsensusProfileMap.keySet()) { - if(aa.description.startsWith(source)) { - - return AAFrequency.extractProfile( - aa.groupRef.hSSConsensusProfileMap.get(source).get(column), - aa.groupRef.getIgnoreGapsConsensus()); + + if (aa.groupRef != null && aa.groupRef.hSSConsensusProfileMap != null + && aa.groupRef.isShowSequenceLogo()) + { + for (String source : aa.groupRef.hSSConsensusProfileMap.keySet()) + { + if (aa.description.startsWith(source)) + { + + return AAFrequency + .extractProfile( + aa.groupRef.hSSConsensusProfileMap.get(source) + .get(column), + aa.groupRef.getIgnoreGapsConsensus()); + } } } - } - - if(hSSconsensus!=null && aa.groupRef == null) { - for (String source : hSSconsensus.keySet()) { - if(aa.description.startsWith(source)) { - - return AAFrequency.extractProfile( - hSSconsensus.get(source).get(column), - av_ignoreGapsConsensus); + + if (hSSconsensus != null && aa.groupRef == null) + { + for (String source : hSSconsensus.keySet()) + { + if (aa.description.startsWith(source)) + { + + return AAFrequency.extractProfile( + hSSconsensus.get(source).get(column), + av_ignoreGapsConsensus); + } } } - } - + } - - if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) + + if (aa.autoCalculated && aa.label.startsWith("StrucConsensus")) + { + // TODO implement group structure consensus + /* + * if (aa.groupRef != null && aa.groupRef.consensusData != null && + * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for + * group selections return StructureFrequency.extractProfile( + * aa.groupRef.consensusData[column], aa.groupRef + * .getIgnoreGapsConsensus()); } + */ + // TODO extend annotation row to enable dynamic and static profile data + // to + // be stored + if (aa.groupRef == null && aa.sequenceRef == null + && hStrucConsensus != null && hStrucConsensus.length > column) { - // TODO implement group structure consensus - /* - * if (aa.groupRef != null && aa.groupRef.consensusData != null && - * aa.groupRef.isShowSequenceLogo()) { //TODO check what happens for - * group selections return StructureFrequency.extractProfile( - * aa.groupRef.consensusData[column], aa.groupRef - * .getIgnoreGapsConsensus()); } - */ - // TODO extend annotation row to enable dynamic and static profile data - // to - // be stored - if (aa.groupRef == null && aa.sequenceRef == null - && hStrucConsensus != null - && hStrucConsensus.length > column) - { - return StructureFrequency.extractProfile(hStrucConsensus[column], - av_ignoreGapsConsensus); - } + return StructureFrequency.extractProfile(hStrucConsensus[column], + av_ignoreGapsConsensus); } - + } + return null; } @@ -570,18 +578,18 @@ public class AnnotationRenderer // settings appropriately // TODO: generalise this to have render styles for consensus/profile // data - if (row.groupRef != null && - (row == row.groupRef.getConsensus() || - (row.groupRef.getSSConsensus(null) !=null && row.groupRef.getSSConsensus(null).contains(row)))) + if (row.groupRef != null && (row == row.groupRef.getConsensus() + || (row.groupRef.getSSConsensus(null) != null + && row.groupRef.getSSConsensus(null).contains(row)))) { renderHistogram = row.groupRef.isShowConsensusHistogram(); renderProfile = row.groupRef.isShowSequenceLogo(); normaliseProfile = row.groupRef.isNormaliseSequenceLogo(); } - else if (row == consensusAnnot - || row == structConsensusAnnot - || row == complementConsensusAnnot - || (ssConsensusAnnot!=null && ssConsensusAnnot.contains(row))) + else if (row == consensusAnnot || row == structConsensusAnnot + || row == complementConsensusAnnot + || (ssConsensusAnnot != null + && ssConsensusAnnot.contains(row))) { renderHistogram = av_renderHistogram; renderProfile = av_renderProfile; @@ -1568,13 +1576,12 @@ public class AnnotationRenderer * {profile type, #values, total count, char1, pct1, char2, pct2...} */ int profl[] = getProfileFor(_aa, column); - - // just try to draw the logo if profl is not null if (profl != null && profl[2] != 0) { - // TODO do we ever have different profiles for different columns ? Move up to where we set _aa_is_dssp3 + // TODO do we ever have different profiles for different columns ? + // Move up to where we set _aa_is_dssp3 boolean isStructureProfile = profl[0] == AlignmentAnnotation.STRUCTURE_PROFILE; boolean isCdnaProfile = profl[0] == AlignmentAnnotation.CDNA_PROFILE; float ht = normaliseProfile ? y - _aa.graphHeight : y1; @@ -1651,8 +1658,11 @@ public class AnnotationRenderer .codonTranslate(s); colour = profcolour.findColour(codonTranslation.charAt(0), column, null); - } else if(_aa_is_dssp3) { - // TODO - would be nice to get rid of the special 'findSSColour' here ? + } + else if (_aa_is_dssp3) + { + // TODO - would be nice to get rid of the special 'findSSColour' + // here ? colour = profcolour.findSSColour(dc[0], column); } else diff --git a/src/jalview/renderer/ResidueShader.java b/src/jalview/renderer/ResidueShader.java index 0b191ec..1feed89 100644 --- a/src/jalview/renderer/ResidueShader.java +++ b/src/jalview/renderer/ResidueShader.java @@ -63,18 +63,18 @@ public class ResidueShader implements ResidueShaderI * the consensus data for each column */ private ProfilesI consensus; - + /* * the ss consensus data for each column for each source */ - + private Map ssConsensusProfileMap; /* * if true, apply shading of colour by conservation */ private boolean conservationColouring; - + private boolean consensusSecondaryStructureColouring; @Override @@ -106,7 +106,7 @@ public class ResidueShader implements ResidueShaderI * setting of the By Conservation slider */ private int conservationIncrement = INITIAL_CONSERVATION; - + private int consensusSecondaryStructureThreshold = 30; public ResidueShader(ColourSchemeI cs) @@ -158,7 +158,7 @@ public class ResidueShader implements ResidueShaderI public void setConsensus(ProfilesI cons) { consensus = cons; - + } /** @@ -198,13 +198,14 @@ public class ResidueShader implements ResidueShaderI } } - + @Override - public void setConsensusSecondaryStructureColouring(boolean colourByConsensusSecondaryStructure) + public void setConsensusSecondaryStructureColouring( + boolean colourByConsensusSecondaryStructure) { - + consensusSecondaryStructureColouring = colourByConsensusSecondaryStructure; - + } /** @@ -254,13 +255,13 @@ public class ResidueShader implements ResidueShaderI { consensusSecondaryStructureThreshold = i; } - + @Override public int getConsensusSecondaryStructureThreshold() { return consensusSecondaryStructureThreshold; } - + /** * @see jalview.renderer.ResidueShaderI#getThreshold() */ @@ -303,7 +304,7 @@ public class ResidueShader implements ResidueShaderI return colour; } - + @Override public Color findSSColour(char symbol, int position) { @@ -312,8 +313,9 @@ public class ResidueShader implements ResidueShaderI return Color.white; // Colour is 'None' } - Color colour = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol); - + Color colour = AlignmentUtils + .getSecondaryStructureAnnotationColour(symbol); + /* * apply PID threshold and consensus fading if in force */ @@ -348,8 +350,8 @@ public class ResidueShader implements ResidueShaderI { colour = Color.white; } - - if(consensusSecondaryStructureColouring) + + if (consensusSecondaryStructureColouring) { colour = applyByConsensusSecondaryStructure(colour, column); } @@ -465,35 +467,36 @@ public class ResidueShader implements ResidueShaderI return ColorUtils.bleachColour(currentColour, bleachFactor); } - - - protected Color applyByConsensusSecondaryStructure(Color currentColour, int column) + + protected Color applyByConsensusSecondaryStructure(Color currentColour, + int column) { - if (ssConsensusProfileMap == null && - ssConsensusProfileMap.get(Constants.SS_ALL_PROVIDERS) == null) + if (ssConsensusProfileMap == null && ssConsensusProfileMap + .get(Constants.SS_ALL_PROVIDERS) == null) { return currentColour; } - - ProfilesI consensusSSProfileForAllSources = - ssConsensusProfileMap.get(Constants.SS_ALL_PROVIDERS); + + ProfilesI consensusSSProfileForAllSources = ssConsensusProfileMap + .get(Constants.SS_ALL_PROVIDERS); ProfileI profile = consensusSSProfileForAllSources.get(column); - - if(profile != null) - { - float pid = profile.getSSPercentageIdentity(ignoreGaps); - if(pid == 0) { - return Color.white; - } + if (profile != null) + { + float pid = profile.getSSPercentageIdentity(ignoreGaps); + + if (pid == 0) + { + return Color.white; + } - float bleachFactor = 1f - (pid/100); - bleachFactor *= (consensusSecondaryStructureThreshold/20); + float bleachFactor = 1f - (pid / 100); + bleachFactor *= (consensusSecondaryStructureThreshold / 20); + + return ColorUtils.bleachColour(currentColour, bleachFactor); - return ColorUtils.bleachColour(currentColour, bleachFactor); - } - + return currentColour; } @@ -521,7 +524,8 @@ public class ResidueShader implements ResidueShaderI return ssConsensusProfileMap; } - public void setSSConsensusProfileMap(Map ssConsensusProfileMap) + public void setSSConsensusProfileMap( + Map ssConsensusProfileMap) { this.ssConsensusProfileMap = ssConsensusProfileMap; } diff --git a/src/jalview/renderer/ResidueShaderI.java b/src/jalview/renderer/ResidueShaderI.java index c35f208..8e6c754 100644 --- a/src/jalview/renderer/ResidueShaderI.java +++ b/src/jalview/renderer/ResidueShaderI.java @@ -34,8 +34,9 @@ public interface ResidueShaderI { public abstract void setConsensus(ProfilesI cons); - - public abstract void setSSConsensusProfileMap(Map ssConsensusProfileMap); + + public abstract void setSSConsensusProfileMap( + Map ssConsensusProfileMap); public abstract boolean conservationApplied(); diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java index 04097a8..8e64f8f 100755 --- a/src/jalview/schemes/ClustalxColourScheme.java +++ b/src/jalview/schemes/ClustalxColourScheme.java @@ -364,62 +364,72 @@ public class ClustalxColourScheme extends ResidueColourScheme { return false; } + public String toRuleRep() { makeColours(); - HashMap cols=new HashMap(); - for (String res:ResidueProperties.aa) { + HashMap cols = new HashMap(); + for (String res : ResidueProperties.aa) + { StringBuilder sb = new StringBuilder(); - - int rnum=ResidueProperties.aaIndex[res.charAt(0)]; - if (rnum<0 || rnum>=residueColour.length) + + int rnum = ResidueProperties.aaIndex[res.charAt(0)]; + if (rnum < 0 || rnum >= residueColour.length) { continue; } - + ConsensusColour cc = residueColour[rnum]; - if (cc==null) + if (cc == null) { continue; } - //sb.append("Residue "+res+" ("+rnum+")"); - //sb.append("\t"); + // sb.append("Residue "+res+" ("+rnum+")"); + // sb.append("\t"); sb.append(cc.c.toString()); - double f=0; + double f = 0; sb.append("\t"); - for (Consensus cons: cc.cons) { - if (cons.threshold==0 || f!=cons.threshold) + for (Consensus cons : cc.cons) + { + if (cons.threshold == 0 || f != cons.threshold) { - if (f!=0) + if (f != 0) { - sb.append("}, {"); - } else { - sb.append("{"); + sb.append("}, {"); + } + else + { + sb.append("{"); } - sb.append(cons.threshold); - sb.append(","); - f=cons.threshold; - } else { + sb.append(cons.threshold); + sb.append(","); + f = cons.threshold; + } + else + { sb.append(","); } sb.append(cons.maskstr); } sb.append("}"); - String clxrep=sb.toString(); + String clxrep = sb.toString(); String xres = cols.get(clxrep); - if (xres==null) { xres = "";} - xres+=res; + if (xres == null) + { + xres = ""; + } + xres += res; cols.put(clxrep, xres); } StringBuilder sb = new StringBuilder(); - for (String clxrep:cols.keySet()) + for (String clxrep : cols.keySet()) { sb.append(cols.get(clxrep)); sb.append("\t"); sb.append(clxrep); sb.append("\n"); - + } return sb.toString(); } diff --git a/src/jalview/schemes/ResidueProperties.java b/src/jalview/schemes/ResidueProperties.java index 2fcb95f..9d83069 100755 --- a/src/jalview/schemes/ResidueProperties.java +++ b/src/jalview/schemes/ResidueProperties.java @@ -41,7 +41,7 @@ public class ResidueProperties public static final int[] nucleotideIndex; public static final int[] purinepyrimidineIndex; - + public static final int[] secondaryStructureIndex; public static final Map aa3Hash = new HashMap<>(); @@ -197,13 +197,13 @@ public class ResidueProperties purinepyrimidineIndex['N'] = 2; purinepyrimidineIndex['n'] = 2; } - + static { secondaryStructureIndex = new int[255]; for (int i = 0; i < 255; i++) { - secondaryStructureIndex[i] = 3; + secondaryStructureIndex[i] = 3; } secondaryStructureIndex['H'] = 0; @@ -398,12 +398,12 @@ public class ResidueProperties Color.white, // all other nucleotides Color.white // Gap }; - - //Secondary structure - public static final Color[] secondarystructure = { Color.red, // H - Color.green, // E - Color.gray // C - }; + + // Secondary structure + public static final Color[] secondarystructure = { Color.red, // H + Color.green, // E + Color.gray // C + }; // Zappo public static final Color[] zappo = { Color.pink, // A diff --git a/src/jalview/structure/StructureSelectionManager.java b/src/jalview/structure/StructureSelectionManager.java index 73c4c0f..c3c3b3e 100644 --- a/src/jalview/structure/StructureSelectionManager.java +++ b/src/jalview/structure/StructureSelectionManager.java @@ -696,18 +696,22 @@ public class StructureSelectionManager StructureMapping nwMapping = getNWMappings(seq, pdbFile, maxChainId, maxChain, pdb, maxAlignseq); seqToStrucMapping.add(nwMapping); - ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); + ds.addPDBId(maxChain.sequence.getAllPDBEntries().get(0)); } - - //JAL-4392 TODO: Unable to match PDBProvider with Annotation without matching struct file path + + // JAL-4392 TODO: Unable to match PDBProvider with Annotation without + // matching struct file path String ssAnnotDescriptionInPDB = null; - String ssStructFilePathNameInPDB = pdb.getInFile(); //Structure file name in PDB data model - //Secondary structure annotations in pdb data model - AlignmentAnnotation[] ssAnnotationsInPDB = pdb.getSeqs().get(0).getAnnotation(Constants.SS_ANNOTATION_LABEL); - if(ssAnnotationsInPDB != null && ssAnnotationsInPDB.length>0) { + String ssStructFilePathNameInPDB = pdb.getInFile(); // Structure file name + // in PDB data model + // Secondary structure annotations in pdb data model + AlignmentAnnotation[] ssAnnotationsInPDB = pdb.getSeqs().get(0) + .getAnnotation(Constants.SS_ANNOTATION_LABEL); + if (ssAnnotationsInPDB != null && ssAnnotationsInPDB.length > 0) + { ssAnnotDescriptionInPDB = ssAnnotationsInPDB[0].description; } - + // Match the PDB entry using file path in the pdb data model and get the // provider if (ssStructFilePathNameInPDB != null @@ -729,7 +733,8 @@ public class StructureSelectionManager // Add provider value as property to the ss annotation if (provider != null) { - // TODO - JAL-2880 JAL-4441 this should be applied to all structure derived annotations, not just secondary structure! + // TODO - JAL-2880 JAL-4441 this should be applied to all structure + // derived annotations, not just secondary structure! AlignmentAnnotation[] ssAnnotList = ds .getAnnotation(Constants.SS_ANNOTATION_LABEL); if (ssAnnotList != null) @@ -751,8 +756,7 @@ public class StructureSelectionManager } } } - - + if (forStructureView) { for (StructureMapping sm : seqToStrucMapping) diff --git a/src/jalview/util/Constants.java b/src/jalview/util/Constants.java index 27513ab..5f01895 100644 --- a/src/jalview/util/Constants.java +++ b/src/jalview/util/Constants.java @@ -28,31 +28,35 @@ import java.util.Map; */ public class Constants { - - //character used to represent secondary structures + + // character used to represent secondary structures public static final char HELIX = 'H'; + public static final char SHEET = 'E'; + public static final char COIL = 'C'; - //label in secondary structure annotation data model from 3d structures + // label in secondary structure annotation data model from 3d structures public static final String SS_ANNOTATION_LABEL = "Secondary Structure"; - - //label in secondary structure annotation data model from JPred - public static final String SS_ANNOTATION_FROM_JPRED_LABEL = "jnetpred"; - + + // label in secondary structure annotation data model from JPred + public static final String SS_ANNOTATION_FROM_JPRED_LABEL = "jnetpred"; + public static final Map SECONDARY_STRUCTURE_LABELS = new HashMap<>(); - static { - SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_LABEL, "3D Structures"); - SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_FROM_JPRED_LABEL, "JPred"); - // Add other secondary structure labels here if needed - } - - public static final String SS_PROVIDER_PROPERTY = "SS_PROVIDER"; - - //generic secondary structure provider options - public static final String SS_ALL_PROVIDERS = "All"; + static + { + SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_LABEL, "3D Structures"); + SECONDARY_STRUCTURE_LABELS.put(SS_ANNOTATION_FROM_JPRED_LABEL, "JPred"); + // Add other secondary structure labels here if needed + } + + public static final String SS_PROVIDER_PROPERTY = "SS_PROVIDER"; + + // generic secondary structure provider options + public static final String SS_ALL_PROVIDERS = "All"; + public static final String SS_NONE_PROVIDER = "None"; - - //Secondary structure consensus label + + // Secondary structure consensus label public static final String SECONDARY_STRUCTURE_CONSENSUS_LABEL = "Secondary Structure Consensus"; } diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 94a1424..80c9957 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -252,7 +252,7 @@ public abstract class AlignmentViewport { return viewStyle.getAbovePIDThreshold(); } - + @Override public boolean getByConsensusSecondaryStructureSelected() { @@ -287,8 +287,8 @@ public abstract class AlignmentViewport public int getIncrement() { return viewStyle.getIncrement(); - } - + } + /** * @param inc * @see jalview.api.ViewStyleI#setConsensusSecondaryStructureThreshold(int) @@ -298,7 +298,7 @@ public abstract class AlignmentViewport { viewStyle.setConsensusSecondaryStructureThreshold(val); } - + /** * @return * @see jalview.api.ViewStyleI#getConsensusSecondaryStructureThreshold() @@ -307,8 +307,7 @@ public abstract class AlignmentViewport public int getConsensusSecondaryStructureThreshold() { return viewStyle.getConsensusSecondaryStructureThreshold(); - } - + } /** * @param b @@ -409,7 +408,7 @@ public abstract class AlignmentViewport { viewStyle.setAbovePIDThreshold(b); } - + @Override public void setByConsensusSecondaryStructureSelected(boolean b) { @@ -743,7 +742,7 @@ public abstract class AlignmentViewport } protected AlignmentAnnotation consensus; - + protected List secondaryStructureConsensus; protected AlignmentAnnotation complementConsensus; @@ -757,7 +756,7 @@ public abstract class AlignmentViewport protected AlignmentAnnotation quality; protected AlignmentAnnotation[] groupConsensus; - + protected AlignmentAnnotation[] groupSSConsensus; protected AlignmentAnnotation[] groupConservation; @@ -766,10 +765,8 @@ public abstract class AlignmentViewport * results of alignment consensus analysis for visible portion of view */ protected ProfilesI hconsensus = null; - + protected Map hSSConsensusProfileMap = null; - - /** * results of cDNA complement consensus visible portion of view @@ -789,7 +786,7 @@ public abstract class AlignmentViewport { hconservation = cons; } - + @Override public List getSecondaryStructureSources() { @@ -802,15 +799,17 @@ public abstract class AlignmentViewport { viewStyle.setSecondaryStructureSources(secondaryStructureSources); } - + protected void setSecondaryStructureSources(AlignmentAnnotation[] aa) { List sources = null; - - if(aa!=null) { + + if (aa != null) + { sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa); - if(sources != null) { - sources.add(0,Constants.SS_ALL_PROVIDERS); + if (sources != null) + { + sources.add(0, Constants.SS_ALL_PROVIDERS); viewStyle.setSecondaryStructureSources(sources); } } @@ -833,13 +832,14 @@ public abstract class AlignmentViewport { this.hconsensus = hconsensus; } - + @Override - public void setSequenceSSConsensusHash(Map hSSConsensusProfileMap) + public void setSequenceSSConsensusHash( + Map hSSConsensusProfileMap) { this.hSSConsensusProfileMap = hSSConsensusProfileMap; } - + @Override public void setComplementConsensusHash( Hashtable[] hconsensus) @@ -858,7 +858,6 @@ public abstract class AlignmentViewport { return hSSConsensusProfileMap; } - @Override public Hashtable[] getComplementConsensusHash() @@ -898,13 +897,11 @@ public abstract class AlignmentViewport return consensus; } - @Override public List getAlignmentSecondaryStructureConsensusAnnotation() { return secondaryStructureConsensus; } - @Override public AlignmentAnnotation getAlignmentGapAnnotation() @@ -997,9 +994,6 @@ public abstract class AlignmentViewport } } } - - - /** * trigger update of Secondary Structure consensus annotation @@ -1012,21 +1006,31 @@ public abstract class AlignmentViewport return; } List ssSources = viewStyle.getSecondaryStructureSources(); - if (secondaryStructureConsensus.size() != ssSources.size()) { - - for(String source : ssSources) { + if (secondaryStructureConsensus.size() != ssSources.size()) + { + + for (String source : ssSources) + { boolean ssConsensusForSourcePresent = false; - for(AlignmentAnnotation aa : secondaryStructureConsensus) { - if(aa.description.startsWith(source)) { + for (AlignmentAnnotation aa : secondaryStructureConsensus) + { + if (aa.description.startsWith(source)) + { ssConsensusForSourcePresent = true; break; } } - - if(!ssConsensusForSourcePresent) { - AlignmentAnnotation ssConsensus = new AlignmentAnnotation(MessageManager.getString("label.ssconsensus_label") + " "+source, - source + " " + MessageManager.getString("label.ssconsensus_descr"), - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + + if (!ssConsensusForSourcePresent) + { + AlignmentAnnotation ssConsensus = new AlignmentAnnotation( + MessageManager.getString("label.ssconsensus_label") + " " + + source, + source + " " + + MessageManager + .getString("label.ssconsensus_descr"), + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); ssConsensus.hasText = true; ssConsensus.autoCalculated = true; @@ -1035,19 +1039,19 @@ public abstract class AlignmentViewport { ssConsensus.visible = true; alignment.addAnnotation(ssConsensus); - + } } } } - if (calculator - .getRegisteredWorkersOfClass(SecondaryStructureConsensusThread.class) == null) + if (calculator.getRegisteredWorkersOfClass( + SecondaryStructureConsensusThread.class) == null) { - calculator.registerWorker(new SecondaryStructureConsensusThread(this, ap)); + calculator.registerWorker( + new SecondaryStructureConsensusThread(this, ap)); } ap.adjustAnnotationHeight(); - } // --------START Structure Conservation @@ -1154,7 +1158,6 @@ public abstract class AlignmentViewport * should consensus rows be shown for groups */ protected boolean showGroupConsensus = false; - protected boolean showGroupSSConsensus = false; @@ -1162,7 +1165,7 @@ public abstract class AlignmentViewport * should consensus profile be rendered by default */ protected boolean showSequenceLogo = false; - + /** * should consensus profile be rendered normalised to row height */ @@ -1172,7 +1175,7 @@ public abstract class AlignmentViewport * should consensus histograms be rendered by default */ protected boolean showConsensusHistogram = true; - + /** * @return the showConsensusProfile */ @@ -1181,7 +1184,7 @@ public abstract class AlignmentViewport { return showSequenceLogo; } - + /** * @param showSequenceLogo * the new value @@ -1196,14 +1199,15 @@ public abstract class AlignmentViewport calculator.updateAnnotationFor(ConsensusThread.class); calculator.updateAnnotationFor(ComplementConsensusThread.class); calculator.updateAnnotationFor(StrucConsensusThread.class); - - //to do - calculator.updateAnnotationFor(SecondaryStructureConsensusThread.class); + // to do + + calculator + .updateAnnotationFor(SecondaryStructureConsensusThread.class); } this.showSequenceLogo = showSequenceLogo; } - + /** * @param showConsensusHistogram * the showConsensusHistogram to set @@ -1237,13 +1241,12 @@ public abstract class AlignmentViewport { return showGroupConsensus; } - + public boolean isShowGroupSSConsensus() { return showGroupSSConsensus; } - /** * @param showGroupConsensus * the showGroupConsensus to set @@ -1252,12 +1255,12 @@ public abstract class AlignmentViewport { this.showGroupConsensus = showGroupConsensus; } - + public void setShowGroupSSConsensus(boolean showGroupSSConsensus) { this.showGroupSSConsensus = showGroupSSConsensus; } - + /** * @param showSSConsensus * the showSSConsensus to set @@ -1266,7 +1269,7 @@ public abstract class AlignmentViewport { this.showSSConsensus = showSSConsensus; } - + /** * * @return flag to indicate if the consensus histogram should be rendered by @@ -1501,7 +1504,7 @@ public abstract class AlignmentViewport protected boolean showQuality = true; - protected boolean showConsensus = true; + protected boolean showConsensus = true; protected boolean showSSConsensus = true; @@ -2149,19 +2152,26 @@ public abstract class AlignmentViewport setSecondaryStructureSources(alignment.getAlignmentAnnotation()); List secondaryStructureSources = getSecondaryStructureSources(); - if(secondaryStructureSources!=null) { + if (secondaryStructureSources != null) + { secondaryStructureConsensus = new ArrayList(); - for (String ssSource : secondaryStructureSources) { - - AlignmentAnnotation ssConsensus = new AlignmentAnnotation(MessageManager.getString("label.ssconsensus_label") + " "+ssSource, - ssSource + " " + MessageManager.getString("label.ssconsensus_descr"), - new Annotation[1], 0f, 100f, AlignmentAnnotation.BAR_GRAPH); + for (String ssSource : secondaryStructureSources) + { + + AlignmentAnnotation ssConsensus = new AlignmentAnnotation( + MessageManager.getString("label.ssconsensus_label") + " " + + ssSource, + ssSource + " " + + MessageManager + .getString("label.ssconsensus_descr"), + new Annotation[1], 0f, 100f, + AlignmentAnnotation.BAR_GRAPH); secondaryStructureConsensus.add(ssConsensus); } - + } - + initConsensus(consensus); initSSConsensus(secondaryStructureConsensus); initGapCounts(); @@ -2169,7 +2179,6 @@ public abstract class AlignmentViewport } } - /** * If this is a protein alignment and there are mappings to cDNA, adds the * cDNA consensus annotation and returns true, else returns false. @@ -2220,21 +2229,24 @@ public abstract class AlignmentViewport alignment.addAnnotation(aa); } } - - private void initSSConsensus(List secondaryStructureConsensuses) + + private void initSSConsensus( + List secondaryStructureConsensuses) { - if(secondaryStructureConsensuses == null) { + if (secondaryStructureConsensuses == null) + { return; } - for(AlignmentAnnotation aa : secondaryStructureConsensuses) { + for (AlignmentAnnotation aa : secondaryStructureConsensuses) + { aa.hasText = true; aa.autoCalculated = true; - + if (showSSConsensus) { alignment.addAnnotation(aa); } - + } } @@ -2436,21 +2448,25 @@ public abstract class AlignmentViewport updateCalcs = true; alignment.addAnnotation(sg.getConsensus(), 0); } - if(sscons) - { + if (sscons) + { updateCalcs = true; List secondaryStructureSources = getSecondaryStructureSources(); - if(secondaryStructureSources !=null) { - List ssAa = sg.getSSConsensus(secondaryStructureSources); - if(ssAa != null) { - for(AlignmentAnnotation aa : ssAa) { + if (secondaryStructureSources != null) + { + List ssAa = sg + .getSSConsensus(secondaryStructureSources); + if (ssAa != null) + { + for (AlignmentAnnotation aa : ssAa) + { // Setting annotation visibility to true for the secondary // structure consensus for all providers if (aa.label.contains(Constants.SS_ALL_PROVIDERS)) { aa.visible = true; } - alignment.addAnnotation(aa, 0); + alignment.addAnnotation(aa, 0); } } } @@ -3243,8 +3259,8 @@ public abstract class AlignmentViewport + ((ignoreGapsInConsensusCalculation) ? " without gaps" : "")); return sq; } - - //to do jal-4386 + + // to do jal-4386 public SequenceI getSSConsensusSeq() { if (secondaryStructureConsensus == null) @@ -3256,23 +3272,23 @@ public abstract class AlignmentViewport return null; } StringBuffer seqs = new StringBuffer(); -// for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++) -// { -// Annotation annotation = secondaryStructureConsensus.annotations[i]; -// if (annotation != null) -// { -// String description = annotation.description; -// if (description != null && description.startsWith("[")) -// { -// // consensus is a tie - just pick the first one -// seqs.append(description.charAt(1)); -// } -// else -// { -// seqs.append(annotation.displayCharacter); -// } -// } -// } + // for (int i = 0; i < secondaryStructureConsensus.annotations.length; i++) + // { + // Annotation annotation = secondaryStructureConsensus.annotations[i]; + // if (annotation != null) + // { + // String description = annotation.description; + // if (description != null && description.startsWith("[")) + // { + // // consensus is a tie - just pick the first one + // seqs.append(description.charAt(1)); + // } + // else + // { + // seqs.append(annotation.displayCharacter); + // } + // } + // } SequenceI sq = new Sequence("Sec Str Consensus", seqs.toString()); sq.setDescription("Percentage Identity Sec Str Consensus " diff --git a/src/jalview/viewmodel/PaSiMapModel.java b/src/jalview/viewmodel/PaSiMapModel.java index a0e5174..8568af4 100644 --- a/src/jalview/viewmodel/PaSiMapModel.java +++ b/src/jalview/viewmodel/PaSiMapModel.java @@ -69,8 +69,8 @@ public class PaSiMapModel * @param modelName * @param params */ - public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, boolean nuc, - ScoreModelI modelName) + public PaSiMapModel(AlignmentViewport seqData, SequenceI[] sqs, + boolean nuc, ScoreModelI modelName) { inputData = seqData; seqs = sqs; @@ -79,8 +79,8 @@ public class PaSiMapModel } /** - * Performs the PaSiMap calculation (in the same thread) and extracts result data - * needed for visualisation by PaSiMapPanel + * Performs the PaSiMap calculation (in the same thread) and extracts result + * data needed for visualisation by PaSiMapPanel */ public void calculate(PairwiseAlignPanel pap) { @@ -100,7 +100,8 @@ public class PaSiMapModel top = width; points = new Vector<>(); - Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, 1); + Point[] scores = pasimap.getComponents(width - 1, width - 2, width - 3, + 1); for (int i = 0; i < height; i++) { @@ -142,8 +143,9 @@ public class PaSiMapModel /** * Updates the 3D coordinates for the list of points to the given dimensions. * Principal dimension is getTop(). Next greatest eigenvector is getTop()-1. - * Note - pasimap.getComponents starts counting the spectrum from rank-2 to zero, - * rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 ..) + * Note - pasimap.getComponents starts counting the spectrum from rank-2 to + * zero, rather than rank-1, so getComponents(dimN ...) == updateRcView(dimN+1 + * ..) * * @param dim1 * @param dim2 @@ -207,13 +209,15 @@ public class PaSiMapModel csv.append("\"" + seqs[s].getName() + "\""); if (!transformed) { - double[] fl = pasimap.component(s); - for (int d = fl.length - 1; d >= 0; d--) - { - csv.append(","); - csv.append(fl[d]); - } - } else { + double[] fl = pasimap.component(s); + for (int d = fl.length - 1; d >= 0; d--) + { + csv.append(","); + csv.append(fl[d]); + } + } + else + { Point p = points.get(s).coord; csv.append(",").append(p.x); csv.append(",").append(p.y); diff --git a/src/jalview/viewmodel/styles/ViewStyle.java b/src/jalview/viewmodel/styles/ViewStyle.java index c9a1ad3..1e803b8 100644 --- a/src/jalview/viewmodel/styles/ViewStyle.java +++ b/src/jalview/viewmodel/styles/ViewStyle.java @@ -66,7 +66,7 @@ public class ViewStyle implements ViewStyleI private boolean colourByReferenceSeq = false; boolean conservationColourSelected = false; - + boolean byConsensusSecondaryStructureSelected = false; /** @@ -75,7 +75,7 @@ public class ViewStyle implements ViewStyleI private boolean displayReferenceSeq = false; private int increment; - + private int consensusSecondaryStructureThreshold; /** @@ -193,8 +193,10 @@ public class ViewStyle implements ViewStyleI setColourAppliesToAllGroups(vs.getColourAppliesToAllGroups()); setColourByReferenceSeq(vs.isColourByReferenceSeq()); setColourText(vs.getColourText()); - setByConsensusSecondaryStructureSelected(vs.getByConsensusSecondaryStructureSelected()); - setConsensusSecondaryStructureThreshold(vs.getConsensusSecondaryStructureThreshold()); + setByConsensusSecondaryStructureSelected( + vs.getByConsensusSecondaryStructureSelected()); + setConsensusSecondaryStructureThreshold( + vs.getConsensusSecondaryStructureThreshold()); setConservationColourSelected(vs.isConservationColourSelected()); setConservationSelected(vs.getConservationSelected()); setDisplayReferenceSeq(vs.isDisplayReferenceSeq()); @@ -262,14 +264,16 @@ public class ViewStyle implements ViewStyleI && getColourText() == vs.getColourText() && isConservationColourSelected() == vs .isConservationColourSelected() - && getByConsensusSecondaryStructureSelected() == vs.getByConsensusSecondaryStructureSelected() + && getByConsensusSecondaryStructureSelected() == vs + .getByConsensusSecondaryStructureSelected() && getConservationSelected() == vs.getConservationSelected() && isDisplayReferenceSeq() == vs.isDisplayReferenceSeq() && getFontSize() == vs.getFontSize() && getFontStyle() == vs.getFontStyle() && getIdWidth() == vs.getIdWidth() && getIncrement() == vs.getIncrement() - && getConsensusSecondaryStructureThreshold() == vs.getConsensusSecondaryStructureThreshold() + && getConsensusSecondaryStructureThreshold() == vs + .getConsensusSecondaryStructureThreshold() && isRenderGaps() == vs.isRenderGaps() && isRightAlignIds() == vs.isRightAlignIds() && getScaleAboveWrapped() == vs.getScaleAboveWrapped() @@ -298,7 +302,8 @@ public class ViewStyle implements ViewStyleI && isUpperCasebold() == vs.isUpperCasebold() && getWrapAlignment() == vs.getWrapAlignment() && getWrappedWidth() == vs.getWrappedWidth() - && getSecondaryStructureSources() == vs.getSecondaryStructureSources() + && getSecondaryStructureSources() == vs + .getSecondaryStructureSources() && isShowStructureProvider() == vs.isShowStructureProvider()); /* * and compare non-primitive types; syntax below will match null with null @@ -386,11 +391,11 @@ public class ViewStyle implements ViewStyleI private boolean showComplementFeatures; private boolean showComplementFeaturesOnTop; - + /** - * secondary structure annotation rows shown in the view - */ - private List secondaryStructureSources = List.of( new String[0] ); + * secondary structure annotation rows shown in the view + */ + private List secondaryStructureSources = List.of(new String[0]); private boolean showStructureProvider; @@ -410,6 +415,7 @@ public class ViewStyle implements ViewStyleI { return byConsensusSecondaryStructureSelected; } + /** * DOCUMENT ME! * @@ -582,13 +588,12 @@ public class ViewStyle implements ViewStyleI { return threshold; } - + @Override public int getConsensusSecondaryStructureThreshold() { return consensusSecondaryStructureThreshold; } - /** * @return the thresholdTextColour @@ -708,7 +713,7 @@ public class ViewStyle implements ViewStyleI { abovePIDThreshold = b; } - + @Override public void setByConsensusSecondaryStructureSelected(boolean b) { @@ -808,7 +813,7 @@ public class ViewStyle implements ViewStyleI { increment = inc; } - + /** * * @param val @@ -820,7 +825,6 @@ public class ViewStyle implements ViewStyleI { consensusSecondaryStructureThreshold = val; } - /** * DOCUMENT ME! @@ -1195,7 +1199,7 @@ public class ViewStyle implements ViewStyleI { return showComplementFeaturesOnTop; } - + @Override public List getSecondaryStructureSources() { @@ -1203,7 +1207,8 @@ public class ViewStyle implements ViewStyleI } @Override - public void setSecondaryStructureSources(List secondaryStructureSources) + public void setSecondaryStructureSources( + List secondaryStructureSources) { this.secondaryStructureSources = secondaryStructureSources; } @@ -1211,8 +1216,9 @@ public class ViewStyle implements ViewStyleI @Override public void setShowStructureProvider(boolean showStructureProvider) { - this.showStructureProvider=showStructureProvider; + this.showStructureProvider = showStructureProvider; } + @Override public boolean isShowStructureProvider() { diff --git a/src/jalview/workers/SecondaryStructureConsensusThread.java b/src/jalview/workers/SecondaryStructureConsensusThread.java index 6629f27..13e22fd 100644 --- a/src/jalview/workers/SecondaryStructureConsensusThread.java +++ b/src/jalview/workers/SecondaryStructureConsensusThread.java @@ -92,7 +92,7 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker calcMan.workerComplete(this); return; } - + setSecondaryStructureSources(); eraseSSConsensus(aWidth); computeSSConsensus(alignment); @@ -125,7 +125,8 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker protected void eraseSSConsensus(int aWidth) { List ssConsensuses = getSSConsensusAnnotation(); - for(AlignmentAnnotation ssConsensus : ssConsensuses) { + for (AlignmentAnnotation ssConsensus : ssConsensuses) + { if (ssConsensus != null) { ssConsensus.annotations = new Annotation[aWidth]; @@ -147,13 +148,13 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker SequenceI[] aseqs = getSequences(); int width = alignment.getWidth(); Map hSSConsensusProfileMap = new HashMap(); - List ssSources = getSecondaryStructureSources(); - for(String ssSource : ssSources) { - ProfilesI hSSConsensus = AAFrequency.calculateSS(aseqs, width, 0, width, - true, ssSource); + List ssSources = getSecondaryStructureSources(); + for (String ssSource : ssSources) + { + ProfilesI hSSConsensus = AAFrequency.calculateSS(aseqs, width, 0, + width, true, ssSource); hSSConsensusProfileMap.put(ssSource, hSSConsensus); } - alignViewport.setSequenceSSConsensusHash(hSSConsensusProfileMap); setColourSchemeConsensus(hSSConsensusProfileMap); @@ -170,7 +171,8 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker /** * @param hconsensus */ - protected void setColourSchemeConsensus(Map ssConsensusProfileMap) + protected void setColourSchemeConsensus( + Map ssConsensusProfileMap) { ResidueShaderI cs = alignViewport.getResidueShading(); if (cs != null) @@ -186,9 +188,10 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker */ protected List getSSConsensusAnnotation() { - return alignViewport.getAlignmentSecondaryStructureConsensusAnnotation(); + return alignViewport + .getAlignmentSecondaryStructureConsensusAnnotation(); } - + /** * Get the Consensus annotation for the alignment * @@ -197,16 +200,19 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker protected void setSecondaryStructureSources() { List sources = null; - AlignmentAnnotation[] aa = alignViewport.getAlignment().getAlignmentAnnotation(); - if(aa!=null) { + AlignmentAnnotation[] aa = alignViewport.getAlignment() + .getAlignmentAnnotation(); + if (aa != null) + { sources = AlignmentUtils.extractSSSourceInAlignmentAnnotation(aa); - if(sources != null) { + if (sources != null) + { sources.add(0, Constants.SS_ALL_PROVIDERS); alignViewport.setSecondaryStructureSources(sources); } } } - + protected List getSecondaryStructureSources() { return alignViewport.getSecondaryStructureSources(); @@ -236,29 +242,34 @@ public class SecondaryStructureConsensusThread extends AlignCalcWorker { List ssConsensuses = getSSConsensusAnnotation(); Map ssConsensusProfileMap = getViewportSSConsensus(); - for(AlignmentAnnotation ssConsensus : ssConsensuses) { + for (AlignmentAnnotation ssConsensus : ssConsensuses) + { ProfilesI ssConsensusProfile = null; - for(String source: ssConsensusProfileMap.keySet()) { - if(ssConsensus.description.startsWith(source)) { + for (String source : ssConsensusProfileMap.keySet()) + { + if (ssConsensus.description.startsWith(source)) + { ssConsensusProfile = ssConsensusProfileMap.get(source); break; } } - if(ssConsensusProfile==null) { - continue; - } - if (immediate || !calcMan.isWorking(this) && ssConsensus != null - && ssConsensusProfile != null) - { - if(ssConsensusProfile.get(0)!=null) - ssConsensus.setNoOfSequencesIncluded(ssConsensusProfile.get(0).getSeqWithSSCount()); - deriveSSConsensus(ssConsensus, ssConsensusProfile); - AlignmentAnnotation gap = getGapAnnotation(); - if (gap != null) + if (ssConsensusProfile == null) { - deriveGap(gap, ssConsensusProfile); + continue; + } + if (immediate || !calcMan.isWorking(this) && ssConsensus != null + && ssConsensusProfile != null) + { + if (ssConsensusProfile.get(0) != null) + ssConsensus.setNoOfSequencesIncluded( + ssConsensusProfile.get(0).getSeqWithSSCount()); + deriveSSConsensus(ssConsensus, ssConsensusProfile); + AlignmentAnnotation gap = getGapAnnotation(); + if (gap != null) + { + deriveGap(gap, ssConsensusProfile); + } } - } } } diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index ab8fbf5..79dfb0a 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -5,7 +5,6 @@ // Generated on: 2024.07.25 at 04:43:38 PM BST // - package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -18,11 +17,16 @@ 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>
@@ -61,286 +65,295 @@ 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;
+
+  /**
+   * 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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the alcodon property.
+   */
+  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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the alcodMap property.
+   */
+  public List getAlcodMap()
+  {
+    if (alcodMap == null)
+    {
+      alcodMap = new ArrayList();
+    }
+    return this.alcodMap;
+  }
 
-    protected List alcodon;
-    protected List 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
+  {
 
     /**
-     * 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);
-     * 
    
+     * a Mapping entry and an associated protein sequence
      * 
+     */
+    @XmlElement(name = "Mapping", required = true)
+    protected Mapping mapping;
+
+    /**
+     * internal jalview id for the dnasq for this mapping.
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link AlcodonFrame.Alcodon }
-     * 
    
+     */
+    @XmlAttribute(name = "dnasq", required = true)
+    protected String dnasq;
+
+    /**
+     * a Mapping entry and an associated protein sequence
      * 
+     * @return possible object is {@link Mapping }
      * 
-     * @return
-     *     The value of the alcodon property.
      */
-    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);
-     * 
    
-     * 
+     * Sets the value of the mapping property.
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link AlcodonFrame.AlcodMap }
-     * 
    
+     * @param value
+     *          allowed object is {@link Mapping }
      * 
-     * 
-     * @return
-     *     The value of the alcodMap property.
+     * @see #getMapping()
      */
-    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
    .
+     * internal jalview id for the dnasq for this mapping.
      * 
-     * 
    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 }
      * 
+     * @see #getDnasq()
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "mapping"
-    })
-    public static class AlcodMap {
+    public void setDnasq(String value)
+    {
+      this.dnasq = value;
+    }
 
-        /**
-         * a Mapping entry and an associated protein
-         * 										sequence
-         * 
-         */
-        @XmlElement(name = "Mapping", required = true)
-        protected Mapping mapping;
-        /**
-         * internal jalview id for the dnasq for this
-         * 									mapping.
-         * 
-         */
-        @XmlAttribute(name = "dnasq", required = true)
-        protected String dnasq;
+  }
 
-        /**
-         * 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 }
-         *     
-         * @see #getMapping()
-         */
-        public void setMapping(Mapping value) {
-            this.mapping = value;
-        }
+    @XmlAttribute(name = "pos1")
+    protected BigInteger pos1;
 
-        /**
-         * internal jalview id for the dnasq for this
-         * 									mapping.
-         * 
-         * @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 }
-         *     
-         * @see #getDnasq()
-         */
-        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;
     }
 
-
     /**
-     * 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).
+     * Sets the value of the pos1 property.
      * 
-     * 
    Java class for anonymous complex type
    .
+     * @param value
+     *          allowed object is {@link BigInteger }
      * 
-     * 
    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>
-     * 
    
+     */
+    public void setPos1(BigInteger value)
+    {
+      this.pos1 = value;
+    }
+
+    /**
+     * Gets the value of the pos2 property.
      * 
+     * @return possible 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;
-        }
+    public BigInteger getPos2()
+    {
+      return pos2;
+    }
 
-        /**
-         * Gets the value of the pos3 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link BigInteger }
-         *     
-         */
-        public BigInteger getPos3() {
-            return pos3;
-        }
+    /**
+     * Sets the value of the pos2 property.
+     * 
+     * @param value
+     *          allowed object is {@link BigInteger }
+     * 
+     */
+    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 4c2a9a3..f96a980 100644
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,11 +16,16 @@ 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>
@@ -70,772 +74,796 @@ 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)
+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;
+
+  /**
+   * height in pixels for the graph if this is a graph-type annotation.
+   * 
+   */
+  @XmlAttribute(name = "graphHeight")
+  protected Integer graphHeight;
+
+  @XmlAttribute(name = "id")
+  protected String id;
+
+  @XmlAttribute(name = "scoreOnly")
+  protected Boolean scoreOnly;
+
+  @XmlAttribute(name = "score")
+  protected Double score;
+
+  @XmlAttribute(name = "visible")
+  protected Boolean visible;
+
+  @XmlAttribute(name = "centreColLabels")
+  protected Boolean centreColLabels;
+
+  @XmlAttribute(name = "scaleColLabels")
+  protected Boolean scaleColLabels;
+
+  @XmlAttribute(name = "showAllColLabels")
+  protected Boolean showAllColLabels;
+
+  /**
+   * is an autocalculated annotation row
+   * 
+   */
+  @XmlAttribute(name = "autoCalculated")
+  protected Boolean autoCalculated;
+
+  /**
+   * is to be shown below the alignment - introduced in Jalview 2.8 for
+   * visualizing T-COFFEE alignment scores
+   * 
+   */
+  @XmlAttribute(name = "belowAlignment")
+  protected Boolean belowAlignment;
+
+  /**
+   * Optional string identifier used to group sets of annotation produced by a
+   * particular calculation. Values are opaque strings but have semantic meaning
+   * to Jalview's renderer, data importer and calculation system.
+   * 
+   */
+  @XmlAttribute(name = "calcId")
+  protected String calcId;
+
+  /**
+   * Gets the value of the annotationElement property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the annotationElement property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getAnnotationElement().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list
+   * {@link AnnotationElement }
+   * 
    
+   * 
+   * 
+   * @return The value of the annotationElement property.
+   */
+  public List getAnnotationElement()
+  {
+    if (annotationElement == null)
+    {
+      annotationElement = new ArrayList();
+    }
+    return this.annotationElement;
+  }
+
+  /**
+   * 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 MapOnAMatrixType }
+   * 
    
+   * 
+   * 
+   * @return The value of the contactmatrix property.
+   */
+  public List getContactmatrix()
+  {
+    if (contactmatrix == null)
+    {
+      contactmatrix = new ArrayList();
+    }
+    return this.contactmatrix;
+  }
+
+  /**
+   * Gets the value of the property property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the property property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getProperty().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link Property }
+   * 
    
+   * 
+   * 
+   * @return The value of the property property.
+   */
+  public List getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList();
+    }
+    return this.property;
+  }
+
+  /**
+   * Gets the value of the graph property.
+   * 
+   */
+  public boolean isGraph()
+  {
+    return graph;
+  }
+
+  /**
+   * Sets the value of the graph property.
+   * 
+   */
+  public void setGraph(boolean value)
+  {
+    this.graph = value;
+  }
+
+  /**
+   * Gets the value of the graphType property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getGraphType()
+  {
+    return graphType;
+  }
+
+  /**
+   * Sets the value of the graphType property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setGraphType(Integer value)
+  {
+    this.graphType = value;
+  }
+
+  /**
+   * Gets the value of the sequenceRef property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSequenceRef()
+  {
+    return sequenceRef;
+  }
+
+  /**
+   * Sets the value of the sequenceRef property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSequenceRef(String value)
+  {
+    this.sequenceRef = value;
+  }
+
+  /**
+   * Gets the value of the groupRef property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getGroupRef()
+  {
+    return groupRef;
+  }
+
+  /**
+   * Sets the value of the groupRef property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setGroupRef(String value)
+  {
+    this.groupRef = value;
+  }
+
+  /**
+   * Gets the value of the graphColour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getGraphColour()
+  {
+    return graphColour;
+  }
+
+  /**
+   * Sets the value of the graphColour property.
+   * 
+   * @param value
+   *          allowed object is {@link 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;
+  }
+
+  /**
+   * height in pixels for the graph if this is a graph-type annotation.
+   * 
+   * @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 }
+   * 
+   * @see #getGraphHeight()
+   */
+  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;
+  }
+
+  /**
+   * is an autocalculated annotation row
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public boolean isAutoCalculated()
+  {
+    if (autoCalculated == null)
+    {
+      return false;
+    }
+    else
+    {
+      return autoCalculated;
+    }
+  }
+
+  /**
+   * Sets the value of the autoCalculated property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   * @see #isAutoCalculated()
+   */
+  public void setAutoCalculated(Boolean value)
+  {
+    this.autoCalculated = value;
+  }
+
+  /**
+   * is to be shown below the alignment - introduced in Jalview 2.8 for
+   * visualizing T-COFFEE alignment scores
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public boolean isBelowAlignment()
+  {
+    if (belowAlignment == null)
+    {
+      return true;
+    }
+    else
+    {
+      return belowAlignment;
+    }
+  }
+
+  /**
+   * Sets the value of the belowAlignment property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   * @see #isBelowAlignment()
+   */
+  public void setBelowAlignment(Boolean value)
+  {
+    this.belowAlignment = value;
+  }
+
+  /**
+   * Optional string identifier used to group sets of annotation produced by a
+   * particular calculation. Values are opaque strings but have semantic meaning
+   * to Jalview's renderer, data importer and calculation system.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getCalcId()
+  {
+    return calcId;
+  }
+
+  /**
+   * Sets the value of the calcId property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getCalcId()
+   */
+  public void setCalcId(String value)
+  {
+    this.calcId = value;
+  }
+
+  /**
+   * 
    
+   * Java class for anonymous complex type
+   * 
    
+   * .
+   * 
+   * 
    
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
    
+   * 
+   * 
    +   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
    
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(name = "")
+  public static class ThresholdLine
+  {
+
+    @XmlAttribute(name = "label")
     protected String label;
-    protected String description;
-    protected Annotation.ThresholdLine thresholdLine;
-    protected List contactmatrix;
-    protected List property;
-    @XmlAttribute(name = "graph", required = true)
-    protected boolean graph;
-    @XmlAttribute(name = "graphType")
-    protected Integer graphType;
-    @XmlAttribute(name = "sequenceRef")
-    protected String sequenceRef;
-    @XmlAttribute(name = "groupRef")
-    protected String groupRef;
-    @XmlAttribute(name = "graphColour")
-    protected Integer graphColour;
-    @XmlAttribute(name = "graphGroup")
-    protected Integer graphGroup;
-    /**
-     * height in pixels for the graph if this is a
-     * 						graph-type annotation.
-     * 
-     */
-    @XmlAttribute(name = "graphHeight")
-    protected Integer graphHeight;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "scoreOnly")
-    protected Boolean scoreOnly;
-    @XmlAttribute(name = "score")
-    protected Double score;
-    @XmlAttribute(name = "visible")
-    protected Boolean visible;
-    @XmlAttribute(name = "centreColLabels")
-    protected Boolean centreColLabels;
-    @XmlAttribute(name = "scaleColLabels")
-    protected Boolean scaleColLabels;
-    @XmlAttribute(name = "showAllColLabels")
-    protected Boolean showAllColLabels;
-    /**
-     * is an autocalculated annotation row
-     * 
-     */
-    @XmlAttribute(name = "autoCalculated")
-    protected Boolean autoCalculated;
-    /**
-     * is to be shown below the alignment - introduced
-     * 						in Jalview 2.8 for visualizing T-COFFEE alignment scores
-     * 
-     */
-    @XmlAttribute(name = "belowAlignment")
-    protected Boolean belowAlignment;
-    /**
-     * Optional string identifier used to group sets of
-     * 						annotation produced by a particular calculation. Values are opaque
-     * 						strings but have semantic meaning to Jalview's renderer, data
-     * 						importer and calculation system.
-     * 
-     */
-    @XmlAttribute(name = "calcId")
-    protected String calcId;
-
-    /**
-     * Gets the value of the annotationElement property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the annotationElement property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getAnnotationElement().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link AnnotationElement }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the annotationElement property.
-     */
-    public List getAnnotationElement() {
-        if (annotationElement == null) {
-            annotationElement = new ArrayList();
-        }
-        return this.annotationElement;
-    }
-
-    /**
-     * 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 MapOnAMatrixType }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the contactmatrix property.
-     */
-    public List getContactmatrix() {
-        if (contactmatrix == null) {
-            contactmatrix = new ArrayList();
-        }
-        return this.contactmatrix;
-    }
-
-    /**
-     * Gets the value of the property property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the property property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getProperty().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link Property }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the property property.
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
-    }
-
-    /**
-     * Gets the value of the graph property.
-     * 
-     */
-    public boolean isGraph() {
-        return graph;
-    }
-
-    /**
-     * Sets the value of the graph property.
-     * 
-     */
-    public void setGraph(boolean value) {
-        this.graph = value;
-    }
-
-    /**
-     * Gets the value of the graphType property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getGraphType() {
-        return graphType;
-    }
-
-    /**
-     * Sets the value of the graphType property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setGraphType(Integer value) {
-        this.graphType = value;
-    }
-
-    /**
-     * Gets the value of the sequenceRef property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSequenceRef() {
-        return sequenceRef;
-    }
-
-    /**
-     * Sets the value of the sequenceRef property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSequenceRef(String value) {
-        this.sequenceRef = value;
-    }
-
-    /**
-     * Gets the value of the groupRef property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getGroupRef() {
-        return groupRef;
-    }
-
-    /**
-     * Sets the value of the groupRef property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setGroupRef(String value) {
-        this.groupRef = value;
-    }
-
-    /**
-     * Gets the value of the graphColour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getGraphColour() {
-        return graphColour;
-    }
-
-    /**
-     * Sets the value of the graphColour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link 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;
-    }
-
-    /**
-     * height in pixels for the graph if this is a
-     * 						graph-type annotation.
-     * 
-     * @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 }
-     *     
-     * @see #getGraphHeight()
-     */
-    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;
-    }
+    @XmlAttribute(name = "value")
+    protected Float value;
 
-    /**
-     * 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;
-    }
+    @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;
-    }
-
-    /**
-     * is an autocalculated annotation row
+     *          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 }
-     *     
-     * @see #isAutoCalculated()
-     */
-    public void setAutoCalculated(Boolean value) {
-        this.autoCalculated = value;
-    }
-
-    /**
-     * is to be shown below the alignment - introduced
-     * 						in Jalview 2.8 for visualizing T-COFFEE alignment scores
+     * @return possible object is {@link 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 }
-     *     
-     * @see #isBelowAlignment()
-     */
-    public void setBelowAlignment(Boolean value) {
-        this.belowAlignment = value;
-    }
-
-    /**
-     * Optional string identifier used to group sets of
-     * 						annotation produced by a particular calculation. Values are opaque
-     * 						strings but have semantic meaning to Jalview's renderer, data
-     * 						importer and calculation system.
+     *          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 }
-     *     
-     * @see #getCalcId()
-     */
-    public void setCalcId(String value) {
-        this.calcId = value;
-    }
-
-
-    /**
-     * 
    Java class for anonymous complex type
    .
-     * 
-     * 
    The following schema fragment specifies the expected content contained within this class.
    
-     * 
-     * 
    -     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
    
-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class ThresholdLine {
-
-        @XmlAttribute(name = "label")
-        protected String label;
-        @XmlAttribute(name = "value")
-        protected Float value;
-        @XmlAttribute(name = "colour")
-        protected Integer colour;
-
-        /**
-         * Gets the value of the label property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getLabel() {
-            return label;
-        }
-
-        /**
-         * Sets the value of the label property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setLabel(String value) {
-            this.label = value;
-        }
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setValue(Float value) {
-            this.value = value;
-        }
-
-        /**
-         * Gets the value of the colour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getColour() {
-            return colour;
-        }
-
-        /**
-         * Sets the value of the colour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setColour(Integer value) {
-            this.colour = value;
-        }
-
-    }
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index 4df374f..50bcf19 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,16 @@ 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 +44,215 @@ 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 ac12f03..b52b2a3 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,11 +13,16 @@ 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 +50,159 @@ 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 29cb972..4a59859 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,16 @@ 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">
@@ -41,149 +45,154 @@ 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 }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the row property.
-     */
-    public List getRow() {
-        if (row == null) {
-            row = new ArrayList();
-        }
-        return this.row;
-    }
-
-    /**
-     * Gets the value of the d property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public DoubleVector getD() {
-        return d;
-    }
-
-    /**
-     * Sets the value of the d property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public void setD(DoubleVector value) {
-        this.d = value;
-    }
-
-    /**
-     * Gets the value of the e property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public DoubleVector getE() {
-        return e;
-    }
-
-    /**
-     * Sets the value of the e property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleVector }
-     *     
-     */
-    public void setE(DoubleVector value) {
-        this.e = value;
-    }
-
-    /**
-     * Gets the value of the rows property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getRows() {
-        return rows;
-    }
-
-    /**
-     * Sets the value of the rows property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setRows(Integer value) {
-        this.rows = value;
-    }
-
-    /**
-     * Gets the value of the columns property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getColumns() {
-        return columns;
-    }
-
-    /**
-     * Sets the value of the columns property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setColumns(Integer value) {
-        this.columns = value;
+@XmlType(
+  name = "DoubleMatrix",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "row", "d", "e" })
+public class DoubleMatrix
+{
+
+  protected List row;
+
+  @XmlElement(name = "D")
+  protected DoubleVector d;
+
+  @XmlElement(name = "E")
+  protected DoubleVector e;
+
+  @XmlAttribute(name = "rows")
+  protected Integer rows;
+
+  @XmlAttribute(name = "columns")
+  protected Integer columns;
+
+  /**
+   * Gets the value of the row property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the row property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getRow().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list
+   * {@link DoubleVector }
+   * 
    
+   * 
+   * 
+   * @return The value of the row property.
+   */
+  public List getRow()
+  {
+    if (row == null)
+    {
+      row = new ArrayList();
     }
+    return this.row;
+  }
+
+  /**
+   * Gets the value of the d property.
+   * 
+   * @return possible object is {@link DoubleVector }
+   * 
+   */
+  public DoubleVector getD()
+  {
+    return d;
+  }
+
+  /**
+   * Sets the value of the d property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleVector }
+   * 
+   */
+  public void setD(DoubleVector value)
+  {
+    this.d = value;
+  }
+
+  /**
+   * Gets the value of the e property.
+   * 
+   * @return possible object is {@link DoubleVector }
+   * 
+   */
+  public DoubleVector getE()
+  {
+    return e;
+  }
+
+  /**
+   * Sets the value of the e property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleVector }
+   * 
+   */
+  public void setE(DoubleVector value)
+  {
+    this.e = value;
+  }
+
+  /**
+   * Gets the value of the rows property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getRows()
+  {
+    return rows;
+  }
+
+  /**
+   * Sets the value of the rows property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setRows(Integer value)
+  {
+    this.rows = value;
+  }
+
+  /**
+   * Gets the value of the columns property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getColumns()
+  {
+    return columns;
+  }
+
+  /**
+   * Sets the value of the columns property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setColumns(Integer value)
+  {
+    this.columns = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index 5d5e444..0479f56 100644
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,11 +14,16 @@ 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">
@@ -36,44 +40,50 @@ 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 }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the v property.
-     */
-    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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the v property.
+   */
+  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 7982504..9cbfc46 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,11 +14,16 @@ 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">
@@ -53,319 +57,337 @@ 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 }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the otherData property.
-     */
-    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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the otherData property.
+   */
+  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;
 
     /**
-     * Gets the value of the begin property.
+     * key2 may be used for a sub-attribute of key
      * 
      */
-    public int getBegin() {
-        return begin;
-    }
+    @XmlAttribute(name = "key2")
+    protected String key2;
 
-    /**
-     * Sets the value of the begin property.
-     * 
-     */
-    public void setBegin(int value) {
-        this.begin = value;
-    }
+    @XmlAttribute(name = "value", required = true)
+    protected String value;
 
     /**
-     * Gets the value of the end property.
+     * Gets the value of the key property.
      * 
-     */
-    public int getEnd() {
-        return end;
-    }
-
-    /**
-     * Sets the value of the end property.
+     * @return possible object is {@link String }
      * 
      */
-    public void setEnd(int value) {
-        this.end = value;
+    public String getKey()
+    {
+      return key;
     }
 
     /**
-     * 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.
+     * 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.
+     * key2 may be used for a sub-attribute of key
      * 
-     * @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 }
-     *     
+     * @see #getKey2()
      */
-    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;
-        /**
-         * key2 may be used for a sub-attribute of key
-         * 
-         */
-        @XmlAttribute(name = "key2")
-        protected String key2;
-        @XmlAttribute(name = "value", required = true)
-        protected String value;
-
-        /**
-         * Gets the value of the key property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getKey() {
-            return key;
-        }
-
-        /**
-         * Sets the value of the key property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setKey(String value) {
-            this.key = value;
-        }
-
-        /**
-         * key2 may be used for a sub-attribute of key
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getKey2() {
-            return key2;
-        }
-
-        /**
-         * Sets the value of the key2 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         * @see #getKey2()
-         */
-        public void setKey2(String value) {
-            this.key2 = value;
-        }
-
-        /**
-         * Gets the value of the value property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getValue() {
-            return value;
-        }
-
-        /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setValue(String value) {
-            this.value = value;
-        }
-
+    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 730cb71..6daebb3 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,16 @@ 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">
@@ -40,130 +44,134 @@ 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
+{
 
-    /**
-     * name of feature attribute to filter on, or attribute and sub-attribute
-     * 
-     */
-    @XmlElement(namespace = "")
-    protected List attributeName;
-    @XmlElement(namespace = "", required = true)
-    protected String condition;
-    @XmlElement(namespace = "", required = true)
-    protected String value;
-    @XmlAttribute(name = "by")
-    protected FilterBy by;
+  /**
+   * name of feature attribute to filter on, or attribute and sub-attribute
+   * 
+   */
+  @XmlElement(namespace = "")
+  protected List attributeName;
 
-    /**
-     * name of feature attribute to filter on, or attribute and sub-attribute
-     * 
-     * Gets the value of the attributeName property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the attributeName property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getAttributeName().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the attributeName property.
-     */
-    public List getAttributeName() {
-        if (attributeName == null) {
-            attributeName = new ArrayList();
-        }
-        return this.attributeName;
-    }
+  @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;
+  /**
+   * name of feature attribute to filter on, or attribute and sub-attribute
+   * 
+   * Gets the value of the attributeName property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the attributeName property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getAttributeName().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
    
+   * 
+   * 
+   * @return The value of the attributeName property.
+   */
+  public List getAttributeName()
+  {
+    if (attributeName == null)
+    {
+      attributeName = new ArrayList();
     }
+    return this.attributeName;
+  }
 
-    /**
-     * 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 9656aad..8f64753 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,13 +15,18 @@ 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">
@@ -51,149 +55,161 @@ 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;
 
     /**
-     * Gets the value of the matchCondition property.
+     * If true, matchers are AND-ed, if false they are OR-ed
      * 
-     * @return
-     *     possible object is
-     *     {@link FeatureMatcher }
-     *     
      */
-    public FeatureMatcher getMatchCondition() {
-        return matchCondition;
-    }
+    @XmlAttribute(name = "and", required = true)
+    protected boolean and;
 
     /**
-     * Sets the value of the matchCondition property.
+     * Gets the value of the matcherSet property.
      * 
-     * @param value
-     *     allowed object is
-     *     {@link FeatureMatcher }
-     *     
-     */
-    public void setMatchCondition(FeatureMatcher value) {
-        this.matchCondition = value;
-    }
-
-    /**
-     * Gets the value of the compoundMatcher property.
+     * 
    
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification 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);
+     * 
    
      * 
-     * @return
-     *     possible object is
-     *     {@link FeatureMatcherSet.CompoundMatcher }
-     *     
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link FeatureMatcherSet }
+     * 
    
+     * 
+     * 
+     * @return The value of the matcherSet property.
      */
-    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.
+     * If true, matchers are AND-ed, if false they are OR-ed
      * 
-     * @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;
-        /**
-         * If true, matchers are AND-ed, if false they are OR-ed
-         * 
-         */
-        @XmlAttribute(name = "and", required = true)
-        protected boolean and;
-
-        /**
-         * Gets the value of the matcherSet property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the matcherSet property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getMatcherSet().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link FeatureMatcherSet }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the matcherSet property.
-         */
-        public List getMatcherSet() {
-            if (matcherSet == null) {
-                matcherSet = new ArrayList();
-            }
-            return this.matcherSet;
-        }
-
-        /**
-         * If true, matchers are AND-ed, if false they are OR-ed
-         * 
-         */
-        public boolean isAnd() {
-            return and;
-        }
-
-        /**
-         * Sets the value of the and property.
-         * 
-         */
-        public void setAnd(boolean value) {
-            this.and = value;
-        }
-
+    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 5704bf9..866a0c8 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -5,20 +5,25 @@
 // Generated on: 2024.07.25 at 04:43:38 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;
 
-
 /**
  * Filter may apply to label, score or some feature attribute
  * 
- * 
    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">
@@ -32,47 +37,50 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum FilterBy {
+public enum FilterBy
+{
 
-    @XmlEnumValue("byLabel")
-    BY_LABEL("byLabel"),
-    @XmlEnumValue("byScore")
-    BY_SCORE("byScore"),
-    @XmlEnumValue("byAttribute")
-    BY_ATTRIBUTE("byAttribute");
-    private final String value;
+  @XmlEnumValue("byLabel")
+  BY_LABEL("byLabel"), @XmlEnumValue("byScore")
+  BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
+  BY_ATTRIBUTE("byAttribute");
 
-    FilterBy(String v) {
-        value = v;
-    }
+  private final String value;
 
-    /**
-     * Gets the value associated to the enum constant.
-     * 
-     * @return
-     *     The value linked to the enum.
-     */
-    public String value() {
-        return value;
-    }
+  FilterBy(String v)
+  {
+    value = v;
+  }
+
+  /**
+   * Gets the value associated to the enum constant.
+   * 
+   * @return The value linked to the enum.
+   */
+  public String value()
+  {
+    return value;
+  }
 
-    /**
-     * Gets the enum associated to the value passed as parameter.
-     * 
-     * @param v
-     *     The value to get the enum from.
-     * @return
-     *     The enum which corresponds to the value, if it exists.
-     * @throws IllegalArgumentException
-     *     If no value matches in the enum declaration.
-     */
-    public static FilterBy fromValue(String v) {
-        for (FilterBy c: FilterBy.values()) {
-            if (c.value.equals(v)) {
-                return c;
-            }
-        }
-        throw new IllegalArgumentException(v);
+  /**
+   * Gets the enum associated to the value passed as parameter.
+   * 
+   * @param v
+   *          The value to get the enum from.
+   * @return The enum which corresponds to the value, if it exists.
+   * @throws IllegalArgumentException
+   *           If no value matches in the enum declaration.
+   */
+  public static FilterBy fromValue(String v)
+  {
+    for (FilterBy c : FilterBy.values())
+    {
+      if (c.value.equals(v))
+      {
+        return c;
+      }
     }
+    throw new IllegalArgumentException(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 3f8185c..62d74a5 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -22,11 +21,16 @@ 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">
@@ -375,3401 +379,2741 @@ 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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the jSeq property.
+   */
+  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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the jGroup property.
+   */
+  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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the viewport property.
+   */
+  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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the userColours property.
+   */
+  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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the tree property.
+   */
+  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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the pcaViewer property.
+   */
+  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 }
      * 
    
      * 
      * 
-     * @return
-     *     The value of the jSeq property.
+     * @return The value of the setting property.
      */
-    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 }
      * 
    
      * 
      * 
-     * @return
-     *     The value of the jGroup property.
+     * @return The value of the group property.
      */
-    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>
+     * 
    
+     * 
      * 
-     * @return
-     *     The value of the viewport property.
      */
-    public List getViewport() {
-        if (viewport == null) {
-            viewport = new ArrayList();
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+    public static class Setting
+    {
+
+      /**
+       * name of feature attribute to colour by, or attribute and sub-attribute
+       * 
+       */
+      @XmlElement(namespace = "www.jalview.org")
+      protected List attributeName;
+
+      /**
+       * optional filter(s) applied to the feature type
+       * 
+       */
+      @XmlElement(namespace = "www.jalview.org")
+      protected FeatureMatcherSet matcherSet;
+
+      @XmlAttribute(name = "type", required = true)
+      protected String type;
+
+      @XmlAttribute(name = "colour", required = true)
+      protected int colour;
+
+      @XmlAttribute(name = "display", required = true)
+      protected boolean display;
+
+      @XmlAttribute(name = "order")
+      protected Float order;
+
+      /**
+       * Optional minimum colour for graduated feature colour
+       * 
+       */
+      @XmlAttribute(name = "mincolour")
+      protected Integer mincolour;
+
+      @XmlAttribute(name = "noValueColour")
+      protected NoValueColour noValueColour;
+
+      /**
+       * threshold value for graduated feature colour
+       * 
+       */
+      @XmlAttribute(name = "threshold")
+      protected Float threshold;
+
+      /**
+       * threshold type for graduated feature colour
+       * 
+       */
+      @XmlAttribute(name = "threshstate")
+      protected Integer threshstate;
+
+      @XmlAttribute(name = "max")
+      protected Float max;
+
+      @XmlAttribute(name = "min")
+      protected Float min;
+
+      @XmlAttribute(name = "colourByLabel")
+      protected Boolean colourByLabel;
+
+      @XmlAttribute(name = "autoScale")
+      protected Boolean autoScale;
+
+      /**
+       * name of feature attribute to colour by, or attribute and sub-attribute
+       * 
+       * Gets the value of the attributeName property.
+       * 
+       * 
    
+       * This accessor method returns a reference to the live list, not a
+       * snapshot. Therefore any modification you make to the returned list will
+       * be present inside the JAXB object. This is why there is not a
+       * set method for the attributeName property.
+       * 
    
+       * 
+       * 
    
+       * For example, to add a new item, do as follows:
+       * 
    
+       * 
+       * 
    +       * getAttributeName().add(newItem);
+       * 
    
+       * 
+       * 
+       * 
    
+       * Objects of the following type(s) are allowed in the list {@link String
+       * }
+       * 
    
+       * 
+       * 
+       * @return The value of the attributeName property.
+       */
+      public List getAttributeName()
+      {
+        if (attributeName == null)
+        {
+          attributeName = new ArrayList();
+        }
+        return this.attributeName;
+      }
+
+      /**
+       * optional filter(s) applied to the feature type
+       * 
+       * @return possible object is {@link FeatureMatcherSet }
+       * 
+       */
+      public FeatureMatcherSet getMatcherSet()
+      {
+        return matcherSet;
+      }
+
+      /**
+       * Sets the value of the matcherSet property.
+       * 
+       * @param value
+       *          allowed object is {@link FeatureMatcherSet }
+       * 
+       * @see #getMatcherSet()
+       */
+      public void setMatcherSet(FeatureMatcherSet value)
+      {
+        this.matcherSet = value;
+      }
+
+      /**
+       * Gets the value of the type property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getType()
+      {
+        return type;
+      }
+
+      /**
+       * Sets the value of the type property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setType(String value)
+      {
+        this.type = value;
+      }
+
+      /**
+       * Gets the value of the colour property.
+       * 
+       */
+      public int getColour()
+      {
+        return colour;
+      }
+
+      /**
+       * Sets the value of the colour property.
+       * 
+       */
+      public void setColour(int value)
+      {
+        this.colour = value;
+      }
+
+      /**
+       * Gets the value of the display property.
+       * 
+       */
+      public boolean isDisplay()
+      {
+        return display;
+      }
+
+      /**
+       * Sets the value of the display property.
+       * 
+       */
+      public void setDisplay(boolean value)
+      {
+        this.display = value;
+      }
+
+      /**
+       * Gets the value of the order property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getOrder()
+      {
+        return order;
+      }
+
+      /**
+       * Sets the value of the order property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setOrder(Float value)
+      {
+        this.order = value;
+      }
+
+      /**
+       * Optional minimum colour for graduated feature colour
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getMincolour()
+      {
+        return mincolour;
+      }
+
+      /**
+       * Sets the value of the mincolour property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       * @see #getMincolour()
+       */
+      public void setMincolour(Integer value)
+      {
+        this.mincolour = value;
+      }
+
+      /**
+       * Gets the value of the noValueColour property.
+       * 
+       * @return possible object is {@link NoValueColour }
+       * 
+       */
+      public NoValueColour getNoValueColour()
+      {
+        if (noValueColour == null)
+        {
+          return NoValueColour.MIN;
         }
-        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;
+      }
+
+      /**
+       * threshold value for graduated feature colour
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getThreshold()
+      {
+        return threshold;
+      }
+
+      /**
+       * Sets the value of the threshold property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       * @see #getThreshold()
+       */
+      public void setThreshold(Float value)
+      {
+        this.threshold = value;
+      }
+
+      /**
+       * threshold type for graduated feature colour
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getThreshstate()
+      {
+        return threshstate;
+      }
+
+      /**
+       * Sets the value of the threshstate property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       * @see #getThreshstate()
+       */
+      public void setThreshstate(Integer value)
+      {
+        this.threshstate = value;
+      }
+
+      /**
+       * Gets the value of the max property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getMax()
+      {
+        return max;
+      }
+
+      /**
+       * Sets the value of the max property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setMax(Float value)
+      {
+        this.max = value;
+      }
+
+      /**
+       * Gets the value of the min property.
+       * 
+       * @return possible object is {@link Float }
+       * 
+       */
+      public Float getMin()
+      {
+        return min;
+      }
+
+      /**
+       * Sets the value of the min property.
+       * 
+       * @param value
+       *          allowed object is {@link Float }
+       * 
+       */
+      public void setMin(Float value)
+      {
+        this.min = value;
+      }
+
+      /**
+       * Gets the value of the colourByLabel property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public Boolean isColourByLabel()
+      {
+        return colourByLabel;
+      }
+
+      /**
+       * Sets the value of the colourByLabel property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setColourByLabel(Boolean value)
+      {
+        this.colourByLabel = value;
+      }
+
+      /**
+       * Gets the value of the autoScale property.
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public Boolean isAutoScale()
+      {
+        return autoScale;
+      }
+
+      /**
+       * Sets the value of the autoScale property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       */
+      public void setAutoScale(Boolean value)
+      {
+        this.autoScale = value;
+      }
+
     }
 
+  }
+
+  /**
+   * 
    
+   * 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"/>
+   *         <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}conservationShading"/>
+   *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
    
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "seq", "annotationColours", "secStrProvider" })
+  public static class JGroup
+  {
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List seq;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected AnnotationColourScheme annotationColours;
+
+    @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
+    protected List secStrProvider;
+
+    @XmlAttribute(name = "start")
+    protected Integer start;
+
+    @XmlAttribute(name = "end")
+    protected Integer end;
+
+    @XmlAttribute(name = "name")
+    protected String name;
+
+    @XmlAttribute(name = "colour")
+    protected String colour;
+
+    @XmlAttribute(name = "outlineColour")
+    protected Integer outlineColour;
+
+    @XmlAttribute(name = "displayBoxes")
+    protected Boolean displayBoxes;
+
+    @XmlAttribute(name = "displayText")
+    protected Boolean displayText;
+
+    @XmlAttribute(name = "colourText")
+    protected Boolean colourText;
+
+    @XmlAttribute(name = "textCol1")
+    protected Integer textCol1;
+
+    @XmlAttribute(name = "textCol2")
+    protected Integer textCol2;
+
+    @XmlAttribute(name = "textColThreshold")
+    protected Integer textColThreshold;
+
+    @XmlAttribute(name = "showUnconserved")
+    protected Boolean showUnconserved;
+
     /**
-     * Gets the value of the 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.
    
+     * Optional sequence group ID (only needs to be unique for this alignment)
      * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getUserColours().add(newItem);
-     * 
    
+     */
+    @XmlAttribute(name = "id")
+    protected String id;
+
+    @XmlAttribute(name = "conservationSelected")
+    protected Boolean conservationSelected;
+
+    /**
+     * Conservation shading increment
      * 
+     */
+    @XmlAttribute(name = "consThreshold")
+    protected Integer consThreshold;
+
+    @XmlAttribute(name = "pidSelected")
+    protected Boolean pidSelected;
+
+    /**
+     * Percent Identity Threshold
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.UserColours }
-     * 
    
+     */
+    @XmlAttribute(name = "pidThreshold")
+    protected Integer pidThreshold;
+
+    /**
+     * Secondary structure consensus shading - since 2.11.4
      * 
+     */
+    @XmlAttribute(name = "secstrSelected")
+    protected Boolean secstrSelected;
+
+    /**
+     * Secondary structure consensus increment
      * 
-     * @return
-     *     The value of the userColours property.
      */
-    public List getUserColours() {
-        if (userColours == null) {
-            userColours = new ArrayList();
-        }
-        return this.userColours;
-    }
+    @XmlAttribute(name = "secstrThreshold")
+    protected Integer secstrThreshold;
+
+    @XmlAttribute(name = "showConsensusHistogram")
+    protected Boolean showConsensusHistogram;
+
+    @XmlAttribute(name = "showSequenceLogo")
+    protected Boolean showSequenceLogo;
+
+    @XmlAttribute(name = "normaliseSequenceLogo")
+    protected Boolean normaliseSequenceLogo;
+
+    @XmlAttribute(name = "ignoreGapsinConsensus")
+    protected Boolean ignoreGapsinConsensus;
 
     /**
-     * Gets the value of the tree 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 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 seq property.
+     * 
    
      * 
      * 
    
      * For example, to add a new item, do as follows:
      * 
    
+     * 
      * 
    -     * getTree().add(newItem);
+     * getSeq().add(newItem);
      * 
    
      * 
      * 
      * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Tree }
+     * Objects of the following type(s) are allowed in the list {@link String }
      * 
    
      * 
      * 
-     * @return
-     *     The value of the tree property.
+     * @return The value of the seq property.
      */
-    public List getTree() {
-        if (tree == null) {
-            tree = new ArrayList();
-        }
-        return this.tree;
+    public List getSeq()
+    {
+      if (seq == null)
+      {
+        seq = new ArrayList();
+      }
+      return this.seq;
+    }
+
+    /**
+     * Gets the value of the annotationColours property.
+     * 
+     * @return possible object is {@link AnnotationColourScheme }
+     * 
+     */
+    public AnnotationColourScheme getAnnotationColours()
+    {
+      return annotationColours;
+    }
+
+    /**
+     * Sets the value of the annotationColours property.
+     * 
+     * @param value
+     *          allowed object is {@link AnnotationColourScheme }
+     * 
+     */
+    public void setAnnotationColours(AnnotationColourScheme value)
+    {
+      this.annotationColours = value;
     }
 
     /**
-     * Gets the value of the pcaViewer property.
+     * Gets the value of the secStrProvider property.
      * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the 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 secStrProvider property.
+     * 
    
      * 
      * 
    
      * For example, to add a new item, do as follows:
      * 
    
+     * 
      * 
    -     * getPcaViewer().add(newItem);
+     * getSecStrProvider().add(newItem);
      * 
    
      * 
      * 
      * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer }
+     * Objects of the following type(s) are allowed in the list {@link String }
      * 
    
      * 
      * 
-     * @return
-     *     The value of the pcaViewer property.
+     * @return The value of the secStrProvider property.
      */
-    public List getPcaViewer() {
-        if (pcaViewer == null) {
-            pcaViewer = new ArrayList();
-        }
-        return this.pcaViewer;
+    public List getSecStrProvider()
+    {
+      if (secStrProvider == null)
+      {
+        secStrProvider = new ArrayList();
+      }
+      return this.secStrProvider;
     }
 
     /**
-     * Gets the value of the featureSettings property.
+     * Gets the value of the start property.
+     * 
+     * @return possible object is {@link Integer }
      * 
-     * @return
-     *     possible object is
-     *     {@link JalviewModel.FeatureSettings }
-     *     
      */
-    public JalviewModel.FeatureSettings getFeatureSettings() {
-        return featureSettings;
+    public Integer getStart()
+    {
+      return start;
     }
 
     /**
-     * Sets the value of the featureSettings property.
+     * Sets the value of the start property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link JalviewModel.FeatureSettings }
-     *     
+     *          allowed object is {@link Integer }
+     * 
      */
-    public void setFeatureSettings(JalviewModel.FeatureSettings value) {
-        this.featureSettings = value;
+    public void setStart(Integer value)
+    {
+      this.start = value;
     }
 
-
     /**
-     * 
    Java class for anonymous complex type
    .
+     * Gets the value of the end 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="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 Integer getEnd()
+    {
+      return end;
+    }
+
+    /**
+     * Sets the value of the end property.
      * 
+     * @param value
+     *          allowed object is {@link Integer }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "setting",
-        "group"
-    })
-    public static class FeatureSettings {
-
-        @XmlElement(namespace = "www.jalview.org")
-        protected List setting;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List group;
-
-        /**
-         * Gets the value of the setting property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the setting property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getSetting().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.FeatureSettings.Setting }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the setting property.
-         */
-        public List getSetting() {
-            if (setting == null) {
-                setting = new ArrayList();
-            }
-            return this.setting;
-        }
+    public void setEnd(Integer value)
+    {
+      this.end = value;
+    }
 
-        /**
-         * Gets the value of the group property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the group property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getGroup().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.FeatureSettings.Group }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the group property.
-         */
-        public List getGroup() {
-            if (group == null) {
-                group = new ArrayList();
-            }
-            return this.group;
-        }
+    /**
+     * 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;
+    }
 
-        /**
-         * 
    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;
-            }
+    /**
+     * Gets the value of the colour property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getColour()
+    {
+      return colour;
+    }
 
-        }
+    /**
+     * Sets the value of the colour property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setColour(String value)
+    {
+      this.colour = 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">
-         *       <sequence>
-         *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-         *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-         *       </sequence>
-         *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-         *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
    
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "attributeName",
-            "matcherSet"
-        })
-        public static class Setting {
-
-            /**
-             * name of feature attribute to colour by, or attribute and sub-attribute
-             * 
-             */
-            @XmlElement(namespace = "www.jalview.org")
-            protected List attributeName;
-            /**
-             * optional filter(s) applied to the feature type
-             * 
-             */
-            @XmlElement(namespace = "www.jalview.org")
-            protected FeatureMatcherSet matcherSet;
-            @XmlAttribute(name = "type", required = true)
-            protected String type;
-            @XmlAttribute(name = "colour", required = true)
-            protected int colour;
-            @XmlAttribute(name = "display", required = true)
-            protected boolean display;
-            @XmlAttribute(name = "order")
-            protected Float order;
-            /**
-             * Optional minimum colour
-             * 												for graduated
-             * 												feature
-             * 												colour
-             * 
-             */
-            @XmlAttribute(name = "mincolour")
-            protected Integer mincolour;
-            @XmlAttribute(name = "noValueColour")
-            protected NoValueColour noValueColour;
-            /**
-             * threshold value for
-             * 												graduated feature colour
-             * 
-             */
-            @XmlAttribute(name = "threshold")
-            protected Float threshold;
-            /**
-             * threshold type for
-             * 												graduated feature colour
-             * 
-             */
-            @XmlAttribute(name = "threshstate")
-            protected Integer threshstate;
-            @XmlAttribute(name = "max")
-            protected Float max;
-            @XmlAttribute(name = "min")
-            protected Float min;
-            @XmlAttribute(name = "colourByLabel")
-            protected Boolean colourByLabel;
-            @XmlAttribute(name = "autoScale")
-            protected Boolean autoScale;
-
-            /**
-             * name of feature attribute to colour by, or attribute and sub-attribute
-             * 
-             * Gets the value of the attributeName property.
-             * 
-             * 
    This accessor method returns a reference to the live list,
-             * not a snapshot. Therefore any modification you make to the
-             * returned list will be present inside the JAXB object.
-             * This is why there is not a set method for the attributeName property.
    
-             * 
-             * 
    
-             * For example, to add a new item, do as follows:
-             * 
    
-             * 
    -             * getAttributeName().add(newItem);
-             * 
    
-             * 
-             * 
-             * 
    
-             * Objects of the following type(s) are allowed in the list
-             * {@link String }
-             * 
    
-             * 
-             * 
-             * @return
-             *     The value of the attributeName property.
-             */
-            public List getAttributeName() {
-                if (attributeName == null) {
-                    attributeName = new ArrayList();
-                }
-                return this.attributeName;
-            }
-
-            /**
-             * optional filter(s) applied to the feature type
-             * 
-             * @return
-             *     possible object is
-             *     {@link FeatureMatcherSet }
-             *     
-             */
-            public FeatureMatcherSet getMatcherSet() {
-                return matcherSet;
-            }
-
-            /**
-             * Sets the value of the matcherSet property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link FeatureMatcherSet }
-             *     
-             * @see #getMatcherSet()
-             */
-            public void setMatcherSet(FeatureMatcherSet value) {
-                this.matcherSet = value;
-            }
-
-            /**
-             * Gets the value of the type property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getType() {
-                return type;
-            }
-
-            /**
-             * Sets the value of the type property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setType(String value) {
-                this.type = value;
-            }
-
-            /**
-             * Gets the value of the colour property.
-             * 
-             */
-            public int getColour() {
-                return colour;
-            }
-
-            /**
-             * Sets the value of the colour property.
-             * 
-             */
-            public void setColour(int value) {
-                this.colour = value;
-            }
-
-            /**
-             * Gets the value of the display property.
-             * 
-             */
-            public boolean isDisplay() {
-                return display;
-            }
-
-            /**
-             * Sets the value of the display property.
-             * 
-             */
-            public void setDisplay(boolean value) {
-                this.display = value;
-            }
-
-            /**
-             * Gets the value of the order property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getOrder() {
-                return order;
-            }
-
-            /**
-             * Sets the value of the order property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setOrder(Float value) {
-                this.order = value;
-            }
-
-            /**
-             * Optional minimum colour
-             * 												for graduated
-             * 												feature
-             * 												colour
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getMincolour() {
-                return mincolour;
-            }
-
-            /**
-             * Sets the value of the mincolour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             * @see #getMincolour()
-             */
-            public void setMincolour(Integer value) {
-                this.mincolour = value;
-            }
-
-            /**
-             * Gets the value of the noValueColour property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link NoValueColour }
-             *     
-             */
-            public NoValueColour getNoValueColour() {
-                if (noValueColour == null) {
-                    return NoValueColour.MIN;
-                } else {
-                    return noValueColour;
-                }
-            }
-
-            /**
-             * Sets the value of the noValueColour property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link NoValueColour }
-             *     
-             */
-            public void setNoValueColour(NoValueColour value) {
-                this.noValueColour = value;
-            }
-
-            /**
-             * threshold value for
-             * 												graduated feature colour
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getThreshold() {
-                return threshold;
-            }
-
-            /**
-             * Sets the value of the threshold property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             * @see #getThreshold()
-             */
-            public void setThreshold(Float value) {
-                this.threshold = value;
-            }
-
-            /**
-             * threshold type for
-             * 												graduated feature colour
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getThreshstate() {
-                return threshstate;
-            }
-
-            /**
-             * Sets the value of the threshstate property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             * @see #getThreshstate()
-             */
-            public void setThreshstate(Integer value) {
-                this.threshstate = value;
-            }
-
-            /**
-             * Gets the value of the max property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getMax() {
-                return max;
-            }
-
-            /**
-             * Sets the value of the max property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setMax(Float value) {
-                this.max = value;
-            }
-
-            /**
-             * Gets the value of the min property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getMin() {
-                return min;
-            }
-
-            /**
-             * Sets the value of the min property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setMin(Float value) {
-                this.min = value;
-            }
-
-            /**
-             * Gets the value of the colourByLabel property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isColourByLabel() {
-                return colourByLabel;
-            }
-
-            /**
-             * Sets the value of the colourByLabel property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setColourByLabel(Boolean value) {
-                this.colourByLabel = value;
-            }
-
-            /**
-             * Gets the value of the autoScale property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public Boolean isAutoScale() {
-                return autoScale;
-            }
-
-            /**
-             * Sets the value of the autoScale property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setAutoScale(Boolean value) {
-                this.autoScale = value;
-            }
+    /**
+     * 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;
     }
 
+    /**
+     * Gets the value of the displayText property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isDisplayText()
+    {
+      return displayText;
+    }
 
     /**
-     * 
    Java class for anonymous complex type
    .
+     * Sets the value of the displayText 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="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *         <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}conservationShading"/>
-     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
    
+     */
+    public void setDisplayText(Boolean value)
+    {
+      this.displayText = value;
+    }
+
+    /**
+     * Gets the value of the colourText property.
      * 
+     * @return possible object is {@link Boolean }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "seq",
-        "annotationColours",
-        "secStrProvider"
-    })
-    public static class JGroup {
-
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List seq;
-        @XmlElement(namespace = "www.jalview.org")
-        protected AnnotationColourScheme annotationColours;
-        @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
-        protected List secStrProvider;
-        @XmlAttribute(name = "start")
-        protected Integer start;
-        @XmlAttribute(name = "end")
-        protected Integer end;
-        @XmlAttribute(name = "name")
-        protected String name;
-        @XmlAttribute(name = "colour")
-        protected String colour;
-        @XmlAttribute(name = "outlineColour")
-        protected Integer outlineColour;
-        @XmlAttribute(name = "displayBoxes")
-        protected Boolean displayBoxes;
-        @XmlAttribute(name = "displayText")
-        protected Boolean displayText;
-        @XmlAttribute(name = "colourText")
-        protected Boolean colourText;
-        @XmlAttribute(name = "textCol1")
-        protected Integer textCol1;
-        @XmlAttribute(name = "textCol2")
-        protected Integer textCol2;
-        @XmlAttribute(name = "textColThreshold")
-        protected Integer textColThreshold;
-        @XmlAttribute(name = "showUnconserved")
-        protected Boolean showUnconserved;
-        /**
-         * Optional sequence group ID (only
-         * 									needs to be
-         * 									unique for this
-         * 									alignment)
-         * 
-         */
-        @XmlAttribute(name = "id")
-        protected String id;
-        @XmlAttribute(name = "conservationSelected")
-        protected Boolean conservationSelected;
-        /**
-         * Conservation shading increment
-         * 
-         */
-        @XmlAttribute(name = "consThreshold")
-        protected Integer consThreshold;
-        @XmlAttribute(name = "pidSelected")
-        protected Boolean pidSelected;
-        /**
-         * Percent Identity Threshold
-         * 
-         */
-        @XmlAttribute(name = "pidThreshold")
-        protected Integer pidThreshold;
-        /**
-         * Secondary structure consensus shading - since 2.11.4
-         * 
-         */
-        @XmlAttribute(name = "secstrSelected")
-        protected Boolean secstrSelected;
-        /**
-         * Secondary structure consensus increment
-         * 
-         */
-        @XmlAttribute(name = "secstrThreshold")
-        protected Integer secstrThreshold;
-        @XmlAttribute(name = "showConsensusHistogram")
-        protected Boolean showConsensusHistogram;
-        @XmlAttribute(name = "showSequenceLogo")
-        protected Boolean showSequenceLogo;
-        @XmlAttribute(name = "normaliseSequenceLogo")
-        protected Boolean normaliseSequenceLogo;
-        @XmlAttribute(name = "ignoreGapsinConsensus")
-        protected Boolean ignoreGapsinConsensus;
+    public Boolean isColourText()
+    {
+      return colourText;
+    }
 
-        /**
-         * 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 }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the seq property.
-         */
-        public List getSeq() {
-            if (seq == null) {
-                seq = new ArrayList();
-            }
-            return this.seq;
-        }
+    /**
+     * Sets the value of the colourText property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setColourText(Boolean value)
+    {
+      this.colourText = value;
+    }
 
-        /**
-         * Gets the value of the annotationColours property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link AnnotationColourScheme }
-         *     
-         */
-        public AnnotationColourScheme getAnnotationColours() {
-            return annotationColours;
-        }
+    /**
+     * Gets the value of the textCol1 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol1()
+    {
+      return textCol1;
+    }
 
-        /**
-         * Sets the value of the annotationColours property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link AnnotationColourScheme }
-         *     
-         */
-        public void setAnnotationColours(AnnotationColourScheme value) {
-            this.annotationColours = value;
-        }
+    /**
+     * Sets the value of the textCol1 property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextCol1(Integer value)
+    {
+      this.textCol1 = value;
+    }
 
-        /**
-         * Gets the value of the secStrProvider property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the secStrProvider property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getSecStrProvider().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the secStrProvider property.
-         */
-        public List getSecStrProvider() {
-            if (secStrProvider == null) {
-                secStrProvider = new ArrayList();
-            }
-            return this.secStrProvider;
-        }
+    /**
+     * Gets the value of the textCol2 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol2()
+    {
+      return textCol2;
+    }
 
-        /**
-         * Gets the value of the start property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getStart() {
-            return start;
-        }
+    /**
+     * 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 start property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setStart(Integer value) {
-            this.start = value;
-        }
+    /**
+     * Gets the value of the textColThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextColThreshold()
+    {
+      return textColThreshold;
+    }
 
-        /**
-         * Gets the value of the end property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getEnd() {
-            return end;
-        }
+    /**
+     * 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 end property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setEnd(Integer value) {
-            this.end = value;
-        }
+    /**
+     * Gets the value of the showUnconserved property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowUnconserved()
+    {
+      return showUnconserved;
+    }
 
-        /**
-         * Gets the value of the name property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getName() {
-            return name;
-        }
+    /**
+     * 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 name property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setName(String value) {
-            this.name = value;
-        }
+    /**
+     * Optional sequence group ID (only needs to be unique for this alignment)
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
 
-        /**
-         * Gets the value of the colour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getColour() {
-            return colour;
-        }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     * @see #getId()
+     */
+    public void setId(String value)
+    {
+      this.id = value;
+    }
 
-        /**
-         * Sets the value of the colour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setColour(String value) {
-            this.colour = value;
-        }
+    /**
+     * Gets the value of the conservationSelected property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isConservationSelected()
+    {
+      return conservationSelected;
+    }
 
-        /**
-         * Gets the value of the outlineColour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getOutlineColour() {
-            return outlineColour;
-        }
+    /**
+     * 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 outlineColour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setOutlineColour(Integer value) {
-            this.outlineColour = value;
-        }
+    /**
+     * Conservation shading increment
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getConsThreshold()
+    {
+      return consThreshold;
+    }
 
-        /**
-         * Gets the value of the displayBoxes property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isDisplayBoxes() {
-            return displayBoxes;
-        }
+    /**
+     * Sets the value of the consThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     * @see #getConsThreshold()
+     */
+    public void setConsThreshold(Integer value)
+    {
+      this.consThreshold = value;
+    }
 
-        /**
-         * Sets the value of the displayBoxes property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setDisplayBoxes(Boolean value) {
-            this.displayBoxes = value;
-        }
+    /**
+     * Gets the value of the pidSelected property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isPidSelected()
+    {
+      return pidSelected;
+    }
 
-        /**
-         * Gets the value of the displayText property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isDisplayText() {
-            return displayText;
-        }
+    /**
+     * 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 displayText property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setDisplayText(Boolean value) {
-            this.displayText = value;
-        }
+    /**
+     * Percent Identity Threshold
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getPidThreshold()
+    {
+      return pidThreshold;
+    }
 
-        /**
-         * Gets the value of the colourText property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isColourText() {
-            return colourText;
-        }
+    /**
+     * Sets the value of the pidThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     * @see #getPidThreshold()
+     */
+    public void setPidThreshold(Integer value)
+    {
+      this.pidThreshold = value;
+    }
 
-        /**
-         * Sets the value of the colourText property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setColourText(Boolean value) {
-            this.colourText = value;
-        }
+    /**
+     * Secondary structure consensus shading - since 2.11.4
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isSecstrSelected()
+    {
+      if (secstrSelected == null)
+      {
+        return false;
+      }
+      else
+      {
+        return secstrSelected;
+      }
+    }
 
-        /**
-         * Gets the value of the textCol1 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextCol1() {
-            return textCol1;
-        }
+    /**
+     * Sets the value of the secstrSelected property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     * @see #isSecstrSelected()
+     */
+    public void setSecstrSelected(Boolean value)
+    {
+      this.secstrSelected = value;
+    }
 
-        /**
-         * Sets the value of the textCol1 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setTextCol1(Integer value) {
-            this.textCol1 = value;
-        }
+    /**
+     * Secondary structure consensus increment
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getSecstrThreshold()
+    {
+      return secstrThreshold;
+    }
 
-        /**
-         * Gets the value of the textCol2 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextCol2() {
-            return textCol2;
-        }
+    /**
+     * Sets the value of the secstrThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     * @see #getSecstrThreshold()
+     */
+    public void setSecstrThreshold(Integer value)
+    {
+      this.secstrThreshold = value;
+    }
 
-        /**
-         * Sets the value of the 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;
-        }
-
-        /**
-         * Optional sequence group ID (only
-         * 									needs to be
-         * 									unique for this
-         * 									alignment)
-         * 
-         * @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 }
-         *     
-         * @see #getId()
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
-
-        /**
-         * Gets the value of the conservationSelected property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isConservationSelected() {
-            return conservationSelected;
-        }
-
-        /**
-         * Sets the value of the conservationSelected property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setConservationSelected(Boolean value) {
-            this.conservationSelected = value;
-        }
-
-        /**
-         * Conservation shading increment
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getConsThreshold() {
-            return consThreshold;
-        }
-
-        /**
-         * Sets the value of the consThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         * @see #getConsThreshold()
-         */
-        public void setConsThreshold(Integer value) {
-            this.consThreshold = value;
-        }
-
-        /**
-         * Gets the value of the pidSelected property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isPidSelected() {
-            return pidSelected;
-        }
+    /**
+     * 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 pidSelected property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setPidSelected(Boolean value) {
-            this.pidSelected = value;
-        }
+    /**
+     * Sets the value of the showConsensusHistogram property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowConsensusHistogram(Boolean value)
+    {
+      this.showConsensusHistogram = value;
+    }
 
-        /**
-         * Percent Identity Threshold
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getPidThreshold() {
-            return pidThreshold;
-        }
+    /**
+     * 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 pidThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         * @see #getPidThreshold()
-         */
-        public void setPidThreshold(Integer value) {
-            this.pidThreshold = value;
-        }
+    /**
+     * Sets the value of the showSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowSequenceLogo(Boolean value)
+    {
+      this.showSequenceLogo = value;
+    }
 
-        /**
-         * Secondary structure consensus shading - since 2.11.4
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isSecstrSelected() {
-            if (secstrSelected == null) {
-                return false;
-            } else {
-                return secstrSelected;
-            }
-        }
+    /**
+     * Gets the value of the normaliseSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isNormaliseSequenceLogo()
+    {
+      if (normaliseSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return normaliseSequenceLogo;
+      }
+    }
 
-        /**
-         * Sets the value of the secstrSelected property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isSecstrSelected()
-         */
-        public void setSecstrSelected(Boolean value) {
-            this.secstrSelected = value;
-        }
+    /**
+     * Sets the value of the normaliseSequenceLogo property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setNormaliseSequenceLogo(Boolean value)
+    {
+      this.normaliseSequenceLogo = value;
+    }
 
-        /**
-         * Secondary structure consensus increment
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getSecstrThreshold() {
-            return secstrThreshold;
-        }
+    /**
+     * 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 secstrThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         * @see #getSecstrThreshold()
-         */
-        public void setSecstrThreshold(Integer value) {
-            this.secstrThreshold = 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;
-            }
-        }
+  }
+
+  /**
+   * 
    
+   * 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;
 
-        /**
-         * Sets the value of the showConsensusHistogram property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowConsensusHistogram(Boolean value) {
-            this.showConsensusHistogram = value;
-        }
+    /**
+     * Reference to a viewer showing RNA structure for this sequence. Schema
+     * supports one viewer showing multiple annotations for multiple sequences,
+     * though currently only one annotation for one sequence (gapped or trimmed)
+     * is used
+     * 
+     */
+    @XmlElement(namespace = "www.jalview.org")
+    protected List rnaViewer;
 
-        /**
-         * Gets the value of the showSequenceLogo property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowSequenceLogo() {
-            if (showSequenceLogo == null) {
-                return false;
-            } else {
-                return showSequenceLogo;
-            }
-        }
+    @XmlAttribute(name = "colour")
+    protected Integer colour;
 
-        /**
-         * Sets the value of the showSequenceLogo property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowSequenceLogo(Boolean value) {
-            this.showSequenceLogo = value;
-        }
+    @XmlAttribute(name = "start", required = true)
+    protected int start;
 
-        /**
-         * Gets the value of the normaliseSequenceLogo property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isNormaliseSequenceLogo() {
-            if (normaliseSequenceLogo == null) {
-                return false;
-            } else {
-                return normaliseSequenceLogo;
-            }
-        }
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
 
-        /**
-         * Sets the value of the normaliseSequenceLogo property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setNormaliseSequenceLogo(Boolean value) {
-            this.normaliseSequenceLogo = value;
-        }
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
 
-        /**
-         * Gets the value of the ignoreGapsinConsensus property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isIgnoreGapsinConsensus() {
-            if (ignoreGapsinConsensus == null) {
-                return true;
-            } else {
-                return ignoreGapsinConsensus;
-            }
-        }
+    @XmlAttribute(name = "hidden")
+    protected Boolean hidden;
 
-        /**
-         * Sets the value of the ignoreGapsinConsensus property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setIgnoreGapsinConsensus(Boolean value) {
-            this.ignoreGapsinConsensus = value;
-        }
+    @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 }
+     * 
    
+     * 
+     * 
+     * @return The value of the features property.
+     */
+    public List getFeatures()
+    {
+      if (features == null)
+      {
+        features = new ArrayList();
+      }
+      return this.features;
     }
 
-
     /**
-     * 
    Java class for anonymous complex type
    .
+     * 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.
+     * 
    
      * 
-     * 
    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="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>
+     * getPdbids().add(newItem);
      * 
    
      * 
      * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JSeq.Pdbids }
+     * 
    
+     * 
+     * 
+     * @return The value of the pdbids property.
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "features",
-        "pdbids",
-        "hiddenSequences",
-        "rnaViewer"
-    })
-    public static class JSeq {
-
-        @XmlElement(namespace = "www.jalview.org")
-        protected List features;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List pdbids;
-        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-        protected List hiddenSequences;
-        /**
-         * Reference to a viewer showing
-         * 										RNA structure for this sequence.
-         * 										Schema supports one viewer
-         * 										showing multiple annotations for
-         * 										multiple sequences, though
-         * 										currently only one annotation
-         * 										for one sequence (gapped or
-         * 										trimmed) is used
-         * 
-         */
-        @XmlElement(namespace = "www.jalview.org")
-        protected List rnaViewer;
-        @XmlAttribute(name = "colour")
-        protected Integer colour;
-        @XmlAttribute(name = "start", required = true)
-        protected int start;
-        @XmlAttribute(name = "end", required = true)
-        protected int end;
-        @XmlAttribute(name = "id", required = true)
-        protected String id;
-        @XmlAttribute(name = "hidden")
-        protected Boolean hidden;
-        @XmlAttribute(name = "viewreference")
-        protected Boolean viewreference;
-
-        /**
-         * Gets the value of the features property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the features property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getFeatures().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link Feature }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the features property.
-         */
-        public List getFeatures() {
-            if (features == null) {
-                features = new ArrayList();
-            }
-            return this.features;
-        }
+    public List getPdbids()
+    {
+      if (pdbids == null)
+      {
+        pdbids = new ArrayList();
+      }
+      return this.pdbids;
+    }
 
-        /**
-         * Gets the value of the pdbids property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the pdbids property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getPdbids().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.JSeq.Pdbids }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the pdbids property.
-         */
-        public List getPdbids() {
-            if (pdbids == null) {
-                pdbids = new ArrayList();
-            }
-            return this.pdbids;
+    /**
+     * Gets the value of the hiddenSequences property.
+     * 
+     * 
    
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the hiddenSequences property.
+     * 
    
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    
+     * 
+     * 
    +     * getHiddenSequences().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * 
    
+     * 
+     * 
+     * @return The value of the hiddenSequences property.
+     */
+    public List getHiddenSequences()
+    {
+      if (hiddenSequences == null)
+      {
+        hiddenSequences = new ArrayList();
+      }
+      return this.hiddenSequences;
+    }
+
+    /**
+     * Reference to a viewer showing RNA structure for this sequence. Schema
+     * supports one viewer showing multiple annotations for multiple sequences,
+     * though currently only one annotation for one sequence (gapped or trimmed)
+     * is used
+     * 
+     * Gets the value of the rnaViewer property.
+     * 
+     * 
    
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the rnaViewer property.
+     * 
    
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    
+     * 
+     * 
    +     * getRnaViewer().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JSeq.RnaViewer }
+     * 
    
+     * 
+     * 
+     * @return The value of the rnaViewer property.
+     */
+    public List getRnaViewer()
+    {
+      if (rnaViewer == null)
+      {
+        rnaViewer = new ArrayList();
+      }
+      return this.rnaViewer;
+    }
+
+    /**
+     * Gets the value of the 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 }
+       * 
    
+       * 
+       * 
+       * @return The value of the structureState property.
+       */
+      public List getStructureState()
+      {
+        if (structureState == null)
+        {
+          structureState = new ArrayList();
         }
+        return this.structureState;
+      }
+
+      /**
+       * 
    
+       * Java class for anonymous complex type
+       * 
    
+       * .
+       * 
+       * 
    
+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
    
+       * 
+       * 
    +       * <complexType>
+       *   <simpleContent>
+       *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+       *       <attGroup ref="{www.jalview.org}swingwindow"/>
+       *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+       *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </extension>
+       *   </simpleContent>
+       * </complexType>
+       * 
    
+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "", propOrder = { "value" })
+      public static class StructureState
+      {
+
+        @XmlValue
+        protected String value;
+
+        @XmlAttribute(name = "visible")
+        protected Boolean visible;
 
         /**
-         * Gets the value of the hiddenSequences property.
+         * additional identifier which properly disambiguates the structure view
+         * from any other view with the same attributes. This is not an ID,
+         * because it is possible to have many references to the same physical
+         * structure view from different sequences in an alignment. A
+         * structureState element citing the same viewId will appear for each
+         * instance.
          * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification 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.
    
+         */
+        @XmlAttribute(name = "viewId")
+        protected String viewId;
+
+        /**
+         * Flag set if the alignment panel containing this JSeq should be
+         * included in those used to perform a structure superposition (since
+         * Jalview 2.7).
+         * 
+         */
+        @XmlAttribute(name = "alignwithAlignPanel")
+        protected Boolean alignwithAlignPanel;
+
+        /**
+         * Flag set if the alignment panel containing this JSeq should be
+         * included in those used to colour its associated sequences in this
+         * structureState(since Jalview 2.7).
          * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getHiddenSequences().add(newItem);
-         * 
    
+         */
+        @XmlAttribute(name = "colourwithAlignPanel")
+        protected Boolean colourwithAlignPanel;
+
+        /**
+         * Flag set if the structure display is coloured by the Jmol state,
+         * rather than by one or more linked alignment views.
          * 
+         */
+        @XmlAttribute(name = "colourByJmol")
+        protected Boolean colourByJmol;
+
+        /**
+         * An identifier for the viewer type, currently either JMOL or CHIMERA
          * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link Integer }
-         * 
    
+         */
+        @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 }
          * 
-         * @return
-         *     The value of the hiddenSequences property.
          */
-        public List getHiddenSequences() {
-            if (hiddenSequences == null) {
-                hiddenSequences = new ArrayList();
-            }
-            return this.hiddenSequences;
+        public String getValue()
+        {
+          return value;
         }
 
         /**
-         * Reference to a viewer showing
-         * 										RNA structure for this sequence.
-         * 										Schema supports one viewer
-         * 										showing multiple annotations for
-         * 										multiple sequences, though
-         * 										currently only one annotation
-         * 										for one sequence (gapped or
-         * 										trimmed) is used
-         * 
-         * Gets the value of the rnaViewer property.
+         * Sets the value of the value property.
          * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification 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.
    
+         * @param value
+         *          allowed object is {@link String }
          * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getRnaViewer().add(newItem);
-         * 
    
+         */
+        public void setValue(String value)
+        {
+          this.value = value;
+        }
+
+        /**
+         * Gets the value of the visible property.
          * 
+         * @return possible object is {@link Boolean }
          * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.JSeq.RnaViewer }
-         * 
    
+         */
+        public Boolean isVisible()
+        {
+          return visible;
+        }
+
+        /**
+         * Sets the value of the visible property.
          * 
+         * @param value
+         *          allowed object is {@link Boolean }
          * 
-         * @return
-         *     The value of the rnaViewer property.
          */
-        public List getRnaViewer() {
-            if (rnaViewer == null) {
-                rnaViewer = new ArrayList();
-            }
-            return this.rnaViewer;
+        public void setVisible(Boolean value)
+        {
+          this.visible = value;
         }
 
         /**
-         * Gets the value of the colour property.
+         * additional identifier which properly disambiguates the structure view
+         * from any other view with the same attributes. This is not an ID,
+         * because it is possible to have many references to the same physical
+         * structure view from different sequences in an alignment. A
+         * structureState element citing the same viewId will appear for each
+         * instance.
+         * 
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getColour() {
-            return colour;
+        public String getViewId()
+        {
+          return viewId;
         }
 
         /**
-         * Sets the value of the colour property.
+         * Sets the value of the viewId property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
+         *          allowed object is {@link String }
+         * 
+         * @see #getViewId()
          */
-        public void setColour(Integer value) {
-            this.colour = value;
+        public void setViewId(String value)
+        {
+          this.viewId = value;
         }
 
         /**
-         * Gets the value of the start property.
+         * Flag set if the alignment panel containing this JSeq should be
+         * included in those used to perform a structure superposition (since
+         * Jalview 2.7).
+         * 
+         * @return possible object is {@link Boolean }
          * 
          */
-        public int getStart() {
-            return start;
+        public boolean isAlignwithAlignPanel()
+        {
+          if (alignwithAlignPanel == null)
+          {
+            return true;
+          }
+          else
+          {
+            return alignwithAlignPanel;
+          }
         }
 
         /**
-         * Sets the value of the start property.
+         * Sets the value of the alignwithAlignPanel property.
+         * 
+         * @param value
+         *          allowed object is {@link Boolean }
          * 
+         * @see #isAlignwithAlignPanel()
          */
-        public void setStart(int value) {
-            this.start = value;
+        public void setAlignwithAlignPanel(Boolean value)
+        {
+          this.alignwithAlignPanel = value;
         }
 
         /**
-         * Gets the value of the end property.
+         * Flag set if the alignment panel containing this JSeq should be
+         * included in those used to colour its associated sequences in this
+         * structureState(since Jalview 2.7).
+         * 
+         * @return possible object is {@link Boolean }
          * 
          */
-        public int getEnd() {
-            return end;
+        public boolean isColourwithAlignPanel()
+        {
+          if (colourwithAlignPanel == null)
+          {
+            return false;
+          }
+          else
+          {
+            return colourwithAlignPanel;
+          }
         }
 
         /**
-         * Sets the value of the end property.
+         * Sets the value of the colourwithAlignPanel property.
+         * 
+         * @param value
+         *          allowed object is {@link Boolean }
          * 
+         * @see #isColourwithAlignPanel()
          */
-        public void setEnd(int value) {
-            this.end = value;
+        public void setColourwithAlignPanel(Boolean value)
+        {
+          this.colourwithAlignPanel = value;
         }
 
         /**
-         * Gets the value of the id property.
+         * Flag set if the structure display is coloured by the Jmol state,
+         * rather than by one or more linked alignment views.
+         * 
+         * @return possible object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
          */
-        public String getId() {
-            return id;
+        public boolean isColourByJmol()
+        {
+          if (colourByJmol == null)
+          {
+            return true;
+          }
+          else
+          {
+            return colourByJmol;
+          }
         }
 
         /**
-         * Sets the value of the id property.
+         * Sets the value of the colourByJmol property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
+         *          allowed object is {@link Boolean }
+         * 
+         * @see #isColourByJmol()
          */
-        public void setId(String value) {
-            this.id = value;
+        public void setColourByJmol(Boolean value)
+        {
+          this.colourByJmol = value;
         }
 
         /**
-         * Gets the value of the hidden property.
+         * An identifier for the viewer type, currently either JMOL or CHIMERA
+         * 
+         * @return possible object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public Boolean isHidden() {
-            return hidden;
+        public String getType()
+        {
+          return type;
         }
 
         /**
-         * Sets the value of the hidden property.
+         * Sets the value of the type property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link String }
+         * 
+         * @see #getType()
          */
-        public void setHidden(Boolean value) {
-            this.hidden = value;
+        public void setType(String value)
+        {
+          this.type = value;
         }
 
         /**
-         * Gets the value of the viewreference property.
+         * Gets the value of the width property.
+         * 
+         * @return possible object is {@link Integer }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public Boolean isViewreference() {
-            return viewreference;
+        public Integer getWidth()
+        {
+          return width;
         }
 
         /**
-         * Sets the value of the viewreference property.
+         * Sets the value of the width property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
+         *          allowed object is {@link Integer }
+         * 
          */
-        public void setViewreference(Boolean value) {
-            this.viewreference = value;
+        public void setWidth(Integer value)
+        {
+          this.width = value;
         }
 
-
         /**
-         * 
    Java class for anonymous complex type
    .
+         * Gets the value of the height property.
          * 
-         * 
    The following schema fragment specifies the expected content contained within this class.
    
+         * @return possible object is {@link Integer }
          * 
-         * 
    -         * <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>
-         * 
    
+         */
+        public Integer getHeight()
+        {
+          return height;
+        }
+
+        /**
+         * Sets the value of the height property.
          * 
+         * @param value
+         *          allowed object is {@link Integer }
          * 
          */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "", propOrder = {
-            "structureState"
-        })
-        public static class Pdbids
-            extends Pdbentry
+        public void setHeight(Integer value)
         {
-
-            @XmlElement(namespace = "www.jalview.org")
-            protected List structureState;
-
-            /**
-             * Gets the value of the structureState property.
-             * 
-             * 
    This accessor method returns a reference to the live list,
-             * not a snapshot. Therefore any modification you make to the
-             * returned list will be present inside the JAXB object.
-             * This is why there is not a set method for the structureState property.
    
-             * 
-             * 
    
-             * For example, to add a new item, do as follows:
-             * 
    
-             * 
    -             * getStructureState().add(newItem);
-             * 
    
-             * 
-             * 
-             * 
    
-             * Objects of the following type(s) are allowed in the list
-             * {@link JalviewModel.JSeq.Pdbids.StructureState }
-             * 
    
-             * 
-             * 
-             * @return
-             *     The value of the structureState property.
-             */
-            public List getStructureState() {
-                if (structureState == null) {
-                    structureState = new ArrayList();
-                }
-                return this.structureState;
-            }
-
-
-            /**
-             * 
    Java class for anonymous complex type
    .
-             * 
-             * 
    The following schema fragment specifies the expected content contained within this class.
    
-             * 
-             * 
    -             * <complexType>
-             *   <simpleContent>
-             *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-             *       <attGroup ref="{www.jalview.org}swingwindow"/>
-             *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-             *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     </extension>
-             *   </simpleContent>
-             * </complexType>
-             * 
    
-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "", propOrder = {
-                "value"
-            })
-            public static class StructureState {
-
-                @XmlValue
-                protected String value;
-                @XmlAttribute(name = "visible")
-                protected Boolean visible;
-                /**
-                 * additional
-                 * 																			identifier
-                 * 																			which
-                 * 																			properly
-                 * 																			disambiguates
-                 * 																			the
-                 * 																			structure
-                 * 																			view
-                 * 																			from
-                 * 																			any
-                 * 																			other
-                 * 																			view
-                 * 																			with
-                 * 																			the
-                 * 																			same
-                 * 																			attributes.
-                 * 																			This
-                 * 																			is
-                 * 																			not
-                 * 																			an
-                 * 																			ID,
-                 * 																			because
-                 * 																			it
-                 * 																			is
-                 * 																			possible
-                 * 																			to
-                 * 																			have
-                 * 																			many
-                 * 																			references
-                 * 																			to
-                 * 																			the
-                 * 																			same
-                 * 																			physical
-                 * 																			structure
-                 * 																			view
-                 * 																			from
-                 * 																			different
-                 * 																			sequences
-                 * 																			in
-                 * 																			an
-                 * 																			alignment.
-                 * 																			A
-                 * 																			structureState
-                 * 																			element
-                 * 																			citing
-                 * 																			the
-                 * 																			same
-                 * 																			viewId
-                 * 																			will
-                 * 																			appear
-                 * 																			for
-                 * 																			each
-                 * 																			instance.
-                 * 
-                 */
-                @XmlAttribute(name = "viewId")
-                protected String viewId;
-                /**
-                 * Flag
-                 * 																			set
-                 * 																			if
-                 * 																			the
-                 * 																			alignment
-                 * 																			panel
-                 * 																			containing
-                 * 																			this
-                 * 																			JSeq
-                 * 																			should
-                 * 																			be
-                 * 																			included
-                 * 																			in
-                 * 																			those
-                 * 																			used
-                 * 																			to
-                 * 																			perform
-                 * 																			a
-                 * 																			structure
-                 * 																			superposition
-                 * 																			(since
-                 * 																			Jalview
-                 * 																			2.7).
-                 * 
-                 */
-                @XmlAttribute(name = "alignwithAlignPanel")
-                protected Boolean alignwithAlignPanel;
-                /**
-                 * Flag
-                 * 																			set
-                 * 																			if
-                 * 																			the
-                 * 																			alignment
-                 * 																			panel
-                 * 																			containing
-                 * 																			this
-                 * 																			JSeq
-                 * 																			should
-                 * 																			be
-                 * 																			included
-                 * 																			in
-                 * 																			those
-                 * 																			used
-                 * 																			to
-                 * 																			colour
-                 * 																			its
-                 * 																			associated
-                 * 																			sequences
-                 * 																			in
-                 * 																			this
-                 * 																			structureState(since
-                 * 																			Jalview
-                 * 																			2.7).
-                 * 
-                 */
-                @XmlAttribute(name = "colourwithAlignPanel")
-                protected Boolean colourwithAlignPanel;
-                /**
-                 * Flag
-                 * 																			set
-                 * 																			if
-                 * 																			the
-                 * 																			structure
-                 * 																			display
-                 * 																			is
-                 * 																			coloured
-                 * 																			by
-                 * 																			the
-                 * 																			Jmol
-                 * 																			state,
-                 * 																			rather
-                 * 																			than
-                 * 																			by
-                 * 																			one
-                 * 																			or
-                 * 																			more
-                 * 																			linked
-                 * 																			alignment
-                 * 																			views.
-                 * 
-                 */
-                @XmlAttribute(name = "colourByJmol")
-                protected Boolean colourByJmol;
-                /**
-                 * An
-                 * 																			identifier
-                 * 																			for
-                 * 																			the
-                 * 																			viewer
-                 * 																			type,
-                 * 																			currently
-                 * 																			either
-                 * 																			JMOL
-                 * 																			or
-                 * 																			CHIMERA
-                 * 
-                 */
-                @XmlAttribute(name = "type")
-                protected String type;
-                @XmlAttribute(name = "width")
-                protected Integer width;
-                @XmlAttribute(name = "height")
-                protected Integer height;
-                @XmlAttribute(name = "xpos")
-                protected Integer xpos;
-                @XmlAttribute(name = "ypos")
-                protected Integer ypos;
-
-                /**
-                 * Gets the value of the value property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getValue() {
-                    return value;
-                }
-
-                /**
-                 * Sets the value of the value property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setValue(String value) {
-                    this.value = value;
-                }
-
-                /**
-                 * Gets the value of the visible property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public Boolean isVisible() {
-                    return visible;
-                }
-
-                /**
-                 * Sets the value of the visible property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public void setVisible(Boolean value) {
-                    this.visible = value;
-                }
-
-                /**
-                 * additional
-                 * 																			identifier
-                 * 																			which
-                 * 																			properly
-                 * 																			disambiguates
-                 * 																			the
-                 * 																			structure
-                 * 																			view
-                 * 																			from
-                 * 																			any
-                 * 																			other
-                 * 																			view
-                 * 																			with
-                 * 																			the
-                 * 																			same
-                 * 																			attributes.
-                 * 																			This
-                 * 																			is
-                 * 																			not
-                 * 																			an
-                 * 																			ID,
-                 * 																			because
-                 * 																			it
-                 * 																			is
-                 * 																			possible
-                 * 																			to
-                 * 																			have
-                 * 																			many
-                 * 																			references
-                 * 																			to
-                 * 																			the
-                 * 																			same
-                 * 																			physical
-                 * 																			structure
-                 * 																			view
-                 * 																			from
-                 * 																			different
-                 * 																			sequences
-                 * 																			in
-                 * 																			an
-                 * 																			alignment.
-                 * 																			A
-                 * 																			structureState
-                 * 																			element
-                 * 																			citing
-                 * 																			the
-                 * 																			same
-                 * 																			viewId
-                 * 																			will
-                 * 																			appear
-                 * 																			for
-                 * 																			each
-                 * 																			instance.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getViewId() {
-                    return viewId;
-                }
-
-                /**
-                 * Sets the value of the viewId property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 * @see #getViewId()
-                 */
-                public void setViewId(String value) {
-                    this.viewId = value;
-                }
-
-                /**
-                 * Flag
-                 * 																			set
-                 * 																			if
-                 * 																			the
-                 * 																			alignment
-                 * 																			panel
-                 * 																			containing
-                 * 																			this
-                 * 																			JSeq
-                 * 																			should
-                 * 																			be
-                 * 																			included
-                 * 																			in
-                 * 																			those
-                 * 																			used
-                 * 																			to
-                 * 																			perform
-                 * 																			a
-                 * 																			structure
-                 * 																			superposition
-                 * 																			(since
-                 * 																			Jalview
-                 * 																			2.7).
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isAlignwithAlignPanel() {
-                    if (alignwithAlignPanel == null) {
-                        return true;
-                    } else {
-                        return alignwithAlignPanel;
-                    }
-                }
-
-                /**
-                 * Sets the value of the alignwithAlignPanel property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 * @see #isAlignwithAlignPanel()
-                 */
-                public void setAlignwithAlignPanel(Boolean value) {
-                    this.alignwithAlignPanel = value;
-                }
-
-                /**
-                 * Flag
-                 * 																			set
-                 * 																			if
-                 * 																			the
-                 * 																			alignment
-                 * 																			panel
-                 * 																			containing
-                 * 																			this
-                 * 																			JSeq
-                 * 																			should
-                 * 																			be
-                 * 																			included
-                 * 																			in
-                 * 																			those
-                 * 																			used
-                 * 																			to
-                 * 																			colour
-                 * 																			its
-                 * 																			associated
-                 * 																			sequences
-                 * 																			in
-                 * 																			this
-                 * 																			structureState(since
-                 * 																			Jalview
-                 * 																			2.7).
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isColourwithAlignPanel() {
-                    if (colourwithAlignPanel == null) {
-                        return false;
-                    } else {
-                        return colourwithAlignPanel;
-                    }
-                }
-
-                /**
-                 * Sets the value of the colourwithAlignPanel property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 * @see #isColourwithAlignPanel()
-                 */
-                public void setColourwithAlignPanel(Boolean value) {
-                    this.colourwithAlignPanel = value;
-                }
-
-                /**
-                 * Flag
-                 * 																			set
-                 * 																			if
-                 * 																			the
-                 * 																			structure
-                 * 																			display
-                 * 																			is
-                 * 																			coloured
-                 * 																			by
-                 * 																			the
-                 * 																			Jmol
-                 * 																			state,
-                 * 																			rather
-                 * 																			than
-                 * 																			by
-                 * 																			one
-                 * 																			or
-                 * 																			more
-                 * 																			linked
-                 * 																			alignment
-                 * 																			views.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public boolean isColourByJmol() {
-                    if (colourByJmol == null) {
-                        return true;
-                    } else {
-                        return colourByJmol;
-                    }
-                }
-
-                /**
-                 * Sets the value of the colourByJmol property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 * @see #isColourByJmol()
-                 */
-                public void setColourByJmol(Boolean value) {
-                    this.colourByJmol = value;
-                }
-
-                /**
-                 * An
-                 * 																			identifier
-                 * 																			for
-                 * 																			the
-                 * 																			viewer
-                 * 																			type,
-                 * 																			currently
-                 * 																			either
-                 * 																			JMOL
-                 * 																			or
-                 * 																			CHIMERA
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getType() {
-                    return type;
-                }
-
-                /**
-                 * Sets the value of the type property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 * @see #getType()
-                 */
-                public void setType(String value) {
-                    this.type = value;
-                }
-
-                /**
-                 * Gets the value of the width property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getWidth() {
-                    return width;
-                }
-
-                /**
-                 * Sets the value of the width property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setWidth(Integer value) {
-                    this.width = value;
-                }
-
-                /**
-                 * Gets the value of the height property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getHeight() {
-                    return height;
-                }
-
-                /**
-                 * Sets the value of the height property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setHeight(Integer value) {
-                    this.height = value;
-                }
-
-                /**
-                 * Gets the value of the xpos property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getXpos() {
-                    return xpos;
-                }
-
-                /**
-                 * Sets the value of the xpos property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setXpos(Integer value) {
-                    this.xpos = value;
-                }
-
-                /**
-                 * Gets the value of the ypos property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public Integer getYpos() {
-                    return ypos;
-                }
-
-                /**
-                 * Sets the value of the ypos property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Integer }
-                 *     
-                 */
-                public void setYpos(Integer value) {
-                    this.ypos = value;
-                }
-
-            }
-
+          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>
-         *         <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>
-         * 
    
+         */
+        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 = {
-            "secondaryStructure"
-        })
-        public static class RnaViewer {
-
-            @XmlElement(namespace = "www.jalview.org", required = true)
-            protected List secondaryStructure;
-            @XmlAttribute(name = "title")
-            protected String title;
-            /**
-             * An id unique to the RNA
-             * 												viewer panel
-             * 
-             */
-            @XmlAttribute(name = "viewId")
-            protected String viewId;
-            /**
-             * horizontal position of
-             * 												split pane divider
-             * 
-             */
-            @XmlAttribute(name = "dividerLocation")
-            protected Integer dividerLocation;
-            /**
-             * Index of the selected
-             * 												structure in the viewer
-             * 												panel
-             * 
-             */
-            @XmlAttribute(name = "selectedRna")
-            protected Integer selectedRna;
-            @XmlAttribute(name = "width")
-            protected Integer width;
-            @XmlAttribute(name = "height")
-            protected Integer height;
-            @XmlAttribute(name = "xpos")
-            protected Integer xpos;
-            @XmlAttribute(name = "ypos")
-            protected Integer ypos;
-
-            /**
-             * Gets the value of the secondaryStructure property.
-             * 
-             * 
    This accessor method returns a reference to the live list,
-             * not a snapshot. Therefore any modification you make to the
-             * returned list will be present inside the JAXB object.
-             * This is why there is not a set method for the secondaryStructure property.
    
-             * 
-             * 
    
-             * For example, to add a new item, do as follows:
-             * 
    
-             * 
    -             * getSecondaryStructure().add(newItem);
-             * 
    
-             * 
-             * 
-             * 
    
-             * Objects of the following type(s) are allowed in the list
-             * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-             * 
    
-             * 
-             * 
-             * @return
-             *     The value of the secondaryStructure property.
-             */
-            public List getSecondaryStructure() {
-                if (secondaryStructure == null) {
-                    secondaryStructure = new ArrayList();
-                }
-                return this.secondaryStructure;
-            }
-
-            /**
-             * Gets the value of the title property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getTitle() {
-                return title;
-            }
-
-            /**
-             * Sets the value of the title property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setTitle(String value) {
-                this.title = value;
-            }
-
-            /**
-             * An id unique to the RNA
-             * 												viewer panel
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getViewId() {
-                return viewId;
-            }
-
-            /**
-             * Sets the value of the viewId property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             * @see #getViewId()
-             */
-            public void setViewId(String value) {
-                this.viewId = value;
-            }
-
-            /**
-             * horizontal position of
-             * 												split pane divider
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getDividerLocation() {
-                return dividerLocation;
-            }
-
-            /**
-             * Sets the value of the dividerLocation property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             * @see #getDividerLocation()
-             */
-            public void setDividerLocation(Integer value) {
-                this.dividerLocation = value;
-            }
-
-            /**
-             * Index of the selected
-             * 												structure in the viewer
-             * 												panel
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getSelectedRna() {
-                return selectedRna;
-            }
-
-            /**
-             * Sets the value of the selectedRna property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             * @see #getSelectedRna()
-             */
-            public void setSelectedRna(Integer value) {
-                this.selectedRna = value;
-            }
-
-            /**
-             * Gets the value of the width property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getWidth() {
-                return width;
-            }
-
-            /**
-             * Sets the value of the width property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setWidth(Integer value) {
-                this.width = value;
-            }
-
-            /**
-             * Gets the value of the height property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getHeight() {
-                return height;
-            }
-
-            /**
-             * Sets the value of the height property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setHeight(Integer value) {
-                this.height = value;
-            }
-
-            /**
-             * Gets the value of the xpos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getXpos() {
-                return xpos;
-            }
-
-            /**
-             * Sets the value of the xpos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setXpos(Integer value) {
-                this.xpos = value;
-            }
-
-            /**
-             * Gets the value of the ypos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Integer }
-             *     
-             */
-            public Integer getYpos() {
-                return ypos;
-            }
-
-            /**
-             * Sets the value of the ypos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Integer }
-             *     
-             */
-            public void setYpos(Integer value) {
-                this.ypos = value;
-            }
-
-
-            /**
-             * 
    Java class for anonymous complex type
    .
-             * 
-             * 
    The following schema fragment specifies the expected content contained within this class.
    
-             * 
-             * 
    -             * <complexType>
-             *   <complexContent>
-             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     </restriction>
-             *   </complexContent>
-             * </complexType>
-             * 
    
-             * 
-             * 
-             */
-            @XmlAccessorType(XmlAccessType.FIELD)
-            @XmlType(name = "")
-            public static class SecondaryStructure {
-
-                @XmlAttribute(name = "title")
-                protected String title;
-                /**
-                 * id attribute
-                 * 															of
-                 * 															Annotation
-                 * 															in
-                 * 															vamsasModel
-                 * 															for the
-                 * 															secondary
-                 * 															structure
-                 * 															annotation
-                 * 															shown in the
-                 * 															viewer
-                 * 
-                 */
-                @XmlAttribute(name = "annotationId", required = true)
-                protected String annotationId;
-                /**
-                 * if true the
-                 * 															RNA
-                 * 															structure is
-                 * 															shown with
-                 * 															gaps, if
-                 * 															false
-                 * 															without
-                 * 
-                 */
-                @XmlAttribute(name = "gapped")
-                protected Boolean gapped;
-                /**
-                 * name of the
-                 * 															project jar
-                 * 															entry that
-                 * 															holds the
-                 * 															VARNA viewer
-                 * 															state for
-                 * 															the
-                 * 															structure
-                 * 
-                 */
-                @XmlAttribute(name = "viewerState")
-                protected String viewerState;
-
-                /**
-                 * Gets the value of the title property.
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getTitle() {
-                    return title;
-                }
-
-                /**
-                 * Sets the value of the title property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 */
-                public void setTitle(String value) {
-                    this.title = value;
-                }
-
-                /**
-                 * id attribute
-                 * 															of
-                 * 															Annotation
-                 * 															in
-                 * 															vamsasModel
-                 * 															for the
-                 * 															secondary
-                 * 															structure
-                 * 															annotation
-                 * 															shown in the
-                 * 															viewer
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getAnnotationId() {
-                    return annotationId;
-                }
-
-                /**
-                 * Sets the value of the annotationId property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 * @see #getAnnotationId()
-                 */
-                public void setAnnotationId(String value) {
-                    this.annotationId = value;
-                }
-
-                /**
-                 * if true the
-                 * 															RNA
-                 * 															structure is
-                 * 															shown with
-                 * 															gaps, if
-                 * 															false
-                 * 															without
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link Boolean }
-                 *     
-                 */
-                public Boolean isGapped() {
-                    return gapped;
-                }
-
-                /**
-                 * Sets the value of the gapped property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link Boolean }
-                 *     
-                 * @see #isGapped()
-                 */
-                public void setGapped(Boolean value) {
-                    this.gapped = value;
-                }
-
-                /**
-                 * name of the
-                 * 															project jar
-                 * 															entry that
-                 * 															holds the
-                 * 															VARNA viewer
-                 * 															state for
-                 * 															the
-                 * 															structure
-                 * 
-                 * @return
-                 *     possible object is
-                 *     {@link String }
-                 *     
-                 */
-                public String getViewerState() {
-                    return viewerState;
-                }
-
-                /**
-                 * Sets the value of the viewerState property.
-                 * 
-                 * @param value
-                 *     allowed object is
-                 *     {@link String }
-                 *     
-                 * @see #getViewerState()
-                 */
-                public void setViewerState(String value) {
-                    this.viewerState = value;
-                }
-
-            }
+        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">
+     *         <element name="secondaryStructure" 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"/>
+     *                 <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>
-     *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
      *       </sequence>
      *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
      *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <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>
@@ -3778,1636 +3122,1133 @@ 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;
-        /**
-         * endpoints of X, Y and Z axes in that order
-         * 
-         */
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List axis;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected PcaDataType pcaData;
+    @XmlType(name = "", propOrder = { "secondaryStructure" })
+    public static class RnaViewer
+    {
+
+      @XmlElement(namespace = "www.jalview.org", required = true)
+      protected List secondaryStructure;
+
+      @XmlAttribute(name = "title")
+      protected String title;
+
+      /**
+       * An id unique to the RNA viewer panel
+       * 
+       */
+      @XmlAttribute(name = "viewId")
+      protected String viewId;
+
+      /**
+       * horizontal position of split pane divider
+       * 
+       */
+      @XmlAttribute(name = "dividerLocation")
+      protected Integer dividerLocation;
+
+      /**
+       * Index of the selected structure in the viewer panel
+       * 
+       */
+      @XmlAttribute(name = "selectedRna")
+      protected Integer selectedRna;
+
+      @XmlAttribute(name = "width")
+      protected Integer width;
+
+      @XmlAttribute(name = "height")
+      protected Integer height;
+
+      @XmlAttribute(name = "xpos")
+      protected Integer xpos;
+
+      @XmlAttribute(name = "ypos")
+      protected Integer ypos;
+
+      /**
+       * Gets the value of the secondaryStructure property.
+       * 
+       * 
    
+       * This accessor method returns a reference to the live list, not a
+       * snapshot. Therefore any modification you make to the returned list will
+       * be present inside the JAXB object. This is why there is not a
+       * set method for the secondaryStructure property.
+       * 
    
+       * 
+       * 
    
+       * For example, to add a new item, do as follows:
+       * 
    
+       * 
+       * 
    +       * getSecondaryStructure().add(newItem);
+       * 
    
+       * 
+       * 
+       * 
    
+       * Objects of the following type(s) are allowed in the list
+       * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+       * 
    
+       * 
+       * 
+       * @return The value of the secondaryStructure property.
+       */
+      public List getSecondaryStructure()
+      {
+        if (secondaryStructure == null)
+        {
+          secondaryStructure = new ArrayList();
+        }
+        return this.secondaryStructure;
+      }
+
+      /**
+       * Gets the value of the title property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getTitle()
+      {
+        return title;
+      }
+
+      /**
+       * Sets the value of the title property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setTitle(String value)
+      {
+        this.title = value;
+      }
+
+      /**
+       * An id unique to the RNA viewer panel
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getViewId()
+      {
+        return viewId;
+      }
+
+      /**
+       * Sets the value of the viewId property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       * @see #getViewId()
+       */
+      public void setViewId(String value)
+      {
+        this.viewId = value;
+      }
+
+      /**
+       * horizontal position of split pane divider
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getDividerLocation()
+      {
+        return dividerLocation;
+      }
+
+      /**
+       * Sets the value of the dividerLocation property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       * @see #getDividerLocation()
+       */
+      public void setDividerLocation(Integer value)
+      {
+        this.dividerLocation = value;
+      }
+
+      /**
+       * Index of the selected structure in the viewer panel
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getSelectedRna()
+      {
+        return selectedRna;
+      }
+
+      /**
+       * Sets the value of the selectedRna property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       * @see #getSelectedRna()
+       */
+      public void setSelectedRna(Integer value)
+      {
+        this.selectedRna = value;
+      }
+
+      /**
+       * Gets the value of the width property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getWidth()
+      {
+        return width;
+      }
+
+      /**
+       * Sets the value of the width property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setWidth(Integer value)
+      {
+        this.width = value;
+      }
+
+      /**
+       * Gets the value of the height property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getHeight()
+      {
+        return height;
+      }
+
+      /**
+       * Sets the value of the height property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setHeight(Integer value)
+      {
+        this.height = value;
+      }
+
+      /**
+       * Gets the value of the xpos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getXpos()
+      {
+        return xpos;
+      }
+
+      /**
+       * Sets the value of the xpos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setXpos(Integer value)
+      {
+        this.xpos = value;
+      }
+
+      /**
+       * Gets the value of the ypos property.
+       * 
+       * @return possible object is {@link Integer }
+       * 
+       */
+      public Integer getYpos()
+      {
+        return ypos;
+      }
+
+      /**
+       * Sets the value of the ypos property.
+       * 
+       * @param value
+       *          allowed object is {@link Integer }
+       * 
+       */
+      public void setYpos(Integer value)
+      {
+        this.ypos = value;
+      }
+
+      /**
+       * 
    
+       * Java class for anonymous complex type
+       * 
    
+       * .
+       * 
+       * 
    
+       * The following schema fragment specifies the expected content contained
+       * within this class.
+       * 
    
+       * 
+       * 
    +       * <complexType>
+       *   <complexContent>
+       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </restriction>
+       *   </complexContent>
+       * </complexType>
+       * 
    
+       * 
+       * 
+       */
+      @XmlAccessorType(XmlAccessType.FIELD)
+      @XmlType(name = "")
+      public static class SecondaryStructure
+      {
+
         @XmlAttribute(name = "title")
         protected String title;
-        @XmlAttribute(name = "scoreModelName")
-        protected String scoreModelName;
-        @XmlAttribute(name = "xDim")
-        protected Integer xDim;
-        @XmlAttribute(name = "yDim")
-        protected Integer yDim;
-        @XmlAttribute(name = "zDim")
-        protected Integer zDim;
-        @XmlAttribute(name = "bgColour")
-        protected Integer bgColour;
-        @XmlAttribute(name = "scaleFactor")
-        protected Float scaleFactor;
-        @XmlAttribute(name = "showLabels")
-        protected Boolean showLabels;
-        @XmlAttribute(name = "linkToAllViews")
-        protected Boolean linkToAllViews;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
-        @XmlAttribute(name = "includeGaps")
-        protected Boolean includeGaps;
-        @XmlAttribute(name = "matchGaps")
-        protected Boolean matchGaps;
-        @XmlAttribute(name = "includeGappedColumns")
-        protected Boolean includeGappedColumns;
-        @XmlAttribute(name = "denominateByShortestLength")
-        protected Boolean denominateByShortestLength;
-
-        /**
-         * Gets the value of the sequencePoint property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the sequencePoint property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getSequencePoint().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.PcaViewer.SequencePoint }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the sequencePoint property.
-         */
-        public List getSequencePoint() {
-            if (sequencePoint == null) {
-                sequencePoint = new ArrayList();
-            }
-            return this.sequencePoint;
-        }
-
-        /**
-         * endpoints of X, Y and Z axes in that order
-         * 
-         * Gets the value of the axis property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the axis property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getAxis().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.PcaViewer.Axis }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the axis property.
-         */
-        public List getAxis() {
-            if (axis == null) {
-                axis = new ArrayList();
-            }
-            return this.axis;
-        }
-
-        /**
-         * Gets the value of the 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.
+         * id attribute of Annotation in vamsasModel for the secondary structure
+         * annotation shown in the viewer
          * 
-         * @param value
-         *     allowed object is
-         *     {@link JalviewModel.PcaViewer.SeqPointMax }
-         *     
          */
-        public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
-            this.seqPointMax = value;
-        }
+        @XmlAttribute(name = "annotationId", required = true)
+        protected String annotationId;
 
         /**
-         * Gets the value of the pcaData property.
+         * if true the RNA structure is shown with gaps, if false without
          * 
-         * @return
-         *     possible object is
-         *     {@link PcaDataType }
-         *     
          */
-        public PcaDataType getPcaData() {
-            return pcaData;
-        }
+        @XmlAttribute(name = "gapped")
+        protected Boolean gapped;
 
         /**
-         * Sets the value of the pcaData property.
+         * name of the project jar entry that holds the VARNA viewer state for
+         * the structure
          * 
-         * @param value
-         *     allowed object is
-         *     {@link PcaDataType }
-         *     
          */
-        public void setPcaData(PcaDataType value) {
-            this.pcaData = value;
-        }
+        @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 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;
-        }
-
-        /**
-         * 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 String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getZDim() {
-            return zDim;
+        public String getTitle()
+        {
+          return title;
         }
 
         /**
-         * Sets the value of the zDim property.
+         * Sets the value of the title property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setZDim(Integer value) {
-            this.zDim = value;
-        }
-
-        /**
-         * Gets the value of the bgColour property.
+         *          allowed object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getBgColour() {
-            return bgColour;
+        public void setTitle(String value)
+        {
+          this.title = value;
         }
 
         /**
-         * Sets the value of the bgColour property.
+         * id attribute of Annotation in vamsasModel for the secondary structure
+         * annotation shown in the viewer
          * 
-         * @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 String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
          */
-        public Float getScaleFactor() {
-            return scaleFactor;
+        public String getAnnotationId()
+        {
+          return annotationId;
         }
 
         /**
-         * Sets the value of the scaleFactor property.
+         * Sets the value of the annotationId property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setScaleFactor(Float value) {
-            this.scaleFactor = value;
-        }
-
-        /**
-         * Gets the value of the showLabels property.
+         *          allowed object is {@link String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
+         * @see #getAnnotationId()
          */
-        public Boolean isShowLabels() {
-            return showLabels;
+        public void setAnnotationId(String value)
+        {
+          this.annotationId = value;
         }
 
         /**
-         * Sets the value of the showLabels property.
+         * if true the RNA structure is shown with gaps, if false without
          * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowLabels(Boolean value) {
-            this.showLabels = value;
-        }
-
-        /**
-         * Gets the value of the linkToAllViews property.
+         * @return possible object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
          */
-        public Boolean isLinkToAllViews() {
-            return linkToAllViews;
+        public Boolean isGapped()
+        {
+          return gapped;
         }
 
         /**
-         * Sets the value of the linkToAllViews property.
+         * Sets the value of the gapped property.
          * 
          * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setLinkToAllViews(Boolean value) {
-            this.linkToAllViews = value;
-        }
-
-        /**
-         * Gets the value of the width property.
+         *          allowed object is {@link Boolean }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
+         * @see #isGapped()
          */
-        public Integer getWidth() {
-            return width;
+        public void setGapped(Boolean value)
+        {
+          this.gapped = value;
         }
 
         /**
-         * Sets the value of the width property.
+         * name of the project jar entry that holds the VARNA viewer state for
+         * the structure
          * 
-         * @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 String }
          * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
          */
-        public Integer getHeight() {
-            return height;
+        public String getViewerState()
+        {
+          return viewerState;
         }
 
         /**
-         * Sets the value of the height property.
+         * Sets the value of the viewerState 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.
+         *          allowed object is {@link String }
          * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
+         * @see #getViewerState()
          */
-        public void setXpos(Integer value) {
-            this.xpos = value;
+        public void setViewerState(String value)
+        {
+          this.viewerState = 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;
-        }
+    }
 
-        /**
-         * Gets the value of the includeGaps property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isIncludeGaps() {
-            return includeGaps;
-        }
+  }
+
+  /**
+   * 
    
+   * Java class for anonymous complex type
+   * 
    
+   * .
+   * 
+   * 
    
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
    
+   * 
+   * 
    +   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="sequencePoint" maxOccurs="unbounded">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="axis" maxOccurs="3" minOccurs="3">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="seqPointMin">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="seqPointMax">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}position"/>
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
+   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
    
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
+  public static class PcaViewer
+  {
+
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List sequencePoint;
 
-        /**
-         * Sets the value of the includeGaps property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setIncludeGaps(Boolean value) {
-            this.includeGaps = value;
-        }
+    /**
+     * endpoints of X, Y and Z axes in that order
+     * 
+     */
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected List axis;
 
-        /**
-         * Gets the value of the matchGaps property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isMatchGaps() {
-            return matchGaps;
-        }
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
 
-        /**
-         * Sets the value of the matchGaps property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setMatchGaps(Boolean value) {
-            this.matchGaps = value;
-        }
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
 
-        /**
-         * Gets the value of the includeGappedColumns property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isIncludeGappedColumns() {
-            return includeGappedColumns;
-        }
+    @XmlElement(namespace = "www.jalview.org", required = true)
+    protected PcaDataType pcaData;
 
-        /**
-         * Sets the value of the includeGappedColumns property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setIncludeGappedColumns(Boolean value) {
-            this.includeGappedColumns = value;
-        }
+    @XmlAttribute(name = "title")
+    protected String title;
 
-        /**
-         * Gets the value of the denominateByShortestLength property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isDenominateByShortestLength() {
-            return denominateByShortestLength;
-        }
+    @XmlAttribute(name = "scoreModelName")
+    protected String scoreModelName;
 
-        /**
-         * Sets the value of the denominateByShortestLength property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setDenominateByShortestLength(Boolean value) {
-            this.denominateByShortestLength = value;
-        }
+    @XmlAttribute(name = "xDim")
+    protected Integer xDim;
 
+    @XmlAttribute(name = "yDim")
+    protected Integer yDim;
 
-        /**
-         * 
    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;
-            }
+    @XmlAttribute(name = "zDim")
+    protected Integer zDim;
 
-        }
+    @XmlAttribute(name = "bgColour")
+    protected Integer bgColour;
 
+    @XmlAttribute(name = "scaleFactor")
+    protected Float 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"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
    
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SeqPointMax {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    @XmlAttribute(name = "showLabels")
+    protected Boolean showLabels;
 
-        }
+    @XmlAttribute(name = "linkToAllViews")
+    protected Boolean linkToAllViews;
 
+    @XmlAttribute(name = "width")
+    protected Integer 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"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
    
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SeqPointMin {
-
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    @XmlAttribute(name = "height")
+    protected Integer height;
 
-        }
+    @XmlAttribute(name = "xpos")
+    protected Integer xpos;
 
+    @XmlAttribute(name = "ypos")
+    protected Integer 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">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
    
-         * 
-         * 
-         */
-        @XmlAccessorType(XmlAccessType.FIELD)
-        @XmlType(name = "")
-        public static class SequencePoint {
-
-            @XmlAttribute(name = "sequenceRef")
-            protected String sequenceRef;
-            @XmlAttribute(name = "xPos")
-            protected Float xPos;
-            @XmlAttribute(name = "yPos")
-            protected Float yPos;
-            @XmlAttribute(name = "zPos")
-            protected Float zPos;
-
-            /**
-             * Gets the value of the sequenceRef property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getSequenceRef() {
-                return sequenceRef;
-            }
-
-            /**
-             * Sets the value of the sequenceRef property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             */
-            public void setSequenceRef(String value) {
-                this.sequenceRef = value;
-            }
-
-            /**
-             * Gets the value of the xPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getXPos() {
-                return xPos;
-            }
-
-            /**
-             * Sets the value of the xPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setXPos(Float value) {
-                this.xPos = value;
-            }
-
-            /**
-             * Gets the value of the yPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getYPos() {
-                return yPos;
-            }
-
-            /**
-             * Sets the value of the yPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setYPos(Float value) {
-                this.yPos = value;
-            }
-
-            /**
-             * Gets the value of the zPos property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Float }
-             *     
-             */
-            public Float getZPos() {
-                return zPos;
-            }
-
-            /**
-             * Sets the value of the zPos property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Float }
-             *     
-             */
-            public void setZPos(Float value) {
-                this.zPos = value;
-            }
+    @XmlAttribute(name = "includeGaps")
+    protected Boolean includeGaps;
 
-        }
+    @XmlAttribute(name = "matchGaps")
+    protected Boolean matchGaps;
 
-    }
+    @XmlAttribute(name = "includeGappedColumns")
+    protected Boolean includeGappedColumns;
 
+    @XmlAttribute(name = "denominateByShortestLength")
+    protected Boolean denominateByShortestLength;
 
     /**
-     * 
    Java class for anonymous complex type
    .
+     * Gets the value of the sequencePoint 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 sequencePoint property.
+     * 
    
      * 
-     * 
    -     * <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>
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    
+     * 
+     * 
    +     * getSequencePoint().add(newItem);
      * 
    
      * 
      * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer.SequencePoint }
+     * 
    
+     * 
+     * 
+     * @return The value of the sequencePoint property.
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "title",
-        "newick"
-    })
-    public static class Tree {
+    public List getSequencePoint()
+    {
+      if (sequencePoint == null)
+      {
+        sequencePoint = new ArrayList();
+      }
+      return this.sequencePoint;
+    }
 
-        @XmlElement(namespace = "www.jalview.org")
-        protected String title;
-        @XmlElement(namespace = "www.jalview.org")
-        protected String newick;
-        @XmlAttribute(name = "fontName")
-        protected String fontName;
-        @XmlAttribute(name = "fontSize")
-        protected Integer fontSize;
-        @XmlAttribute(name = "fontStyle")
-        protected Integer fontStyle;
-        @XmlAttribute(name = "threshold")
-        protected Float threshold;
-        @XmlAttribute(name = "showBootstrap")
-        protected Boolean showBootstrap;
-        @XmlAttribute(name = "showDistances")
-        protected Boolean showDistances;
-        @XmlAttribute(name = "markUnlinked")
-        protected Boolean markUnlinked;
-        @XmlAttribute(name = "fitToWindow")
-        protected Boolean fitToWindow;
-        @XmlAttribute(name = "currentTree")
-        protected Boolean currentTree;
-        /**
-         * Set for trees associated with columns of an alignment, sequence or annotation row
-         * 
-         */
-        @XmlAttribute(name = "columnWise")
-        protected Boolean columnWise;
-        /**
-         * Refers to annotation row the tree is provided by
-         * 
-         */
-        @XmlAttribute(name = "columnReference")
-        protected String columnReference;
-        /**
-         * Tree ID added for binding tree
-         * 									visualization
-         * 									settings to vamsas
-         * 									document trees in jalview 2.4.1
-         * 
-         */
-        @XmlAttribute(name = "id")
-        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-        @XmlID
-        @XmlSchemaType(name = "ID")
-        protected String id;
-        @XmlAttribute(name = "linkToAllViews")
-        protected Boolean linkToAllViews;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
+    /**
+     * endpoints of X, Y and Z axes in that order
+     * 
+     * Gets the value of the axis property.
+     * 
+     * 
    
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the axis property.
+     * 
    
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    
+     * 
+     * 
    +     * getAxis().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer.Axis }
+     * 
    
+     * 
+     * 
+     * @return The value of the axis property.
+     */
+    public List getAxis()
+    {
+      if (axis == null)
+      {
+        axis = new ArrayList();
+      }
+      return this.axis;
+    }
 
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getTitle() {
-            return title;
-        }
+    /**
+     * Gets the value of the seqPointMin property.
+     * 
+     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
+    {
+      return seqPointMin;
+    }
 
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setTitle(String value) {
-            this.title = value;
-        }
+    /**
+     * Sets the value of the seqPointMin property.
+     * 
+     * @param value
+     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
+     * 
+     */
+    public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
+    {
+      this.seqPointMin = value;
+    }
 
-        /**
-         * Gets the value of the newick property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getNewick() {
-            return newick;
-        }
+    /**
+     * Gets the value of the seqPointMax property.
+     * 
+     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
+    {
+      return seqPointMax;
+    }
 
-        /**
-         * Sets the value of the newick property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setNewick(String value) {
-            this.newick = value;
-        }
+    /**
+     * Sets the value of the seqPointMax property.
+     * 
+     * @param value
+     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
+     * 
+     */
+    public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
+    {
+      this.seqPointMax = value;
+    }
 
-        /**
-         * Gets the value of the fontName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getFontName() {
-            return fontName;
-        }
+    /**
+     * Gets the value of the pcaData property.
+     * 
+     * @return possible object is {@link PcaDataType }
+     * 
+     */
+    public PcaDataType getPcaData()
+    {
+      return pcaData;
+    }
 
-        /**
-         * Sets the value of the fontName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setFontName(String value) {
-            this.fontName = value;
-        }
+    /**
+     * Sets the value of the pcaData property.
+     * 
+     * @param value
+     *          allowed object is {@link PcaDataType }
+     * 
+     */
+    public void setPcaData(PcaDataType value)
+    {
+      this.pcaData = value;
+    }
 
-        /**
-         * Gets the value of the fontSize property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontSize() {
-            return fontSize;
-        }
+    /**
+     * Gets the value of the title property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getTitle()
+    {
+      return title;
+    }
 
-        /**
-         * Sets the value of the fontSize property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontSize(Integer value) {
-            this.fontSize = value;
-        }
+    /**
+     * Sets the value of the title property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setTitle(String value)
+    {
+      this.title = value;
+    }
 
-        /**
-         * Gets the value of the fontStyle property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontStyle() {
-            return fontStyle;
-        }
+    /**
+     * Gets the value of the scoreModelName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getScoreModelName()
+    {
+      return scoreModelName;
+    }
 
-        /**
-         * Sets the value of the fontStyle property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontStyle(Integer value) {
-            this.fontStyle = value;
-        }
+    /**
+     * Sets the value of the scoreModelName property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setScoreModelName(String value)
+    {
+      this.scoreModelName = value;
+    }
 
-        /**
-         * Gets the value of the threshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getThreshold() {
-            return threshold;
-        }
+    /**
+     * Gets the value of the xDim property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXDim()
+    {
+      return xDim;
+    }
 
-        /**
-         * Sets the value of the threshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setThreshold(Float value) {
-            this.threshold = value;
-        }
+    /**
+     * Sets the value of the xDim property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setXDim(Integer value)
+    {
+      this.xDim = value;
+    }
 
-        /**
-         * Gets the value of the showBootstrap property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowBootstrap() {
-            return showBootstrap;
-        }
+    /**
+     * Gets the value of the yDim property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getYDim()
+    {
+      return yDim;
+    }
 
-        /**
-         * Sets the value of the showBootstrap property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowBootstrap(Boolean value) {
-            this.showBootstrap = value;
-        }
+    /**
+     * Sets the value of the yDim property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setYDim(Integer value)
+    {
+      this.yDim = value;
+    }
 
-        /**
-         * Gets the value of the showDistances property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowDistances() {
-            return showDistances;
-        }
+    /**
+     * Gets the value of the zDim property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getZDim()
+    {
+      return zDim;
+    }
 
-        /**
-         * Sets the value of the showDistances property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowDistances(Boolean value) {
-            this.showDistances = value;
-        }
+    /**
+     * Sets the value of the zDim property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setZDim(Integer value)
+    {
+      this.zDim = value;
+    }
 
-        /**
-         * Gets the value of the markUnlinked property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isMarkUnlinked() {
-            return markUnlinked;
-        }
+    /**
+     * Gets the value of the bgColour property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getBgColour()
+    {
+      return bgColour;
+    }
 
-        /**
-         * Sets the value of the markUnlinked property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setMarkUnlinked(Boolean value) {
-            this.markUnlinked = value;
-        }
+    /**
+     * Sets the value of the bgColour property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setBgColour(Integer value)
+    {
+      this.bgColour = value;
+    }
 
-        /**
-         * Gets the value of the fitToWindow property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isFitToWindow() {
-            return fitToWindow;
-        }
+    /**
+     * Gets the value of the scaleFactor property.
+     * 
+     * @return possible object is {@link Float }
+     * 
+     */
+    public Float getScaleFactor()
+    {
+      return scaleFactor;
+    }
 
-        /**
-         * Sets the value of the fitToWindow property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setFitToWindow(Boolean value) {
-            this.fitToWindow = value;
-        }
+    /**
+     * Sets the value of the scaleFactor property.
+     * 
+     * @param value
+     *          allowed object is {@link Float }
+     * 
+     */
+    public void setScaleFactor(Float value)
+    {
+      this.scaleFactor = value;
+    }
 
-        /**
-         * Gets the value of the currentTree property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isCurrentTree() {
-            return currentTree;
-        }
+    /**
+     * Gets the value of the showLabels property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowLabels()
+    {
+      return showLabels;
+    }
 
-        /**
-         * Sets the value of the currentTree property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setCurrentTree(Boolean value) {
-            this.currentTree = value;
-        }
+    /**
+     * Sets the value of the showLabels property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowLabels(Boolean value)
+    {
+      this.showLabels = value;
+    }
 
-        /**
-         * Set for trees associated with columns of an alignment, sequence or annotation row
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isColumnWise() {
-            if (columnWise == null) {
-                return false;
-            } else {
-                return columnWise;
-            }
-        }
+    /**
+     * Gets the value of the linkToAllViews property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isLinkToAllViews()
+    {
+      return linkToAllViews;
+    }
 
-        /**
-         * Sets the value of the columnWise property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isColumnWise()
-         */
-        public void setColumnWise(Boolean value) {
-            this.columnWise = value;
-        }
+    /**
+     * Sets the value of the linkToAllViews property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setLinkToAllViews(Boolean value)
+    {
+      this.linkToAllViews = value;
+    }
 
-        /**
-         * Refers to annotation row the tree is provided by
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getColumnReference() {
-            return columnReference;
-        }
+    /**
+     * Gets the value of the width property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getWidth()
+    {
+      return width;
+    }
 
-        /**
-         * Sets the value of the columnReference property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         * @see #getColumnReference()
-         */
-        public void setColumnReference(String value) {
-            this.columnReference = value;
-        }
+    /**
+     * Sets the value of the width property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setWidth(Integer value)
+    {
+      this.width = value;
+    }
 
-        /**
-         * Tree ID added for binding tree
-         * 									visualization
-         * 									settings to vamsas
-         * 									document trees in jalview 2.4.1
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getId() {
-            return id;
-        }
+    /**
+     * Gets the value of the height property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getHeight()
+    {
+      return height;
+    }
 
-        /**
-         * Sets the value of the id property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         * @see #getId()
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
+    /**
+     * Sets the value of the height property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setHeight(Integer value)
+    {
+      this.height = value;
+    }
 
-        /**
-         * Gets the value of the linkToAllViews property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isLinkToAllViews() {
-            if (linkToAllViews == null) {
-                return false;
-            } else {
-                return linkToAllViews;
-            }
-        }
+    /**
+     * Gets the value of the xpos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXpos()
+    {
+      return xpos;
+    }
 
-        /**
-         * Sets the value of the linkToAllViews property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setLinkToAllViews(Boolean value) {
-            this.linkToAllViews = value;
-        }
+    /**
+     * Sets the value of the xpos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setXpos(Integer value)
+    {
+      this.xpos = value;
+    }
 
-        /**
-         * Gets the value of the width property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getWidth() {
-            return width;
-        }
+    /**
+     * Gets the value of the ypos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getYpos()
+    {
+      return ypos;
+    }
 
-        /**
-         * Sets the value of the width property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setWidth(Integer value) {
-            this.width = value;
-        }
+    /**
+     * Sets the value of the ypos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setYpos(Integer value)
+    {
+      this.ypos = value;
+    }
 
-        /**
-         * Gets the value of the height property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getHeight() {
-            return height;
-        }
+    /**
+     * Gets the value of the includeGaps property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isIncludeGaps()
+    {
+      return includeGaps;
+    }
 
-        /**
-         * Sets the value of the height property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setHeight(Integer value) {
-            this.height = value;
-        }
+    /**
+     * Sets the value of the includeGaps property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIncludeGaps(Boolean value)
+    {
+      this.includeGaps = value;
+    }
 
-        /**
-         * Gets the value of the xpos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getXpos() {
-            return xpos;
-        }
+    /**
+     * Gets the value of the matchGaps property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isMatchGaps()
+    {
+      return matchGaps;
+    }
 
-        /**
-         * Sets the value of the xpos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setXpos(Integer value) {
-            this.xpos = value;
-        }
+    /**
+     * Sets the value of the matchGaps property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setMatchGaps(Boolean value)
+    {
+      this.matchGaps = value;
+    }
 
-        /**
-         * Gets the value of the ypos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getYpos() {
-            return ypos;
-        }
+    /**
+     * Gets the value of the includeGappedColumns property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isIncludeGappedColumns()
+    {
+      return includeGappedColumns;
+    }
 
-        /**
-         * Sets the value of the ypos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setYpos(Integer value) {
-            this.ypos = value;
-        }
+    /**
+     * Sets the value of the includeGappedColumns property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIncludeGappedColumns(Boolean value)
+    {
+      this.includeGappedColumns = value;
+    }
 
+    /**
+     * 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
    .
+     * 
    
+     * 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="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-     *       </sequence>
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attGroup ref="{www.jalview.org}position"/>
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -5416,158 +4257,214 @@ public class JalviewModel {
      * 
      */
     @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;
-        }
+    @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 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;
-        }
+    /**
+     * 
    
+     * 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;
+      }
 
     }
 
-
     /**
-     * 
    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="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               </extension>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="overview" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attGroup ref="{www.jalview.org}conservationShading"/>
-     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attGroup ref="{www.jalview.org}position"/>
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -5576,2181 +4473,3242 @@ public class JalviewModel {
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "annotationColours",
-        "hiddenColumns",
-        "calcIdParam",
-        "overview",
-        "secStrProvider"
-    })
-    public static class Viewport {
-
-        @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
-        protected AnnotationColourScheme annotationColours;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List hiddenColumns;
-        @XmlElement(namespace = "www.jalview.org")
-        protected List calcIdParam;
-        @XmlElement(namespace = "www.jalview.org")
-        protected JalviewModel.Viewport.Overview overview;
-        @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
-        protected List secStrProvider;
-        @XmlAttribute(name = "bgColour")
-        protected String bgColour;
-        @XmlAttribute(name = "title")
-        protected String title;
-        @XmlAttribute(name = "showFullId")
-        protected Boolean showFullId;
-        @XmlAttribute(name = "rightAlignIds")
-        protected Boolean rightAlignIds;
-        @XmlAttribute(name = "showText")
-        protected Boolean showText;
-        @XmlAttribute(name = "showColourText")
-        protected Boolean showColourText;
-        @XmlAttribute(name = "showUnconserved")
-        protected Boolean showUnconserved;
-        @XmlAttribute(name = "showBoxes")
-        protected Boolean showBoxes;
-        @XmlAttribute(name = "wrapAlignment")
-        protected Boolean wrapAlignment;
-        @XmlAttribute(name = "renderGaps")
-        protected Boolean renderGaps;
-        @XmlAttribute(name = "showSequenceFeatures")
-        protected Boolean showSequenceFeatures;
-        @XmlAttribute(name = "showNPfeatureTooltip")
-        protected Boolean showNPfeatureTooltip;
-        @XmlAttribute(name = "showDbRefTooltip")
-        protected Boolean showDbRefTooltip;
-        @XmlAttribute(name = "followHighlight")
-        protected Boolean followHighlight;
-        @XmlAttribute(name = "followSelection")
-        protected Boolean followSelection;
-        @XmlAttribute(name = "showAnnotation")
-        protected Boolean showAnnotation;
-        @XmlAttribute(name = "showStructureProviders")
-        protected Boolean showStructureProviders;
-        @XmlAttribute(name = "centreColumnLabels")
-        protected Boolean centreColumnLabels;
-        /**
-         * whether a new group has conservation displayed by default
-         * 
-         */
-        @XmlAttribute(name = "showGroupConservation")
-        protected Boolean showGroupConservation;
-        /**
-         * whether a new group has consensus displayed by default
-         * 
-         */
-        @XmlAttribute(name = "showGroupConsensus")
-        protected Boolean showGroupConsensus;
-        /**
-         * whether a new group has secondary structure consensus displayed by default
-         * 
-         */
-        @XmlAttribute(name = "showGroupSecStrConsensus")
-        protected Boolean showGroupSecStrConsensus;
-        @XmlAttribute(name = "startRes")
-        protected Integer startRes;
-        @XmlAttribute(name = "startSeq")
-        protected Integer startSeq;
-        @XmlAttribute(name = "charWidth")
-        protected Integer charWidth;
-        @XmlAttribute(name = "charHeight")
-        protected Integer charHeight;
-        @XmlAttribute(name = "fontName")
-        protected String fontName;
-        @XmlAttribute(name = "fontSize")
-        protected Integer fontSize;
-        @XmlAttribute(name = "fontStyle")
-        protected Integer fontStyle;
-        @XmlAttribute(name = "idWidth")
-        protected Integer idWidth;
-        @XmlAttribute(name = "idWidthManuallyAdjusted")
-        protected Boolean idWidthManuallyAdjusted;
-        @XmlAttribute(name = "scaleProteinAsCdna")
-        protected Boolean scaleProteinAsCdna;
-        @XmlAttribute(name = "viewName")
-        protected String viewName;
-        @XmlAttribute(name = "sequenceSetId")
-        protected String sequenceSetId;
-        @XmlAttribute(name = "gatheredViews")
-        protected Boolean gatheredViews;
-        @XmlAttribute(name = "textCol1")
-        protected Integer textCol1;
-        @XmlAttribute(name = "textCol2")
-        protected Integer textCol2;
-        @XmlAttribute(name = "textColThreshold")
-        protected Integer textColThreshold;
-        /**
-         * unique id used by jalview to
-         * 									synchronize
-         * 									between stored and
-         * 									instantiated views
-         * 
-         */
-        @XmlAttribute(name = "id")
-        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-        @XmlID
-        @XmlSchemaType(name = "ID")
-        protected String id;
-        /**
-         * The viewport id of this viewport's
-         * 									(cdna/protein) coding complement, if any
-         * 
-         */
-        @XmlAttribute(name = "complementId")
-        protected String complementId;
-        @XmlAttribute(name = "showComplementFeatures")
-        protected Boolean showComplementFeatures;
-        @XmlAttribute(name = "showComplementFeaturesOnTop")
-        protected Boolean showComplementFeaturesOnTop;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
-        @XmlAttribute(name = "conservationSelected")
-        protected Boolean conservationSelected;
-        /**
-         * Conservation shading increment
-         * 
-         */
-        @XmlAttribute(name = "consThreshold")
-        protected Integer consThreshold;
-        @XmlAttribute(name = "pidSelected")
-        protected Boolean pidSelected;
-        /**
-         * Percent Identity Threshold
-         * 
-         */
-        @XmlAttribute(name = "pidThreshold")
-        protected Integer pidThreshold;
-        /**
-         * Secondary structure consensus shading - since 2.11.4
-         * 
-         */
-        @XmlAttribute(name = "secstrSelected")
-        protected Boolean secstrSelected;
-        /**
-         * Secondary structure consensus increment
-         * 
-         */
-        @XmlAttribute(name = "secstrThreshold")
-        protected Integer secstrThreshold;
-        @XmlAttribute(name = "showConsensusHistogram")
-        protected Boolean showConsensusHistogram;
-        @XmlAttribute(name = "showSequenceLogo")
-        protected Boolean showSequenceLogo;
-        @XmlAttribute(name = "normaliseSequenceLogo")
-        protected Boolean normaliseSequenceLogo;
-        @XmlAttribute(name = "ignoreGapsinConsensus")
-        protected Boolean ignoreGapsinConsensus;
+    @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 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
+     * 
    
+     * .
+     * 
+     * 
    
+     * 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;
+      }
 
-        /**
-         * Gets the value of the hiddenColumns property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the hiddenColumns property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getHiddenColumns().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.Viewport.HiddenColumns }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the hiddenColumns property.
-         */
-        public List getHiddenColumns() {
-            if (hiddenColumns == null) {
-                hiddenColumns = new ArrayList();
-            }
-            return this.hiddenColumns;
-        }
+    }
 
-        /**
-         * Gets the value of the calcIdParam property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the calcIdParam property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getCalcIdParam().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link JalviewModel.Viewport.CalcIdParam }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the calcIdParam property.
-         */
-        public List getCalcIdParam() {
-            if (calcIdParam == null) {
-                calcIdParam = new ArrayList();
-            }
-            return this.calcIdParam;
-        }
+  }
+
+  /**
+   * 
    
+   * 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;
 
-        /**
-         * Gets the value of the overview property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link JalviewModel.Viewport.Overview }
-         *     
-         */
-        public JalviewModel.Viewport.Overview getOverview() {
-            return overview;
-        }
+    /**
+     * Set for trees associated with columns of an alignment, sequence or
+     * annotation row
+     * 
+     */
+    @XmlAttribute(name = "columnWise")
+    protected Boolean columnWise;
 
-        /**
-         * 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;
-        }
+    /**
+     * Refers to annotation row the tree is provided by
+     * 
+     */
+    @XmlAttribute(name = "columnReference")
+    protected String columnReference;
 
-        /**
-         * Gets the value of the secStrProvider property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the secStrProvider property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getSecStrProvider().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the secStrProvider property.
-         */
-        public List getSecStrProvider() {
-            if (secStrProvider == null) {
-                secStrProvider = new ArrayList();
-            }
-            return this.secStrProvider;
-        }
+    /**
+     * Tree ID added for binding tree visualization settings to vamsas document
+     * trees in jalview 2.4.1
+     * 
+     */
+    @XmlAttribute(name = "id")
+    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+    @XmlID
+    @XmlSchemaType(name = "ID")
+    protected String id;
 
-        /**
-         * Gets the value of the bgColour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getBgColour() {
-            return bgColour;
-        }
+    @XmlAttribute(name = "linkToAllViews")
+    protected Boolean linkToAllViews;
 
-        /**
-         * Sets the value of the bgColour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setBgColour(String value) {
-            this.bgColour = value;
-        }
+    @XmlAttribute(name = "width")
+    protected Integer width;
 
-        /**
-         * Gets the value of the title property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getTitle() {
-            return title;
-        }
+    @XmlAttribute(name = "height")
+    protected Integer height;
 
-        /**
-         * Sets the value of the title property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setTitle(String value) {
-            this.title = value;
-        }
+    @XmlAttribute(name = "xpos")
+    protected Integer xpos;
 
-        /**
-         * Gets the value of the showFullId property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowFullId() {
-            return showFullId;
-        }
+    @XmlAttribute(name = "ypos")
+    protected Integer ypos;
 
-        /**
-         * 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 title property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getTitle()
+    {
+      return title;
+    }
 
-        /**
-         * Gets the value of the rightAlignIds property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isRightAlignIds() {
-            return rightAlignIds;
-        }
+    /**
+     * 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 rightAlignIds property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setRightAlignIds(Boolean value) {
-            this.rightAlignIds = value;
-        }
+    /**
+     * Gets the value of the newick property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getNewick()
+    {
+      return newick;
+    }
 
-        /**
-         * Gets the value of the showText property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowText() {
-            return showText;
-        }
+    /**
+     * 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 showText property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowText(Boolean value) {
-            this.showText = value;
-        }
+    /**
+     * Gets the value of the fontName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getFontName()
+    {
+      return fontName;
+    }
 
-        /**
-         * Gets the value of the showColourText property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowColourText() {
-            return showColourText;
-        }
+    /**
+     * 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 showColourText property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowColourText(Boolean value) {
-            this.showColourText = value;
-        }
+    /**
+     * Gets the value of the fontSize property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontSize()
+    {
+      return fontSize;
+    }
 
-        /**
-         * 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 fontSize property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setFontSize(Integer value)
+    {
+      this.fontSize = 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 fontStyle property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontStyle()
+    {
+      return fontStyle;
+    }
 
-        /**
-         * Gets the value of the showBoxes property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowBoxes() {
-            return showBoxes;
-        }
+    /**
+     * 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 showBoxes property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowBoxes(Boolean value) {
-            this.showBoxes = value;
-        }
+    /**
+     * Gets the value of the threshold property.
+     * 
+     * @return possible object is {@link Float }
+     * 
+     */
+    public Float getThreshold()
+    {
+      return threshold;
+    }
 
-        /**
-         * Gets the value of the wrapAlignment property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isWrapAlignment() {
-            return wrapAlignment;
-        }
+    /**
+     * 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 wrapAlignment property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setWrapAlignment(Boolean value) {
-            this.wrapAlignment = value;
-        }
+    /**
+     * Gets the value of the showBootstrap property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowBootstrap()
+    {
+      return showBootstrap;
+    }
 
-        /**
-         * Gets the value of the renderGaps property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isRenderGaps() {
-            return renderGaps;
-        }
+    /**
+     * 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 renderGaps property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setRenderGaps(Boolean value) {
-            this.renderGaps = value;
-        }
+    /**
+     * Gets the value of the showDistances property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowDistances()
+    {
+      return showDistances;
+    }
 
-        /**
-         * Gets the value of the showSequenceFeatures property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowSequenceFeatures() {
-            return showSequenceFeatures;
-        }
+    /**
+     * 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 showSequenceFeatures property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowSequenceFeatures(Boolean value) {
-            this.showSequenceFeatures = value;
-        }
+    /**
+     * Gets the value of the markUnlinked property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isMarkUnlinked()
+    {
+      return markUnlinked;
+    }
 
-        /**
-         * Gets the value of the showNPfeatureTooltip property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowNPfeatureTooltip() {
-            return showNPfeatureTooltip;
-        }
+    /**
+     * Sets the value of the markUnlinked property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setMarkUnlinked(Boolean value)
+    {
+      this.markUnlinked = 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;
+    }
+
+    /**
+     * 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;
+    }
+
+    /**
+     * Set for trees associated with columns of an alignment, sequence or
+     * annotation row
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isColumnWise()
+    {
+      if (columnWise == null)
+      {
+        return false;
+      }
+      else
+      {
+        return columnWise;
+      }
+    }
+
+    /**
+     * Sets the value of the columnWise property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     * @see #isColumnWise()
+     */
+    public void setColumnWise(Boolean value)
+    {
+      this.columnWise = value;
+    }
+
+    /**
+     * Refers to annotation row the tree is provided by
+     * 
+     * @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 }
+     * 
+     * @see #getColumnReference()
+     */
+    public void setColumnReference(String value)
+    {
+      this.columnReference = value;
+    }
+
+    /**
+     * Tree ID added for binding tree visualization settings to vamsas document
+     * trees in jalview 2.4.1
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     * @see #getId()
+     */
+    public void setId(String value)
+    {
+      this.id = 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;
+    }
+
+    /**
+     * 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">
+   *       <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;
+
+    /**
+     * 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;
+    }
+
+  }
+
+  /**
+   * 
    
+   * Java class for anonymous complex type
+   * 
    
+   * .
+   * 
+   * 
    
+   * The following schema fragment specifies the expected content contained
+   * within this class.
+   * 
    
+   * 
+   * 
    +   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+   *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </extension>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="overview" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="SecStrProvider" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attGroup ref="{www.jalview.org}conservationShading"/>
+   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showStructureProviders" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupSecStrConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
    
+   * 
+   * 
+   */
+  @XmlAccessorType(XmlAccessType.FIELD)
+  @XmlType(
+    name = "",
+    propOrder =
+    { "annotationColours", "hiddenColumns", "calcIdParam", "overview",
+        "secStrProvider" })
+  public static class Viewport
+  {
+
+    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+    protected AnnotationColourScheme annotationColours;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List hiddenColumns;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected List calcIdParam;
+
+    @XmlElement(namespace = "www.jalview.org")
+    protected JalviewModel.Viewport.Overview overview;
+
+    @XmlElement(name = "SecStrProvider", namespace = "www.jalview.org")
+    protected List secStrProvider;
+
+    @XmlAttribute(name = "bgColour")
+    protected String bgColour;
+
+    @XmlAttribute(name = "title")
+    protected String title;
+
+    @XmlAttribute(name = "showFullId")
+    protected Boolean showFullId;
+
+    @XmlAttribute(name = "rightAlignIds")
+    protected Boolean rightAlignIds;
+
+    @XmlAttribute(name = "showText")
+    protected Boolean showText;
+
+    @XmlAttribute(name = "showColourText")
+    protected Boolean showColourText;
+
+    @XmlAttribute(name = "showUnconserved")
+    protected Boolean showUnconserved;
+
+    @XmlAttribute(name = "showBoxes")
+    protected Boolean showBoxes;
+
+    @XmlAttribute(name = "wrapAlignment")
+    protected Boolean wrapAlignment;
+
+    @XmlAttribute(name = "renderGaps")
+    protected Boolean renderGaps;
+
+    @XmlAttribute(name = "showSequenceFeatures")
+    protected Boolean showSequenceFeatures;
+
+    @XmlAttribute(name = "showNPfeatureTooltip")
+    protected Boolean showNPfeatureTooltip;
+
+    @XmlAttribute(name = "showDbRefTooltip")
+    protected Boolean showDbRefTooltip;
+
+    @XmlAttribute(name = "followHighlight")
+    protected Boolean followHighlight;
+
+    @XmlAttribute(name = "followSelection")
+    protected Boolean followSelection;
+
+    @XmlAttribute(name = "showAnnotation")
+    protected Boolean showAnnotation;
+
+    @XmlAttribute(name = "showStructureProviders")
+    protected Boolean showStructureProviders;
+
+    @XmlAttribute(name = "centreColumnLabels")
+    protected Boolean centreColumnLabels;
+
+    /**
+     * whether a new group has conservation displayed by default
+     * 
+     */
+    @XmlAttribute(name = "showGroupConservation")
+    protected Boolean showGroupConservation;
+
+    /**
+     * whether a new group has consensus displayed by default
+     * 
+     */
+    @XmlAttribute(name = "showGroupConsensus")
+    protected Boolean showGroupConsensus;
+
+    /**
+     * whether a new group has secondary structure consensus displayed by
+     * default
+     * 
+     */
+    @XmlAttribute(name = "showGroupSecStrConsensus")
+    protected Boolean showGroupSecStrConsensus;
+
+    @XmlAttribute(name = "startRes")
+    protected Integer startRes;
+
+    @XmlAttribute(name = "startSeq")
+    protected Integer startSeq;
+
+    @XmlAttribute(name = "charWidth")
+    protected Integer charWidth;
+
+    @XmlAttribute(name = "charHeight")
+    protected Integer charHeight;
+
+    @XmlAttribute(name = "fontName")
+    protected String fontName;
+
+    @XmlAttribute(name = "fontSize")
+    protected Integer fontSize;
+
+    @XmlAttribute(name = "fontStyle")
+    protected Integer fontStyle;
+
+    @XmlAttribute(name = "idWidth")
+    protected Integer idWidth;
+
+    @XmlAttribute(name = "idWidthManuallyAdjusted")
+    protected Boolean idWidthManuallyAdjusted;
+
+    @XmlAttribute(name = "scaleProteinAsCdna")
+    protected Boolean scaleProteinAsCdna;
+
+    @XmlAttribute(name = "viewName")
+    protected String viewName;
+
+    @XmlAttribute(name = "sequenceSetId")
+    protected String sequenceSetId;
+
+    @XmlAttribute(name = "gatheredViews")
+    protected Boolean gatheredViews;
+
+    @XmlAttribute(name = "textCol1")
+    protected Integer textCol1;
+
+    @XmlAttribute(name = "textCol2")
+    protected Integer textCol2;
+
+    @XmlAttribute(name = "textColThreshold")
+    protected Integer textColThreshold;
+
+    /**
+     * unique id used by jalview to synchronize between stored and instantiated
+     * views
+     * 
+     */
+    @XmlAttribute(name = "id")
+    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+    @XmlID
+    @XmlSchemaType(name = "ID")
+    protected String id;
+
+    /**
+     * The viewport id of this viewport's (cdna/protein) coding complement, if
+     * any
+     * 
+     */
+    @XmlAttribute(name = "complementId")
+    protected String complementId;
+
+    @XmlAttribute(name = "showComplementFeatures")
+    protected Boolean showComplementFeatures;
+
+    @XmlAttribute(name = "showComplementFeaturesOnTop")
+    protected Boolean showComplementFeaturesOnTop;
+
+    @XmlAttribute(name = "width")
+    protected Integer width;
+
+    @XmlAttribute(name = "height")
+    protected Integer height;
+
+    @XmlAttribute(name = "xpos")
+    protected Integer xpos;
+
+    @XmlAttribute(name = "ypos")
+    protected Integer ypos;
+
+    @XmlAttribute(name = "conservationSelected")
+    protected Boolean conservationSelected;
+
+    /**
+     * Conservation shading increment
+     * 
+     */
+    @XmlAttribute(name = "consThreshold")
+    protected Integer consThreshold;
+
+    @XmlAttribute(name = "pidSelected")
+    protected Boolean pidSelected;
+
+    /**
+     * Percent Identity Threshold
+     * 
+     */
+    @XmlAttribute(name = "pidThreshold")
+    protected Integer pidThreshold;
+
+    /**
+     * Secondary structure consensus shading - since 2.11.4
+     * 
+     */
+    @XmlAttribute(name = "secstrSelected")
+    protected Boolean secstrSelected;
+
+    /**
+     * Secondary structure consensus increment
+     * 
+     */
+    @XmlAttribute(name = "secstrThreshold")
+    protected Integer secstrThreshold;
+
+    @XmlAttribute(name = "showConsensusHistogram")
+    protected Boolean showConsensusHistogram;
+
+    @XmlAttribute(name = "showSequenceLogo")
+    protected Boolean showSequenceLogo;
+
+    @XmlAttribute(name = "normaliseSequenceLogo")
+    protected Boolean normaliseSequenceLogo;
+
+    @XmlAttribute(name = "ignoreGapsinConsensus")
+    protected Boolean ignoreGapsinConsensus;
+
+    /**
+     * 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 }
+     * 
    
+     * 
+     * 
+     * @return The value of the hiddenColumns property.
+     */
+    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 }
+     * 
    
+     * 
+     * 
+     * @return The value of the calcIdParam property.
+     */
+    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 secStrProvider property.
+     * 
+     * 
    
+     * This accessor method returns a reference to the live list, not a
+     * snapshot. Therefore any modification you make to the returned list will
+     * be present inside the JAXB object. This is why there is not a
+     * set method for the secStrProvider property.
+     * 
    
+     * 
+     * 
    
+     * For example, to add a new item, do as follows:
+     * 
    
+     * 
+     * 
    +     * getSecStrProvider().add(newItem);
+     * 
    
+     * 
+     * 
+     * 
    
+     * Objects of the following type(s) are allowed in the list {@link String }
+     * 
    
+     * 
+     * 
+     * @return The value of the secStrProvider property.
+     */
+    public List getSecStrProvider()
+    {
+      if (secStrProvider == null)
+      {
+        secStrProvider = new ArrayList();
+      }
+      return this.secStrProvider;
+    }
+
+    /**
+     * Gets the value of the bgColour property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getBgColour()
+    {
+      return bgColour;
+    }
+
+    /**
+     * 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 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 showFullId property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowFullId()
+    {
+      return showFullId;
+    }
+
+    /**
+     * 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 rightAlignIds property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isRightAlignIds()
+    {
+      return rightAlignIds;
+    }
+
+    /**
+     * 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 showText property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowText()
+    {
+      return showText;
+    }
+
+    /**
+     * 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 showColourText property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowColourText()
+    {
+      return showColourText;
+    }
+
+    /**
+     * 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 showUnconserved property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowUnconserved()
+    {
+      if (showUnconserved == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showUnconserved;
+      }
+    }
 
-        /**
-         * 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 showUnconserved property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowUnconserved(Boolean value)
+    {
+      this.showUnconserved = value;
+    }
 
-        /**
-         * Gets the value of the showDbRefTooltip property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowDbRefTooltip() {
-            return showDbRefTooltip;
-        }
+    /**
+     * Gets the value of the showBoxes property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowBoxes()
+    {
+      return showBoxes;
+    }
 
-        /**
-         * 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 showBoxes property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowBoxes(Boolean value)
+    {
+      this.showBoxes = 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 wrapAlignment property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isWrapAlignment()
+    {
+      return wrapAlignment;
+    }
 
-        /**
-         * 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 wrapAlignment property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setWrapAlignment(Boolean value)
+    {
+      this.wrapAlignment = 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 renderGaps property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isRenderGaps()
+    {
+      return renderGaps;
+    }
 
-        /**
-         * 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 renderGaps property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setRenderGaps(Boolean value)
+    {
+      this.renderGaps = value;
+    }
 
-        /**
-         * Gets the value of the showAnnotation property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowAnnotation() {
-            return showAnnotation;
-        }
+    /**
+     * Gets the value of the showSequenceFeatures property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowSequenceFeatures()
+    {
+      return showSequenceFeatures;
+    }
 
-        /**
-         * 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 showSequenceFeatures property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowSequenceFeatures(Boolean value)
+    {
+      this.showSequenceFeatures = value;
+    }
 
-        /**
-         * Gets the value of the showStructureProviders property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isShowStructureProviders() {
-            return showStructureProviders;
-        }
+    /**
+     * Gets the value of the showNPfeatureTooltip property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowNPfeatureTooltip()
+    {
+      return showNPfeatureTooltip;
+    }
 
-        /**
-         * Sets the value of the showStructureProviders property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowStructureProviders(Boolean value) {
-            this.showStructureProviders = 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 centreColumnLabels property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isCentreColumnLabels() {
-            if (centreColumnLabels == null) {
-                return false;
-            } else {
-                return centreColumnLabels;
-            }
-        }
+    /**
+     * Gets the value of the showDbRefTooltip property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowDbRefTooltip()
+    {
+      return showDbRefTooltip;
+    }
 
-        /**
-         * 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 showDbRefTooltip property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowDbRefTooltip(Boolean value)
+    {
+      this.showDbRefTooltip = value;
+    }
 
-        /**
-         * whether a new group has conservation displayed by default
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowGroupConservation() {
-            if (showGroupConservation == null) {
-                return false;
-            } else {
-                return showGroupConservation;
-            }
-        }
+    /**
+     * 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 showGroupConservation property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isShowGroupConservation()
-         */
-        public void setShowGroupConservation(Boolean value) {
-            this.showGroupConservation = value;
-        }
+    /**
+     * Sets the value of the followHighlight property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setFollowHighlight(Boolean value)
+    {
+      this.followHighlight = value;
+    }
 
-        /**
-         * whether a new group has consensus displayed by default
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowGroupConsensus() {
-            if (showGroupConsensus == null) {
-                return false;
-            } else {
-                return showGroupConsensus;
-            }
-        }
+    /**
+     * 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 showGroupConsensus property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isShowGroupConsensus()
-         */
-        public void setShowGroupConsensus(Boolean value) {
-            this.showGroupConsensus = value;
-        }
+    /**
+     * Sets the value of the followSelection property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setFollowSelection(Boolean value)
+    {
+      this.followSelection = value;
+    }
 
-        /**
-         * whether a new group has secondary structure consensus displayed by default
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowGroupSecStrConsensus() {
-            if (showGroupSecStrConsensus == null) {
-                return false;
-            } else {
-                return showGroupSecStrConsensus;
-            }
-        }
+    /**
+     * Gets the value of the showAnnotation property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowAnnotation()
+    {
+      return showAnnotation;
+    }
 
-        /**
-         * Sets the value of the showGroupSecStrConsensus property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isShowGroupSecStrConsensus()
-         */
-        public void setShowGroupSecStrConsensus(Boolean value) {
-            this.showGroupSecStrConsensus = value;
-        }
+    /**
+     * Sets the value of the showAnnotation property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowAnnotation(Boolean value)
+    {
+      this.showAnnotation = value;
+    }
 
-        /**
-         * Gets the value of the startRes property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getStartRes() {
-            return startRes;
-        }
+    /**
+     * Gets the value of the showStructureProviders property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isShowStructureProviders()
+    {
+      return showStructureProviders;
+    }
 
-        /**
-         * Sets the value of the startRes property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setStartRes(Integer value) {
-            this.startRes = value;
-        }
+    /**
+     * Sets the value of the showStructureProviders property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowStructureProviders(Boolean value)
+    {
+      this.showStructureProviders = value;
+    }
 
-        /**
-         * Gets the value of the startSeq property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getStartSeq() {
-            return startSeq;
-        }
+    /**
+     * 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 startSeq property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setStartSeq(Integer value) {
-            this.startSeq = 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 charWidth property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getCharWidth() {
-            return charWidth;
-        }
+    /**
+     * whether a new group has conservation displayed by default
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowGroupConservation()
+    {
+      if (showGroupConservation == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showGroupConservation;
+      }
+    }
 
-        /**
-         * Sets the value of the charWidth property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setCharWidth(Integer value) {
-            this.charWidth = value;
-        }
+    /**
+     * Sets the value of the showGroupConservation property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     * @see #isShowGroupConservation()
+     */
+    public void setShowGroupConservation(Boolean value)
+    {
+      this.showGroupConservation = value;
+    }
+
+    /**
+     * whether a new group has consensus displayed by default
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowGroupConsensus()
+    {
+      if (showGroupConsensus == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showGroupConsensus;
+      }
+    }
 
-        /**
-         * Gets the value of the charHeight property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getCharHeight() {
-            return charHeight;
-        }
+    /**
+     * Sets the value of the showGroupConsensus property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     * @see #isShowGroupConsensus()
+     */
+    public void setShowGroupConsensus(Boolean value)
+    {
+      this.showGroupConsensus = value;
+    }
 
-        /**
-         * Sets the value of the charHeight property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setCharHeight(Integer value) {
-            this.charHeight = value;
-        }
+    /**
+     * whether a new group has secondary structure consensus displayed by
+     * default
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowGroupSecStrConsensus()
+    {
+      if (showGroupSecStrConsensus == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showGroupSecStrConsensus;
+      }
+    }
 
-        /**
-         * Gets the value of the fontName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getFontName() {
-            return fontName;
-        }
+    /**
+     * Sets the value of the showGroupSecStrConsensus property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     * @see #isShowGroupSecStrConsensus()
+     */
+    public void setShowGroupSecStrConsensus(Boolean value)
+    {
+      this.showGroupSecStrConsensus = value;
+    }
 
-        /**
-         * Sets the value of the fontName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setFontName(String value) {
-            this.fontName = value;
-        }
+    /**
+     * Gets the value of the startRes property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getStartRes()
+    {
+      return startRes;
+    }
 
-        /**
-         * Gets the value of the fontSize property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontSize() {
-            return fontSize;
-        }
+    /**
+     * Sets the value of the startRes property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setStartRes(Integer value)
+    {
+      this.startRes = value;
+    }
 
-        /**
-         * Sets the value of the fontSize property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontSize(Integer value) {
-            this.fontSize = value;
-        }
+    /**
+     * Gets the value of the startSeq property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getStartSeq()
+    {
+      return startSeq;
+    }
 
-        /**
-         * Gets the value of the fontStyle property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getFontStyle() {
-            return fontStyle;
-        }
+    /**
+     * Sets the value of the startSeq property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setStartSeq(Integer value)
+    {
+      this.startSeq = value;
+    }
 
-        /**
-         * Sets the value of the fontStyle property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setFontStyle(Integer value) {
-            this.fontStyle = value;
-        }
+    /**
+     * Gets the value of the charWidth property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getCharWidth()
+    {
+      return charWidth;
+    }
 
-        /**
-         * Gets the value of the idWidth property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getIdWidth() {
-            return idWidth;
-        }
+    /**
+     * 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 idWidth property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setIdWidth(Integer value) {
-            this.idWidth = value;
-        }
+    /**
+     * Gets the value of the charHeight property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getCharHeight()
+    {
+      return charHeight;
+    }
 
-        /**
-         * Gets the value of the idWidthManuallyAdjusted property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isIdWidthManuallyAdjusted() {
-            return idWidthManuallyAdjusted;
-        }
+    /**
+     * 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 idWidthManuallyAdjusted property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setIdWidthManuallyAdjusted(Boolean value) {
-            this.idWidthManuallyAdjusted = value;
-        }
+    /**
+     * Gets the value of the fontName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getFontName()
+    {
+      return fontName;
+    }
 
-        /**
-         * 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 fontName property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setFontName(String value)
+    {
+      this.fontName = 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 fontSize property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontSize()
+    {
+      return fontSize;
+    }
 
-        /**
-         * Gets the value of the viewName property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getViewName() {
-            return viewName;
-        }
+    /**
+     * 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 viewName property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setViewName(String value) {
-            this.viewName = value;
-        }
+    /**
+     * Gets the value of the fontStyle property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getFontStyle()
+    {
+      return fontStyle;
+    }
 
-        /**
-         * Gets the value of the sequenceSetId property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getSequenceSetId() {
-            return sequenceSetId;
-        }
+    /**
+     * 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 sequenceSetId property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setSequenceSetId(String value) {
-            this.sequenceSetId = value;
-        }
+    /**
+     * Gets the value of the idWidth property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getIdWidth()
+    {
+      return idWidth;
+    }
 
-        /**
-         * Gets the value of the gatheredViews property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isGatheredViews() {
-            return gatheredViews;
-        }
+    /**
+     * Sets the value of the idWidth property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setIdWidth(Integer value)
+    {
+      this.idWidth = value;
+    }
 
-        /**
-         * Sets the value of the gatheredViews property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setGatheredViews(Boolean value) {
-            this.gatheredViews = value;
-        }
+    /**
+     * Gets the value of the idWidthManuallyAdjusted property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isIdWidthManuallyAdjusted()
+    {
+      return idWidthManuallyAdjusted;
+    }
 
-        /**
-         * Gets the value of the textCol1 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextCol1() {
-            return textCol1;
-        }
+    /**
+     * Sets the value of the idWidthManuallyAdjusted property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIdWidthManuallyAdjusted(Boolean value)
+    {
+      this.idWidthManuallyAdjusted = value;
+    }
 
-        /**
-         * Sets the value of the textCol1 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setTextCol1(Integer value) {
-            this.textCol1 = 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 textCol2 property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextCol2() {
-            return textCol2;
-        }
+    /**
+     * 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 textCol2 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setTextCol2(Integer value) {
-            this.textCol2 = value;
-        }
+    /**
+     * Gets the value of the viewName property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getViewName()
+    {
+      return viewName;
+    }
 
-        /**
-         * Gets the value of the textColThreshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getTextColThreshold() {
-            return textColThreshold;
-        }
+    /**
+     * Sets the value of the viewName property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setViewName(String value)
+    {
+      this.viewName = value;
+    }
+
+    /**
+     * Gets the value of the sequenceSetId property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getSequenceSetId()
+    {
+      return sequenceSetId;
+    }
 
-        /**
-         * Sets the value of the textColThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setTextColThreshold(Integer value) {
-            this.textColThreshold = value;
-        }
+    /**
+     * Sets the value of the sequenceSetId property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     */
+    public void setSequenceSetId(String value)
+    {
+      this.sequenceSetId = value;
+    }
 
-        /**
-         * unique id used by jalview to
-         * 									synchronize
-         * 									between stored and
-         * 									instantiated views
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getId() {
-            return id;
-        }
+    /**
+     * Gets the value of the gatheredViews property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isGatheredViews()
+    {
+      return gatheredViews;
+    }
 
-        /**
-         * Sets the value of the id property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         * @see #getId()
-         */
-        public void setId(String value) {
-            this.id = value;
-        }
+    /**
+     * Sets the value of the gatheredViews property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setGatheredViews(Boolean value)
+    {
+      this.gatheredViews = value;
+    }
 
-        /**
-         * The viewport id of this viewport's
-         * 									(cdna/protein) coding complement, if any
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getComplementId() {
-            return complementId;
-        }
+    /**
+     * Gets the value of the textCol1 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol1()
+    {
+      return textCol1;
+    }
 
-        /**
-         * Sets the value of the complementId property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         * @see #getComplementId()
-         */
-        public void setComplementId(String value) {
-            this.complementId = 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 showComplementFeatures property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isShowComplementFeatures() {
-            if (showComplementFeatures == null) {
-                return false;
-            } else {
-                return showComplementFeatures;
-            }
-        }
+    /**
+     * Gets the value of the textCol2 property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextCol2()
+    {
+      return textCol2;
+    }
 
-        /**
-         * 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 textCol2 property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextCol2(Integer value)
+    {
+      this.textCol2 = 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 textColThreshold property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getTextColThreshold()
+    {
+      return textColThreshold;
+    }
 
-        /**
-         * 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 textColThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setTextColThreshold(Integer value)
+    {
+      this.textColThreshold = value;
+    }
 
-        /**
-         * Gets the value of the width property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getWidth() {
-            return width;
-        }
+    /**
+     * unique id used by jalview to synchronize between stored and instantiated
+     * views
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getId()
+    {
+      return id;
+    }
 
-        /**
-         * Sets the value of the width property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setWidth(Integer value) {
-            this.width = value;
-        }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     * @see #getId()
+     */
+    public void setId(String value)
+    {
+      this.id = value;
+    }
 
-        /**
-         * Gets the value of the height property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getHeight() {
-            return height;
-        }
+    /**
+     * The viewport id of this viewport's (cdna/protein) coding complement, if
+     * any
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getComplementId()
+    {
+      return complementId;
+    }
 
-        /**
-         * Sets the value of the height property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setHeight(Integer value) {
-            this.height = value;
-        }
+    /**
+     * Sets the value of the complementId property.
+     * 
+     * @param value
+     *          allowed object is {@link String }
+     * 
+     * @see #getComplementId()
+     */
+    public void setComplementId(String value)
+    {
+      this.complementId = value;
+    }
 
-        /**
-         * Gets the value of the xpos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getXpos() {
-            return xpos;
-        }
+    /**
+     * 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 xpos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setXpos(Integer value) {
-            this.xpos = 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 ypos property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getYpos() {
-            return ypos;
-        }
+    /**
+     * 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 ypos property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         */
-        public void setYpos(Integer value) {
-            this.ypos = 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 conservationSelected property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isConservationSelected() {
-            return conservationSelected;
-        }
+    /**
+     * Gets the value of the width property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getWidth()
+    {
+      return width;
+    }
 
-        /**
-         * 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 width property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setWidth(Integer value)
+    {
+      this.width = value;
+    }
 
-        /**
-         * Conservation shading increment
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getConsThreshold() {
-            return consThreshold;
-        }
+    /**
+     * Gets the value of the height property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getHeight()
+    {
+      return height;
+    }
 
-        /**
-         * Sets the value of the consThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         * @see #getConsThreshold()
-         */
-        public void setConsThreshold(Integer value) {
-            this.consThreshold = value;
-        }
+    /**
+     * Sets the value of the height property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setHeight(Integer value)
+    {
+      this.height = value;
+    }
 
-        /**
-         * Gets the value of the pidSelected property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isPidSelected() {
-            return pidSelected;
-        }
+    /**
+     * Gets the value of the xpos property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getXpos()
+    {
+      return xpos;
+    }
 
-        /**
-         * Sets the value of the pidSelected property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setPidSelected(Boolean value) {
-            this.pidSelected = value;
-        }
+    /**
+     * Sets the value of the xpos property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setXpos(Integer value)
+    {
+      this.xpos = value;
+    }
 
-        /**
-         * Percent Identity Threshold
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getPidThreshold() {
-            return pidThreshold;
-        }
+    /**
+     * 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 pidThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         * @see #getPidThreshold()
-         */
-        public void setPidThreshold(Integer value) {
-            this.pidThreshold = value;
-        }
+    /**
+     * Gets the value of the conservationSelected property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isConservationSelected()
+    {
+      return conservationSelected;
+    }
 
-        /**
-         * Secondary structure consensus shading - since 2.11.4
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isSecstrSelected() {
-            if (secstrSelected == null) {
-                return false;
-            } else {
-                return secstrSelected;
-            }
-        }
+    /**
+     * Sets the value of the conservationSelected property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setConservationSelected(Boolean value)
+    {
+      this.conservationSelected = value;
+    }
 
-        /**
-         * Sets the value of the secstrSelected property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isSecstrSelected()
-         */
-        public void setSecstrSelected(Boolean value) {
-            this.secstrSelected = value;
-        }
+    /**
+     * Conservation shading increment
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getConsThreshold()
+    {
+      return consThreshold;
+    }
 
-        /**
-         * Secondary structure consensus increment
-         * 
-         * @return
-         *     possible object is
-         *     {@link Integer }
-         *     
-         */
-        public Integer getSecstrThreshold() {
-            return secstrThreshold;
-        }
+    /**
+     * Sets the value of the consThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     * @see #getConsThreshold()
+     */
+    public void setConsThreshold(Integer value)
+    {
+      this.consThreshold = value;
+    }
 
-        /**
-         * Sets the value of the secstrThreshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Integer }
-         *     
-         * @see #getSecstrThreshold()
-         */
-        public void setSecstrThreshold(Integer value) {
-            this.secstrThreshold = value;
-        }
+    /**
+     * Gets the value of the pidSelected property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isPidSelected()
+    {
+      return pidSelected;
+    }
 
-        /**
-         * 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 pidSelected property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setPidSelected(Boolean value)
+    {
+      this.pidSelected = value;
+    }
 
-        /**
-         * Sets the value of the showConsensusHistogram property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowConsensusHistogram(Boolean value) {
-            this.showConsensusHistogram = value;
-        }
+    /**
+     * Percent Identity Threshold
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getPidThreshold()
+    {
+      return pidThreshold;
+    }
 
-        /**
-         * 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 pidThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     * @see #getPidThreshold()
+     */
+    public void setPidThreshold(Integer value)
+    {
+      this.pidThreshold = value;
+    }
 
-        /**
-         * Sets the value of the showSequenceLogo property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setShowSequenceLogo(Boolean value) {
-            this.showSequenceLogo = value;
-        }
+    /**
+     * Secondary structure consensus shading - since 2.11.4
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isSecstrSelected()
+    {
+      if (secstrSelected == null)
+      {
+        return false;
+      }
+      else
+      {
+        return secstrSelected;
+      }
+    }
 
-        /**
-         * Gets the value of the normaliseSequenceLogo property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isNormaliseSequenceLogo() {
-            if (normaliseSequenceLogo == null) {
-                return false;
-            } else {
-                return normaliseSequenceLogo;
-            }
-        }
+    /**
+     * Sets the value of the secstrSelected property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     * @see #isSecstrSelected()
+     */
+    public void setSecstrSelected(Boolean value)
+    {
+      this.secstrSelected = value;
+    }
 
-        /**
-         * Sets the value of the normaliseSequenceLogo property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setNormaliseSequenceLogo(Boolean value) {
-            this.normaliseSequenceLogo = value;
-        }
+    /**
+     * Secondary structure consensus increment
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getSecstrThreshold()
+    {
+      return secstrThreshold;
+    }
 
-        /**
-         * 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 secstrThreshold property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     * @see #getSecstrThreshold()
+     */
+    public void setSecstrThreshold(Integer value)
+    {
+      this.secstrThreshold = 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;
+      }
+    }
 
+    /**
+     * Sets the value of the showConsensusHistogram property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setShowConsensusHistogram(Boolean value)
+    {
+      this.showConsensusHistogram = 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
-        {
+    /**
+     * Gets the value of the showSequenceLogo property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isShowSequenceLogo()
+    {
+      if (showSequenceLogo == null)
+      {
+        return false;
+      }
+      else
+      {
+        return showSequenceLogo;
+      }
+    }
 
-            /**
-             * handle for the calculation which uses
-             * 														this parameter set
-             * 
-             */
-            @XmlAttribute(name = "calcId", required = true)
-            protected String calcId;
-            /**
-             * should the calculation be performed
-             * 														immediately after loading in order to refresh results
-             * 
-             */
-            @XmlAttribute(name = "needsUpdate")
-            protected Boolean needsUpdate;
-            /**
-             * should the calculation be automatically
-             * 														performed on edits
-             * 
-             */
-            @XmlAttribute(name = "autoUpdate", required = true)
-            protected boolean autoUpdate;
-
-            /**
-             * handle for the calculation which uses
-             * 														this parameter set
-             * 
-             * @return
-             *     possible object is
-             *     {@link String }
-             *     
-             */
-            public String getCalcId() {
-                return calcId;
-            }
-
-            /**
-             * Sets the value of the calcId property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link String }
-             *     
-             * @see #getCalcId()
-             */
-            public void setCalcId(String value) {
-                this.calcId = value;
-            }
-
-            /**
-             * should the calculation be performed
-             * 														immediately after loading in order to refresh results
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public boolean isNeedsUpdate() {
-                if (needsUpdate == null) {
-                    return false;
-                } else {
-                    return needsUpdate;
-                }
-            }
-
-            /**
-             * Sets the value of the needsUpdate property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             * @see #isNeedsUpdate()
-             */
-            public void setNeedsUpdate(Boolean value) {
-                this.needsUpdate = value;
-            }
-
-            /**
-             * should the calculation be automatically
-             * 														performed on edits
-             * 
-             */
-            public boolean isAutoUpdate() {
-                return autoUpdate;
-            }
-
-            /**
-             * Sets the value of the autoUpdate property.
-             * 
-             */
-            public void setAutoUpdate(boolean value) {
-                this.autoUpdate = value;
-            }
+    /**
+     * 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;
+    }
 
-        /**
-         * 
    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;
-            }
+    /**
+     * Gets the value of the ignoreGapsinConsensus property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isIgnoreGapsinConsensus()
+    {
+      if (ignoreGapsinConsensus == null)
+      {
+        return true;
+      }
+      else
+      {
+        return ignoreGapsinConsensus;
+      }
+    }
+
+    /**
+     * Sets the value of the ignoreGapsinConsensus property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIgnoreGapsinConsensus(Boolean value)
+    {
+      this.ignoreGapsinConsensus = value;
+    }
 
+    /**
+     * 
    
+     * Java class for anonymous complex type
+     * 
    
+     * .
+     * 
+     * 
    
+     * The following schema fragment specifies the expected content contained
+     * within this class.
+     * 
    
+     * 
+     * 
    +     * <complexType>
+     *   <complexContent>
+     *     <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
+    {
+
+      /**
+       * handle for the calculation which uses this parameter set
+       * 
+       */
+      @XmlAttribute(name = "calcId", required = true)
+      protected String calcId;
+
+      /**
+       * should the calculation be performed immediately after loading in order
+       * to refresh results
+       * 
+       */
+      @XmlAttribute(name = "needsUpdate")
+      protected Boolean needsUpdate;
+
+      /**
+       * should the calculation be automatically performed on edits
+       * 
+       */
+      @XmlAttribute(name = "autoUpdate", required = true)
+      protected boolean autoUpdate;
+
+      /**
+       * handle for the calculation which uses this parameter set
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getCalcId()
+      {
+        return calcId;
+      }
+
+      /**
+       * Sets the value of the calcId property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       * @see #getCalcId()
+       */
+      public void setCalcId(String value)
+      {
+        this.calcId = value;
+      }
+
+      /**
+       * should the calculation be performed immediately after loading in order
+       * to refresh results
+       * 
+       * @return possible object is {@link Boolean }
+       * 
+       */
+      public boolean isNeedsUpdate()
+      {
+        if (needsUpdate == null)
+        {
+          return false;
         }
+        else
+        {
+          return needsUpdate;
+        }
+      }
+
+      /**
+       * Sets the value of the needsUpdate property.
+       * 
+       * @param value
+       *          allowed object is {@link Boolean }
+       * 
+       * @see #isNeedsUpdate()
+       */
+      public void setNeedsUpdate(Boolean value)
+      {
+        this.needsUpdate = value;
+      }
+
+      /**
+       * should the calculation be automatically performed on edits
+       * 
+       */
+      public boolean isAutoUpdate()
+      {
+        return autoUpdate;
+      }
+
+      /**
+       * Sets the value of the autoUpdate property.
+       * 
+       */
+      public void setAutoUpdate(boolean value)
+      {
+        this.autoUpdate = value;
+      }
 
+    }
 
-        /**
-         * 
    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 b48ca13..f7bac13 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,16 @@ 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">
@@ -71,567 +75,592 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
-    "version",
-    "colour",
-    "filter"
-})
-public class JalviewUserColours {
+@XmlType(
+  name = "JalviewUserColours",
+  namespace = "www.jalview.org/colours",
+  propOrder =
+  { "version", "colour", "filter" })
+public class JalviewUserColours
+{
+
+  /**
+   * Jalview colour scheme document version.
+   * 
+   */
+  @XmlElement(name = "Version", namespace = "")
+  protected String version;
+
+  @XmlElement(namespace = "")
+  protected List colour;
+
+  @XmlElement(namespace = "")
+  protected List filter;
+
+  @XmlAttribute(name = "schemeName")
+  protected String schemeName;
+
+  /**
+   * Jalview colour scheme document version.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getVersion()
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * 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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the colour property.
+   */
+  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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the filter property.
+   */
+  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
+  {
 
     /**
-     * Jalview colour scheme document version.
+     * name of feature attribute to colour by, or attribute and sub-attribute
      * 
      */
-    @XmlElement(name = "Version", namespace = "")
-    protected String version;
-    @XmlElement(namespace = "")
-    protected List colour;
     @XmlElement(namespace = "")
-    protected List filter;
-    @XmlAttribute(name = "schemeName")
-    protected String schemeName;
+    protected List attributeName;
 
     /**
-     * Jalview colour scheme document version.
+     * Single letter residue code for an alignment colour scheme, or feature
+     * type for a feature colour scheme
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getVersion() {
-        return version;
-    }
+    @XmlAttribute(name = "Name")
+    protected String name;
 
-    /**
-     * Sets the value of the version property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getVersion()
-     */
-    public void setVersion(String value) {
-        this.version = value;
-    }
+    @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 colour property.
+     * name of feature attribute to colour by, or attribute and sub-attribute
      * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification 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.
    
+     * 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:
      * 
    
+     * 
      * 
    -     * getColour().add(newItem);
+     * getAttributeName().add(newItem);
      * 
    
      * 
      * 
      * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewUserColours.Colour }
+     * Objects of the following type(s) are allowed in the list {@link String }
      * 
    
      * 
      * 
-     * @return
-     *     The value of the colour property.
+     * @return The value of the attributeName property.
      */
-    public List getColour() {
-        if (colour == null) {
-            colour = new ArrayList();
-        }
-        return this.colour;
+    public List getAttributeName()
+    {
+      if (attributeName == null)
+      {
+        attributeName = new ArrayList();
+      }
+      return this.attributeName;
     }
 
     /**
-     * Gets the value of the filter property.
+     * Single letter residue code for an alignment colour scheme, or feature
+     * type for a feature colour scheme
      * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification 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.
    
+     * @return possible object is {@link String }
      * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getFilter().add(newItem);
-     * 
    
+     */
+    public String getName()
+    {
+      return name;
+    }
+
+    /**
+     * Sets the value of the name property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewUserColours.Filter }
-     * 
    
+     * @see #getName()
+     */
+    public void setName(String value)
+    {
+      this.name = value;
+    }
+
+    /**
+     * Gets the value of the rgb property.
+     * 
+     * @return possible object is {@link String }
+     * 
+     */
+    public String getRGB()
+    {
+      return rgb;
+    }
+
+    /**
+     * Sets the value of the rgb property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     The value of the filter property.
      */
-    public List getFilter() {
-        if (filter == null) {
-            filter = new ArrayList();
-        }
-        return this.filter;
+    public void setRGB(String value)
+    {
+      this.rgb = value;
     }
 
     /**
-     * Gets the value of the schemeName property.
+     * Gets the value of the minRGB property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getSchemeName() {
-        return schemeName;
+    public String getMinRGB()
+    {
+      return minRGB;
     }
 
     /**
-     * Sets the value of the schemeName property.
+     * Sets the value of the minRGB property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setSchemeName(String value) {
-        this.schemeName = value;
+    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;
+      }
+    }
 
     /**
-     * 
    Java class for anonymous complex type
    .
+     * Sets the value of the noValueColour property.
      * 
-     * 
    The following schema fragment specifies the expected content contained within this class.
    
+     * @param value
+     *          allowed object is {@link NoValueColour }
      * 
-     * 
    -     * <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 setNoValueColour(NoValueColour value)
+    {
+      this.noValueColour = value;
+    }
+
+    /**
+     * Gets the value of the threshType property.
      * 
+     * @return possible object is {@link ThresholdType }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "attributeName"
-    })
-    public static class Colour {
-
-        /**
-         * name of feature attribute to colour by, or attribute and sub-attribute
-         * 
-         */
-        @XmlElement(namespace = "")
-        protected List attributeName;
-        /**
-         * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme
-         * 
-         */
-        @XmlAttribute(name = "Name")
-        protected String name;
-        @XmlAttribute(name = "RGB", required = true)
-        protected String rgb;
-        @XmlAttribute(name = "minRGB")
-        protected String minRGB;
-        @XmlAttribute(name = "noValueColour")
-        protected NoValueColour noValueColour;
-        @XmlAttribute(name = "threshType")
-        protected ThresholdType threshType;
-        @XmlAttribute(name = "threshold")
-        protected Float threshold;
-        @XmlAttribute(name = "max")
-        protected Float max;
-        @XmlAttribute(name = "min")
-        protected Float min;
-        @XmlAttribute(name = "colourByLabel")
-        protected Boolean colourByLabel;
-        @XmlAttribute(name = "autoScale")
-        protected Boolean autoScale;
-
-        /**
-         * name of feature attribute to colour by, or attribute and sub-attribute
-         * 
-         * Gets the value of the attributeName property.
-         * 
-         * 
    This accessor method returns a reference to the live list,
-         * not a snapshot. Therefore any modification you make to the
-         * returned list will be present inside the JAXB object.
-         * This is why there is not a set method for the attributeName property.
    
-         * 
-         * 
    
-         * For example, to add a new item, do as follows:
-         * 
    
-         * 
    -         * getAttributeName().add(newItem);
-         * 
    
-         * 
-         * 
-         * 
    
-         * Objects of the following type(s) are allowed in the list
-         * {@link String }
-         * 
    
-         * 
-         * 
-         * @return
-         *     The value of the attributeName property.
-         */
-        public List getAttributeName() {
-            if (attributeName == null) {
-                attributeName = new ArrayList();
-            }
-            return this.attributeName;
-        }
-
-        /**
-         * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getName() {
-            return name;
-        }
-
-        /**
-         * Sets the value of the name property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         * @see #getName()
-         */
-        public void setName(String value) {
-            this.name = value;
-        }
-
-        /**
-         * Gets the value of the rgb property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getRGB() {
-            return rgb;
-        }
-
-        /**
-         * Sets the value of the rgb property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setRGB(String value) {
-            this.rgb = value;
-        }
-
-        /**
-         * Gets the value of the minRGB property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getMinRGB() {
-            return minRGB;
-        }
-
-        /**
-         * Sets the value of the minRGB property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setMinRGB(String value) {
-            this.minRGB = value;
-        }
-
-        /**
-         * Gets the value of the noValueColour property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link NoValueColour }
-         *     
-         */
-        public NoValueColour getNoValueColour() {
-            if (noValueColour == null) {
-                return NoValueColour.MIN;
-            } else {
-                return noValueColour;
-            }
-        }
-
-        /**
-         * Sets the value of the noValueColour property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link NoValueColour }
-         *     
-         */
-        public void setNoValueColour(NoValueColour value) {
-            this.noValueColour = value;
-        }
-
-        /**
-         * Gets the value of the threshType property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link ThresholdType }
-         *     
-         */
-        public ThresholdType getThreshType() {
-            return threshType;
-        }
-
-        /**
-         * Sets the value of the threshType property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link ThresholdType }
-         *     
-         */
-        public void setThreshType(ThresholdType value) {
-            this.threshType = value;
-        }
-
-        /**
-         * Gets the value of the threshold property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getThreshold() {
-            return threshold;
-        }
-
-        /**
-         * Sets the value of the threshold property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setThreshold(Float value) {
-            this.threshold = value;
-        }
-
-        /**
-         * Gets the value of the max property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getMax() {
-            return max;
-        }
-
-        /**
-         * Sets the value of the max property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setMax(Float value) {
-            this.max = value;
-        }
-
-        /**
-         * Gets the value of the min property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Float }
-         *     
-         */
-        public Float getMin() {
-            return min;
-        }
-
-        /**
-         * Sets the value of the min property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Float }
-         *     
-         */
-        public void setMin(Float value) {
-            this.min = value;
-        }
-
-        /**
-         * Gets the value of the colourByLabel property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isColourByLabel() {
-            return colourByLabel;
-        }
-
-        /**
-         * Sets the value of the colourByLabel property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setColourByLabel(Boolean value) {
-            this.colourByLabel = value;
-        }
-
-        /**
-         * Gets the value of the autoScale property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public Boolean isAutoScale() {
-            return autoScale;
-        }
-
-        /**
-         * Sets the value of the autoScale property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         */
-        public void setAutoScale(Boolean value) {
-            this.autoScale = value;
-        }
+    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;
+    }
 
     /**
-     * 
    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="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 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 }
      * 
      */
-    @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 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="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 }
+     * 
+     */
+    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 72fada5..e6e6125 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -18,14 +17,18 @@ 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
    .
+ * 
    
+ * Java class for mapListType 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="mapListType">
@@ -63,312 +66,323 @@ 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
+{
 
-    /**
-     * a region from start to end inclusive
-     * 
-     */
-    protected List mapListFrom;
-    /**
-     * a region from start to end inclusive
-     * 
-     */
-    protected List mapListTo;
-    /**
-     * number of dictionary symbol widths involved in
-     * 					each
-     * 					mapped position on this sequence (for example, 3 for a dna
-     * 					sequence exon
-     * 					region that is being mapped to a protein sequence).
-     * 					This is optional,
-     * 					since the unit can be usually be inferred from the
-     * 					dictionary type of
-     * 					each sequence involved in the mapping.
-     * 
-     */
-    @XmlAttribute(name = "mapFromUnit", required = true)
-    @XmlSchemaType(name = "positiveInteger")
-    protected BigInteger mapFromUnit;
-    /**
-     * number of dictionary symbol widths involved in
-     * 					each
-     * 					mapped position on this sequence (for example, 3 for a dna
-     * 					sequence exon
-     * 					region that is being mapped to a protein sequence).
-     * 					This is optional,
-     * 					since the unit can be usually be inferred from the
-     * 					dictionary type of
-     * 					each sequence involved in the mapping.
-     * 
-     */
-    @XmlAttribute(name = "mapToUnit", required = true)
-    @XmlSchemaType(name = "positiveInteger")
-    protected BigInteger mapToUnit;
+  /**
+   * a region from start to end inclusive
+   * 
+   */
+  protected List mapListFrom;
+
+  /**
+   * a region from start to end inclusive
+   * 
+   */
+  protected List mapListTo;
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   * 
+   */
+  @XmlAttribute(name = "mapFromUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapFromUnit;
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   * 
+   */
+  @XmlAttribute(name = "mapToUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapToUnit;
+
+  /**
+   * a region from start to end inclusive
+   * 
+   * Gets the value of the mapListFrom property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the mapListFrom property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getMapListFrom().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list
+   * {@link MapListType.MapListFrom }
+   * 
    
+   * 
+   * 
+   * @return The value of the mapListFrom property.
+   */
+  public List getMapListFrom()
+  {
+    if (mapListFrom == null)
+    {
+      mapListFrom = new ArrayList();
+    }
+    return this.mapListFrom;
+  }
+
+  /**
+   * a region from start to end inclusive
+   * 
+   * Gets the value of the mapListTo property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the mapListTo property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getMapListTo().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list
+   * {@link MapListType.MapListTo }
+   * 
    
+   * 
+   * 
+   * @return The value of the mapListTo property.
+   */
+  public List getMapListTo()
+  {
+    if (mapListTo == null)
+    {
+      mapListTo = new ArrayList();
+    }
+    return this.mapListTo;
+  }
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   * 
+   * @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 }
+   * 
+   * @see #getMapFromUnit()
+   */
+  public void setMapFromUnit(BigInteger value)
+  {
+    this.mapFromUnit = value;
+  }
+
+  /**
+   * number of dictionary symbol widths involved in each mapped position on this
+   * sequence (for example, 3 for a dna sequence exon region that is being
+   * mapped to a protein sequence). This is optional, since the unit can be
+   * usually be inferred from the dictionary type of each sequence involved in
+   * the mapping.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getMapToUnit()
+  {
+    return mapToUnit;
+  }
+
+  /**
+   * Sets the value of the mapToUnit property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   * @see #getMapToUnit()
+   */
+  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;
 
     /**
-     * a region from start to end inclusive
-     * 
-     * Gets the value of the mapListFrom property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the mapListFrom property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getMapListFrom().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link MapListType.MapListFrom }
-     * 
    
+     * Gets the value of the start property.
      * 
-     * 
-     * @return
-     *     The value of the mapListFrom property.
      */
-    public List getMapListFrom() {
-        if (mapListFrom == null) {
-            mapListFrom = new ArrayList();
-        }
-        return this.mapListFrom;
+    public int getStart()
+    {
+      return start;
     }
 
     /**
-     * a region from start to end inclusive
-     * 
-     * Gets the value of the mapListTo property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the mapListTo property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getMapListTo().add(newItem);
-     * 
    
+     * Sets the value of the start property.
      * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link MapListType.MapListTo }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the mapListTo property.
      */
-    public List getMapListTo() {
-        if (mapListTo == null) {
-            mapListTo = new ArrayList();
-        }
-        return this.mapListTo;
+    public void setStart(int value)
+    {
+      this.start = value;
     }
 
     /**
-     * number of dictionary symbol widths involved in
-     * 					each
-     * 					mapped position on this sequence (for example, 3 for a dna
-     * 					sequence exon
-     * 					region that is being mapped to a protein sequence).
-     * 					This is optional,
-     * 					since the unit can be usually be inferred from the
-     * 					dictionary type of
-     * 					each sequence involved in the mapping.
+     * 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 }
-     *     
-     * @see #getMapFromUnit()
      */
-    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;
+
     /**
-     * number of dictionary symbol widths involved in
-     * 					each
-     * 					mapped position on this sequence (for example, 3 for a dna
-     * 					sequence exon
-     * 					region that is being mapped to a protein sequence).
-     * 					This is optional,
-     * 					since the unit can be usually be inferred from the
-     * 					dictionary type of
-     * 					each sequence involved in the mapping.
+     * 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 }
-     *     
-     * @see #getMapToUnit()
      */
-    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/MapOnAMatrixType.java b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java
index b4b1105..c7e9e33 100644
--- a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java
+++ b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,14 +14,19 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Defines a mapping from the local frame to a matrix
- * 				and its associated data specified by MatrixType
+ * Defines a mapping from the local frame to a matrix and its associated data
+ * specified by MatrixType
  * 
- * 
    Java class for MapOnAMatrixType complex type
    .
+ * 
    
+ * Java class for MapOnAMatrixType 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="MapOnAMatrixType">
@@ -42,135 +46,134 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MapOnAMatrixType", propOrder = {
-    "property",
-    "mapping"
-})
-public class MapOnAMatrixType {
+@XmlType(name = "MapOnAMatrixType", propOrder = { "property", "mapping" })
+public class MapOnAMatrixType
+{
 
-    protected List property;
-    /**
-     * mapping from the matrix row and column positions
-     * 						to
-     * 						associated reference frame
-     * 
-     */
-    protected MapListType mapping;
-    /**
-     * reference to the matrix type this Map refers to
-     * 
-     */
-    @XmlAttribute(name = "matrix", required = true)
-    protected String matrix;
-    @XmlAttribute(name = "id")
-    protected String id;
+  protected List property;
 
-    /**
-     * Gets the value of the property property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the property property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getProperty().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link Property }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the property property.
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
-    }
+  /**
+   * mapping from the matrix row and column positions to associated reference
+   * frame
+   * 
+   */
+  protected MapListType mapping;
 
-    /**
-     * mapping from the matrix row and column positions
-     * 						to
-     * 						associated reference frame
-     * 
-     * @return
-     *     possible object is
-     *     {@link MapListType }
-     *     
-     */
-    public MapListType getMapping() {
-        return mapping;
-    }
+  /**
+   * reference to the matrix type this Map refers to
+   * 
+   */
+  @XmlAttribute(name = "matrix", required = true)
+  protected String matrix;
 
-    /**
-     * Sets the value of the mapping property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link MapListType }
-     *     
-     * @see #getMapping()
-     */
-    public void setMapping(MapListType value) {
-        this.mapping = value;
-    }
+  @XmlAttribute(name = "id")
+  protected String id;
 
-    /**
-     * reference to the matrix type this Map refers to
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getMatrix() {
-        return matrix;
+  /**
+   * Gets the value of the property property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the property property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getProperty().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link Property }
+   * 
    
+   * 
+   * 
+   * @return The value of the property property.
+   */
+  public List getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList();
     }
+    return this.property;
+  }
 
-    /**
-     * Sets the value of the matrix property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getMatrix()
-     */
-    public void setMatrix(String value) {
-        this.matrix = value;
-    }
+  /**
+   * mapping from the matrix row and column positions to associated reference
+   * frame
+   * 
+   * @return possible object is {@link MapListType }
+   * 
+   */
+  public MapListType getMapping()
+  {
+    return mapping;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Sets the value of the mapping property.
+   * 
+   * @param value
+   *          allowed object is {@link MapListType }
+   * 
+   * @see #getMapping()
+   */
+  public void setMapping(MapListType value)
+  {
+    this.mapping = value;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * reference to the matrix type this Map refers to
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getMatrix()
+  {
+    return matrix;
+  }
+
+  /**
+   * Sets the value of the matrix property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getMatrix()
+   */
+  public void setMatrix(String value)
+  {
+    this.matrix = value;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index fcfd7e4..0e7cfff 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -15,18 +14,20 @@ 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>
@@ -52,96 +53,91 @@ 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;
-    /**
-     * Biotype of the mapping e.g. CdsToPeptide
-     * 
-     */
-    @XmlAttribute(name = "mappingType")
-    protected String mappingType;
+  @XmlElement(name = "Sequence")
+  protected Sequence sequence;
+
+  protected String dseqFor;
+
+  /**
+   * Biotype of the mapping e.g. CdsToPeptide
+   * 
+   */
+  @XmlAttribute(name = "mappingType")
+  protected String mappingType;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Sequence }
-     *     
-     */
-    public Sequence getSequence() {
-        return sequence;
-    }
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link Sequence }
+   * 
+   */
+  public Sequence getSequence()
+  {
+    return sequence;
+  }
 
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Sequence }
-     *     
-     */
-    public void setSequence(Sequence value) {
-        this.sequence = value;
-    }
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link Sequence }
+   * 
+   */
+  public void setSequence(Sequence value)
+  {
+    this.sequence = value;
+  }
 
-    /**
-     * Gets the value of the dseqFor property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDseqFor() {
-        return dseqFor;
-    }
+  /**
+   * Gets the value of the dseqFor property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDseqFor()
+  {
+    return dseqFor;
+  }
 
-    /**
-     * Sets the value of the dseqFor property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDseqFor(String value) {
-        this.dseqFor = value;
-    }
+  /**
+   * Sets the value of the dseqFor property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDseqFor(String value)
+  {
+    this.dseqFor = value;
+  }
 
-    /**
-     * Biotype of the mapping e.g. CdsToPeptide
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getMappingType() {
-        return mappingType;
-    }
+  /**
+   * Biotype of the mapping e.g. CdsToPeptide
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getMappingType()
+  {
+    return mappingType;
+  }
 
-    /**
-     * Sets the value of the mappingType property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getMappingType()
-     */
-    public void setMappingType(String value) {
-        this.mappingType = value;
-    }
+  /**
+   * Sets the value of the mappingType property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getMappingType()
+   */
+  public void setMappingType(String value)
+  {
+    this.mappingType = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java
index 0fd8ef5..b781bea 100644
--- a/src/jalview/xml/binding/jalview/MatrixType.java
+++ b/src/jalview/xml/binding/jalview/MatrixType.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,16 +16,19 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Represents matrix data imported to Jalview, and the
- * 				results of any derived calculations (independent of a particular
- * 				view
- * 				on the matrix).
+ * Represents matrix data imported to Jalview, and the results of any derived
+ * calculations (independent of a particular view on the matrix).
  * 
- * 
    Java class for MatrixType complex type
    .
+ * 
    
+ * 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">
@@ -52,315 +54,325 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MatrixType", propOrder = {
-    "elements",
-    "groups",
-    "newick",
-    "property"
-})
-public class MatrixType {
+@XmlType(
+  name = "MatrixType",
+  propOrder =
+  { "elements", "groups", "newick", "property" })
+public class MatrixType
+{
 
-    /**
-     * serialised representation of matrix as one or
-     * 						more sets of comma separated values
-     * 
-     */
-    @XmlElement(required = true)
-    protected String elements;
-    /**
-     * Comma separated series of longs formed from
-     * 						bitsets defining partitions on the rows/columns of the matrix
-     * 
-     */
-    protected List groups;
-    /**
-     * tree computed for this
-     * 
-     */
-    protected List newick;
-    protected List property;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "rows", required = true)
-    protected BigInteger rows;
-    @XmlAttribute(name = "cols", required = true)
-    protected BigInteger cols;
-    @XmlAttribute(name = "treeMethod")
-    protected String treeMethod;
-    @XmlAttribute(name = "cutHeight")
-    protected Double cutHeight;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
+  /**
+   * serialised representation of matrix as one or more sets of comma separated
+   * values
+   * 
+   */
+  @XmlElement(required = true)
+  protected String elements;
 
-    /**
-     * serialised representation of matrix as one or
-     * 						more sets of comma separated values
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getElements() {
-        return elements;
-    }
+  /**
+   * Comma separated series of longs formed from bitsets defining partitions on
+   * the rows/columns of the matrix
+   * 
+   */
+  protected List groups;
 
-    /**
-     * Sets the value of the elements property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getElements()
-     */
-    public void setElements(String value) {
-        this.elements = value;
-    }
+  /**
+   * tree computed for this
+   * 
+   */
+  protected List newick;
 
-    /**
-     * Comma separated series of longs formed from
-     * 						bitsets defining partitions on the rows/columns of the matrix
-     * 
-     * Gets the value of the groups property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the groups property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getGroups().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the groups property.
-     */
-    public List getGroups() {
-        if (groups == null) {
-            groups = new ArrayList();
-        }
-        return this.groups;
-    }
+  protected List property;
 
-    /**
-     * tree computed for this
-     * 
-     * Gets the value of the newick property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the newick property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getNewick().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the newick property.
-     */
-    public List getNewick() {
-        if (newick == null) {
-            newick = new ArrayList();
-        }
-        return this.newick;
-    }
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the property property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the property property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getProperty().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link Property }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the property property.
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
-    }
+  @XmlAttribute(name = "rows", required = true)
+  protected BigInteger rows;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  @XmlAttribute(name = "cols", required = true)
+  protected BigInteger cols;
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  @XmlAttribute(name = "treeMethod")
+  protected String treeMethod;
 
-    /**
-     * Gets the value of the rows property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getRows() {
-        return rows;
-    }
+  @XmlAttribute(name = "cutHeight")
+  protected Double cutHeight;
 
-    /**
-     * Sets the value of the rows property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setRows(BigInteger value) {
-        this.rows = value;
-    }
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
 
-    /**
-     * Gets the value of the cols property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getCols() {
-        return cols;
-    }
+  /**
+   * serialised representation of matrix as one or more sets of comma separated
+   * values
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getElements()
+  {
+    return elements;
+  }
 
-    /**
-     * Sets the value of the cols property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setCols(BigInteger value) {
-        this.cols = value;
-    }
+  /**
+   * Sets the value of the elements property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getElements()
+   */
+  public void setElements(String value)
+  {
+    this.elements = value;
+  }
 
-    /**
-     * Gets the value of the treeMethod property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getTreeMethod() {
-        return treeMethod;
+  /**
+   * Comma separated series of longs formed from bitsets defining partitions on
+   * the rows/columns of the matrix
+   * 
+   * Gets the value of the groups property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the groups property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getGroups().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
    
+   * 
+   * 
+   * @return The value of the groups property.
+   */
+  public List getGroups()
+  {
+    if (groups == null)
+    {
+      groups = new ArrayList();
     }
+    return this.groups;
+  }
 
-    /**
-     * Sets the value of the treeMethod property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setTreeMethod(String value) {
-        this.treeMethod = value;
+  /**
+   * tree computed for this
+   * 
+   * Gets the value of the newick property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the newick property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getNewick().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
    
+   * 
+   * 
+   * @return The value of the newick property.
+   */
+  public List getNewick()
+  {
+    if (newick == null)
+    {
+      newick = new ArrayList();
     }
+    return this.newick;
+  }
 
-    /**
-     * Gets the value of the cutHeight property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Double }
-     *     
-     */
-    public Double getCutHeight() {
-        return cutHeight;
+  /**
+   * Gets the value of the property property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the property property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getProperty().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link Property }
+   * 
    
+   * 
+   * 
+   * @return The value of the property property.
+   */
+  public List getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList();
     }
+    return this.property;
+  }
 
-    /**
-     * Sets the value of the cutHeight property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Double }
-     *     
-     */
-    public void setCutHeight(Double value) {
-        this.cutHeight = value;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Gets the value of the rows property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getRows()
+  {
+    return rows;
+  }
+
+  /**
+   * Sets the value of the rows property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setRows(BigInteger value)
+  {
+    this.rows = value;
+  }
+
+  /**
+   * Gets the value of the cols property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getCols()
+  {
+    return cols;
+  }
+
+  /**
+   * Sets the value of the cols property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setCols(BigInteger value)
+  {
+    this.cols = value;
+  }
+
+  /**
+   * Gets the value of the treeMethod property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getTreeMethod()
+  {
+    return treeMethod;
+  }
+
+  /**
+   * Sets the value of the treeMethod property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setTreeMethod(String value)
+  {
+    this.treeMethod = value;
+  }
+
+  /**
+   * Gets the value of the cutHeight property.
+   * 
+   * @return possible object is {@link Double }
+   * 
+   */
+  public Double getCutHeight()
+  {
+    return cutHeight;
+  }
+
+  /**
+   * Sets the value of the cutHeight property.
+   * 
+   * @param value
+   *          allowed object is {@link Double }
+   * 
+   */
+  public void setCutHeight(Double value)
+  {
+    this.cutHeight = value;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
index baa9eed..29d8d1f 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -5,20 +5,25 @@
 // Generated on: 2024.07.25 at 04:43:38 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;
 
-
 /**
  * Graduated feature colour if no score (or attribute) value
  * 
- * 
    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">
@@ -32,47 +37,50 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum NoValueColour {
+public enum NoValueColour
+{
 
-    @XmlEnumValue("None")
-    NONE("None"),
-    @XmlEnumValue("Min")
-    MIN("Min"),
-    @XmlEnumValue("Max")
-    MAX("Max");
-    private final String value;
+  @XmlEnumValue("None")
+  NONE("None"), @XmlEnumValue("Min")
+  MIN("Min"), @XmlEnumValue("Max")
+  MAX("Max");
 
-    NoValueColour(String v) {
-        value = v;
-    }
+  private final String value;
 
-    /**
-     * Gets the value associated to the enum constant.
-     * 
-     * @return
-     *     The value linked to the enum.
-     */
-    public String value() {
-        return value;
-    }
+  NoValueColour(String v)
+  {
+    value = v;
+  }
+
+  /**
+   * Gets the value associated to the enum constant.
+   * 
+   * @return The value linked to the enum.
+   */
+  public String value()
+  {
+    return value;
+  }
 
-    /**
-     * Gets the enum associated to the value passed as parameter.
-     * 
-     * @param v
-     *     The value to get the enum from.
-     * @return
-     *     The enum which corresponds to the value, if it exists.
-     * @throws IllegalArgumentException
-     *     If no value matches in the enum declaration.
-     */
-    public static NoValueColour fromValue(String v) {
-        for (NoValueColour c: NoValueColour.values()) {
-            if (c.value.equals(v)) {
-                return c;
-            }
-        }
-        throw new IllegalArgumentException(v);
+  /**
+   * Gets the enum associated to the value passed as parameter.
+   * 
+   * @param v
+   *          The value to get the enum from.
+   * @return The enum which corresponds to the value, if it exists.
+   * @throws IllegalArgumentException
+   *           If no value matches in the enum declaration.
+   */
+  public static NoValueColour fromValue(String v)
+  {
+    for (NoValueColour c : NoValueColour.values())
+    {
+      if (c.value.equals(v))
+      {
+        return c;
+      }
     }
+    throw new IllegalArgumentException(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index 8ac2701..31706a5 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.JAXBElement;
@@ -13,512 +12,588 @@ 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 static final QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
-    private static final QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
-    private static final QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
-    /**
-     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
-     * 
-     */
-    public ObjectFactory() {
-    }
-
-    /**
-     * Create an instance of {@link MapListType }
-     * 
-     */
-    public MapListType createMapListType() {
-        return new MapListType();
-    }
-
-    /**
-     * Create an instance of {@link Sequence }
-     * 
-     */
-    public Sequence createSequence() {
-        return new Sequence();
-    }
-
-    /**
-     * Create an instance of {@link AlcodonFrame }
-     * 
-     */
-    public AlcodonFrame createAlcodonFrame() {
-        return new AlcodonFrame();
-    }
-
-    /**
-     * Create an instance of {@link Annotation }
-     * 
-     */
-    public Annotation createAnnotation() {
-        return new Annotation();
-    }
-
-    /**
-     * Create an instance of {@link SequenceSet }
-     * 
-     */
-    public SequenceSet createSequenceSet() {
-        return new SequenceSet();
-    }
-
-    /**
-     * Create an instance of {@link FeatureMatcherSet }
-     * 
-     */
-    public FeatureMatcherSet createFeatureMatcherSet() {
-        return new FeatureMatcherSet();
-    }
-
-    /**
-     * Create an instance of {@link JalviewUserColours }
-     * 
-     */
-    public JalviewUserColours createJalviewUserColours() {
-        return new JalviewUserColours();
-    }
-
-    /**
-     * Create an instance of {@link Pdbentry }
-     * 
-     */
-    public Pdbentry createPdbentry() {
-        return new Pdbentry();
-    }
-
-    /**
-     * Create an instance of {@link Feature }
-     * 
-     */
-    public Feature createFeature() {
-        return new Feature();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel }
-     * 
-     */
-    public JalviewModel createJalviewModel() {
-        return new JalviewModel();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.FeatureSettings }
-     * 
-     */
-    public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
-        return new JalviewModel.FeatureSettings();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer }
-     * 
-     */
-    public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
-        return new JalviewModel.PcaViewer();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport }
-     * 
-     */
-    public JalviewModel.Viewport createJalviewModelViewport() {
-        return new JalviewModel.Viewport();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq }
-     * 
-     */
-    public JalviewModel.JSeq createJalviewModelJSeq() {
-        return new JalviewModel.JSeq();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
-     * 
-     */
-    public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
-        return new JalviewModel.JSeq.RnaViewer();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.Pdbids }
-     * 
-     */
-    public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
-        return new JalviewModel.JSeq.Pdbids();
-    }
-
-    /**
-     * Create an instance of {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme createAnnotationColourScheme() {
-        return new AnnotationColourScheme();
-    }
-
-    /**
-     * Create an instance of {@link PcaDataType }
-     * 
-     */
-    public PcaDataType createPcaDataType() {
-        return new PcaDataType();
-    }
-
-    /**
-     * Create an instance of {@link DoubleVector }
-     * 
-     */
-    public DoubleVector createDoubleVector() {
-        return new DoubleVector();
-    }
-
-    /**
-     * Create an instance of {@link DoubleMatrix }
-     * 
-     */
-    public DoubleMatrix createDoubleMatrix() {
-        return new DoubleMatrix();
-    }
-
-    /**
-     * Create an instance of {@link Mapping }
-     * 
-     */
-    public Mapping createMapping() {
-        return new Mapping();
-    }
-
-    /**
-     * Create an instance of {@link MapListType.MapListFrom }
-     * 
-     */
-    public MapListType.MapListFrom createMapListTypeMapListFrom() {
-        return new MapListType.MapListFrom();
-    }
-
-    /**
-     * Create an instance of {@link MapListType.MapListTo }
-     * 
-     */
-    public MapListType.MapListTo createMapListTypeMapListTo() {
-        return new MapListType.MapListTo();
-    }
-
-    /**
-     * Create an instance of {@link SequenceType }
-     * 
-     */
-    public SequenceType createSequenceType() {
-        return new SequenceType();
-    }
-
-    /**
-     * Create an instance of {@link Sequence.DBRef }
-     * 
-     */
-    public Sequence.DBRef createSequenceDBRef() {
-        return new Sequence.DBRef();
-    }
-
-    /**
-     * Create an instance of {@link AlcodonFrame.Alcodon }
-     * 
-     */
-    public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
-        return new AlcodonFrame.Alcodon();
-    }
-
-    /**
-     * Create an instance of {@link AlcodonFrame.AlcodMap }
-     * 
-     */
-    public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
-        return new AlcodonFrame.AlcodMap();
-    }
-
-    /**
-     * Create an instance of {@link AnnotationElement }
-     * 
-     */
-    public AnnotationElement createAnnotationElement() {
-        return new AnnotationElement();
-    }
-
-    /**
-     * Create an instance of {@link Annotation.ThresholdLine }
-     * 
-     */
-    public Annotation.ThresholdLine createAnnotationThresholdLine() {
-        return new Annotation.ThresholdLine();
-    }
-
-    /**
-     * Create an instance of {@link MapOnAMatrixType }
-     * 
-     */
-    public MapOnAMatrixType createMapOnAMatrixType() {
-        return new MapOnAMatrixType();
-    }
-
-    /**
-     * Create an instance of {@link jalview.xml.binding.jalview.Property }
-     * 
-     */
-    public jalview.xml.binding.jalview.Property createProperty() {
-        return new jalview.xml.binding.jalview.Property();
-    }
-
-    /**
-     * Create an instance of {@link SequenceSet.SequenceSetProperties }
-     * 
-     */
-    public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
-        return new SequenceSet.SequenceSetProperties();
-    }
-
-    /**
-     * Create an instance of {@link MatrixType }
-     * 
-     */
-    public MatrixType createMatrixType() {
-        return new MatrixType();
-    }
-
-    /**
-     * Create an instance of {@link VAMSAS }
-     * 
-     */
-    public VAMSAS createVAMSAS() {
-        return new VAMSAS();
-    }
-
-    /**
-     * Create an instance of {@link FeatureMatcher }
-     * 
-     */
-    public FeatureMatcher createFeatureMatcher() {
-        return new FeatureMatcher();
-    }
-
-    /**
-     * Create an instance of {@link WebServiceParameterSet }
-     * 
-     */
-    public WebServiceParameterSet createWebServiceParameterSet() {
-        return new WebServiceParameterSet();
-    }
-
-    /**
-     * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
-     * 
-     */
-    public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
-        return new FeatureMatcherSet.CompoundMatcher();
-    }
-
-    /**
-     * Create an instance of {@link JalviewUserColours.Colour }
-     * 
-     */
-    public JalviewUserColours.Colour createJalviewUserColoursColour() {
-        return new JalviewUserColours.Colour();
-    }
-
-    /**
-     * Create an instance of {@link JalviewUserColours.Filter }
-     * 
-     */
-    public JalviewUserColours.Filter createJalviewUserColoursFilter() {
-        return new JalviewUserColours.Filter();
-    }
-
-    /**
-     * Create an instance of {@link Pdbentry.Property }
-     * 
-     */
-    public Pdbentry.Property createPdbentryProperty() {
-        return new Pdbentry.Property();
-    }
-
-    /**
-     * Create an instance of {@link Feature.OtherData }
-     * 
-     */
-    public Feature.OtherData createFeatureOtherData() {
-        return new Feature.OtherData();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JGroup }
-     * 
-     */
-    public JalviewModel.JGroup createJalviewModelJGroup() {
-        return new JalviewModel.JGroup();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.UserColours }
-     * 
-     */
-    public JalviewModel.UserColours createJalviewModelUserColours() {
-        return new JalviewModel.UserColours();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Tree }
-     * 
-     */
-    public JalviewModel.Tree createJalviewModelTree() {
-        return new JalviewModel.Tree();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
-     * 
-     */
-    public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
-        return new JalviewModel.FeatureSettings.Setting();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.FeatureSettings.Group }
-     * 
-     */
-    public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
-        return new JalviewModel.FeatureSettings.Group();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
-     * 
-     */
-    public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
-        return new JalviewModel.PcaViewer.SequencePoint();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.Axis }
-     * 
-     */
-    public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
-        return new JalviewModel.PcaViewer.Axis();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
-        return new JalviewModel.PcaViewer.SeqPointMin();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
-        return new JalviewModel.PcaViewer.SeqPointMax();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
-     * 
-     */
-    public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
-        return new JalviewModel.Viewport.HiddenColumns();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
-     * 
-     */
-    public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
-        return new JalviewModel.Viewport.CalcIdParam();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.Viewport.Overview }
-     * 
-     */
-    public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
-        return new JalviewModel.Viewport.Overview();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-     * 
-     */
-    public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
-        return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
-    }
-
-    /**
-     * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
-     * 
-     */
-    public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
-        return new JalviewModel.JSeq.Pdbids.StructureState();
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
-     * 
-     * @param value
-     *     Java instance representing xml element's value.
-     * @return
-     *     the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
-     */
-    @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
-    public JAXBElement createJalviewModel(JalviewModel value) {
-        return new JAXBElement(_JalviewModel_QNAME, JalviewModel.class, null, value);
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
-     * 
-     * @param value
-     *     Java instance representing xml element's value.
-     * @return
-     *     the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
-     */
-    @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
-    public JAXBElement createJalviewUserColours(JalviewUserColours value) {
-        return new JAXBElement(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
-     * 
-     * @param value
-     *     Java instance representing xml element's value.
-     * @return
-     *     the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
-     */
-    @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
-    public JAXBElement createWebServiceParameterSet(WebServiceParameterSet value) {
-        return new JAXBElement(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
-    }
+public class ObjectFactory
+{
+
+  private static final QName _JalviewModel_QNAME = new QName(
+          "www.jalview.org", "JalviewModel");
+
+  private static final QName _JalviewUserColours_QNAME = new QName(
+          "www.jalview.org/colours", "JalviewUserColours");
+
+  private static final QName _WebServiceParameterSet_QNAME = new QName(
+          "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+
+  /**
+   * Create a new ObjectFactory that can be used to create new instances of
+   * schema derived classes for package: jalview.xml.binding.jalview
+   * 
+   */
+  public ObjectFactory()
+  {
+  }
+
+  /**
+   * Create an instance of {@link MapListType }
+   * 
+   */
+  public MapListType createMapListType()
+  {
+    return new MapListType();
+  }
+
+  /**
+   * Create an instance of {@link Sequence }
+   * 
+   */
+  public Sequence createSequence()
+  {
+    return new Sequence();
+  }
+
+  /**
+   * Create an instance of {@link AlcodonFrame }
+   * 
+   */
+  public AlcodonFrame createAlcodonFrame()
+  {
+    return new AlcodonFrame();
+  }
+
+  /**
+   * Create an instance of {@link Annotation }
+   * 
+   */
+  public Annotation createAnnotation()
+  {
+    return new Annotation();
+  }
+
+  /**
+   * Create an instance of {@link SequenceSet }
+   * 
+   */
+  public SequenceSet createSequenceSet()
+  {
+    return new SequenceSet();
+  }
+
+  /**
+   * Create an instance of {@link FeatureMatcherSet }
+   * 
+   */
+  public FeatureMatcherSet createFeatureMatcherSet()
+  {
+    return new FeatureMatcherSet();
+  }
+
+  /**
+   * Create an instance of {@link JalviewUserColours }
+   * 
+   */
+  public JalviewUserColours createJalviewUserColours()
+  {
+    return new JalviewUserColours();
+  }
+
+  /**
+   * Create an instance of {@link Pdbentry }
+   * 
+   */
+  public Pdbentry createPdbentry()
+  {
+    return new Pdbentry();
+  }
+
+  /**
+   * Create an instance of {@link Feature }
+   * 
+   */
+  public Feature createFeature()
+  {
+    return new Feature();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel }
+   * 
+   */
+  public JalviewModel createJalviewModel()
+  {
+    return new JalviewModel();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.FeatureSettings }
+   * 
+   */
+  public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
+  {
+    return new JalviewModel.FeatureSettings();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer }
+   * 
+   */
+  public JalviewModel.PcaViewer createJalviewModelPcaViewer()
+  {
+    return new JalviewModel.PcaViewer();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport }
+   * 
+   */
+  public JalviewModel.Viewport createJalviewModelViewport()
+  {
+    return new JalviewModel.Viewport();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq }
+   * 
+   */
+  public JalviewModel.JSeq createJalviewModelJSeq()
+  {
+    return new JalviewModel.JSeq();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+   * 
+   */
+  public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
+  {
+    return new JalviewModel.JSeq.RnaViewer();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+   * 
+   */
+  public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
+  {
+    return new JalviewModel.JSeq.Pdbids();
+  }
+
+  /**
+   * Create an instance of {@link AnnotationColourScheme }
+   * 
+   */
+  public AnnotationColourScheme createAnnotationColourScheme()
+  {
+    return new AnnotationColourScheme();
+  }
+
+  /**
+   * Create an instance of {@link PcaDataType }
+   * 
+   */
+  public PcaDataType createPcaDataType()
+  {
+    return new PcaDataType();
+  }
+
+  /**
+   * Create an instance of {@link DoubleVector }
+   * 
+   */
+  public DoubleVector createDoubleVector()
+  {
+    return new DoubleVector();
+  }
+
+  /**
+   * Create an instance of {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix createDoubleMatrix()
+  {
+    return new DoubleMatrix();
+  }
+
+  /**
+   * Create an instance of {@link Mapping }
+   * 
+   */
+  public Mapping createMapping()
+  {
+    return new Mapping();
+  }
+
+  /**
+   * Create an instance of {@link MapListType.MapListFrom }
+   * 
+   */
+  public MapListType.MapListFrom createMapListTypeMapListFrom()
+  {
+    return new MapListType.MapListFrom();
+  }
+
+  /**
+   * Create an instance of {@link MapListType.MapListTo }
+   * 
+   */
+  public MapListType.MapListTo createMapListTypeMapListTo()
+  {
+    return new MapListType.MapListTo();
+  }
+
+  /**
+   * Create an instance of {@link SequenceType }
+   * 
+   */
+  public SequenceType createSequenceType()
+  {
+    return new SequenceType();
+  }
+
+  /**
+   * Create an instance of {@link Sequence.DBRef }
+   * 
+   */
+  public Sequence.DBRef createSequenceDBRef()
+  {
+    return new Sequence.DBRef();
+  }
+
+  /**
+   * Create an instance of {@link AlcodonFrame.Alcodon }
+   * 
+   */
+  public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
+  {
+    return new AlcodonFrame.Alcodon();
+  }
+
+  /**
+   * Create an instance of {@link AlcodonFrame.AlcodMap }
+   * 
+   */
+  public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
+  {
+    return new AlcodonFrame.AlcodMap();
+  }
+
+  /**
+   * Create an instance of {@link AnnotationElement }
+   * 
+   */
+  public AnnotationElement createAnnotationElement()
+  {
+    return new AnnotationElement();
+  }
+
+  /**
+   * Create an instance of {@link Annotation.ThresholdLine }
+   * 
+   */
+  public Annotation.ThresholdLine createAnnotationThresholdLine()
+  {
+    return new Annotation.ThresholdLine();
+  }
+
+  /**
+   * Create an instance of {@link MapOnAMatrixType }
+   * 
+   */
+  public MapOnAMatrixType createMapOnAMatrixType()
+  {
+    return new MapOnAMatrixType();
+  }
+
+  /**
+   * Create an instance of {@link jalview.xml.binding.jalview.Property }
+   * 
+   */
+  public jalview.xml.binding.jalview.Property createProperty()
+  {
+    return new jalview.xml.binding.jalview.Property();
+  }
+
+  /**
+   * Create an instance of {@link SequenceSet.SequenceSetProperties }
+   * 
+   */
+  public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
+  {
+    return new SequenceSet.SequenceSetProperties();
+  }
+
+  /**
+   * Create an instance of {@link MatrixType }
+   * 
+   */
+  public MatrixType createMatrixType()
+  {
+    return new MatrixType();
+  }
+
+  /**
+   * Create an instance of {@link VAMSAS }
+   * 
+   */
+  public VAMSAS createVAMSAS()
+  {
+    return new VAMSAS();
+  }
+
+  /**
+   * Create an instance of {@link FeatureMatcher }
+   * 
+   */
+  public FeatureMatcher createFeatureMatcher()
+  {
+    return new FeatureMatcher();
+  }
+
+  /**
+   * Create an instance of {@link WebServiceParameterSet }
+   * 
+   */
+  public WebServiceParameterSet createWebServiceParameterSet()
+  {
+    return new WebServiceParameterSet();
+  }
+
+  /**
+   * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+   * 
+   */
+  public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
+  {
+    return new FeatureMatcherSet.CompoundMatcher();
+  }
+
+  /**
+   * Create an instance of {@link JalviewUserColours.Colour }
+   * 
+   */
+  public JalviewUserColours.Colour createJalviewUserColoursColour()
+  {
+    return new JalviewUserColours.Colour();
+  }
+
+  /**
+   * Create an instance of {@link JalviewUserColours.Filter }
+   * 
+   */
+  public JalviewUserColours.Filter createJalviewUserColoursFilter()
+  {
+    return new JalviewUserColours.Filter();
+  }
+
+  /**
+   * Create an instance of {@link Pdbentry.Property }
+   * 
+   */
+  public Pdbentry.Property createPdbentryProperty()
+  {
+    return new Pdbentry.Property();
+  }
+
+  /**
+   * Create an instance of {@link Feature.OtherData }
+   * 
+   */
+  public Feature.OtherData createFeatureOtherData()
+  {
+    return new Feature.OtherData();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JGroup }
+   * 
+   */
+  public JalviewModel.JGroup createJalviewModelJGroup()
+  {
+    return new JalviewModel.JGroup();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.UserColours }
+   * 
+   */
+  public JalviewModel.UserColours createJalviewModelUserColours()
+  {
+    return new JalviewModel.UserColours();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Tree }
+   * 
+   */
+  public JalviewModel.Tree createJalviewModelTree()
+  {
+    return new JalviewModel.Tree();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+   * 
+   */
+  public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
+  {
+    return new JalviewModel.FeatureSettings.Setting();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+   * 
+   */
+  public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
+  {
+    return new JalviewModel.FeatureSettings.Group();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+   * 
+   */
+  public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
+  {
+    return new JalviewModel.PcaViewer.SequencePoint();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+   * 
+   */
+  public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
+  {
+    return new JalviewModel.PcaViewer.Axis();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+   * 
+   */
+  public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
+  {
+    return new JalviewModel.PcaViewer.SeqPointMin();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+   * 
+   */
+  public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
+  {
+    return new JalviewModel.PcaViewer.SeqPointMax();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+   * 
+   */
+  public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
+  {
+    return new JalviewModel.Viewport.HiddenColumns();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+   * 
+   */
+  public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
+  {
+    return new JalviewModel.Viewport.CalcIdParam();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.Viewport.Overview }
+   * 
+   */
+  public JalviewModel.Viewport.Overview createJalviewModelViewportOverview()
+  {
+    return new JalviewModel.Viewport.Overview();
+  }
+
+  /**
+   * Create an instance of
+   * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+   * 
+   */
+  public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
+  {
+    return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+  }
+
+  /**
+   * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+   * 
+   */
+  public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
+  {
+    return new JalviewModel.JSeq.Pdbids.StructureState();
+  }
+
+  /**
+   * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
+   * }{@code >}
+   * 
+   * @param value
+   *          Java instance representing xml element's value.
+   * @return the new instance of {@link JAXBElement
+   *         }{@code <}{@link JalviewModel }{@code >}
+   */
+  @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+  public JAXBElement createJalviewModel(JalviewModel value)
+  {
+    return new JAXBElement(_JalviewModel_QNAME,
+            JalviewModel.class, null, value);
+  }
+
+  /**
+   * Create an instance of {@link JAXBElement
+   * }{@code <}{@link JalviewUserColours }{@code >}
+   * 
+   * @param value
+   *          Java instance representing xml element's value.
+   * @return the new instance of {@link JAXBElement
+   *         }{@code <}{@link JalviewUserColours }{@code >}
+   */
+  @XmlElementDecl(
+    namespace = "www.jalview.org/colours",
+    name = "JalviewUserColours")
+  public JAXBElement createJalviewUserColours(
+          JalviewUserColours value)
+  {
+    return new JAXBElement(_JalviewUserColours_QNAME,
+            JalviewUserColours.class, null, value);
+  }
+
+  /**
+   * Create an instance of {@link JAXBElement
+   * }{@code <}{@link WebServiceParameterSet }{@code >}
+   * 
+   * @param value
+   *          Java instance representing xml element's value.
+   * @return the new instance of {@link JAXBElement
+   *         }{@code <}{@link WebServiceParameterSet }{@code >}
+   */
+  @XmlElementDecl(
+    namespace = "www.jalview.org/xml/wsparamset",
+    name = "WebServiceParameterSet")
+  public JAXBElement createWebServiceParameterSet(
+          WebServiceParameterSet value)
+  {
+    return new JAXBElement(
+            _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
+            null, value);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
index b807190..dc175e2 100644
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +12,18 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * The results of a PCA calculation
  * 
- * 
    Java class for PcaDataType complex type
    .
+ * 
    
+ * 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">
@@ -38,90 +42,90 @@ 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 f7e4d73..032b932 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,16 @@ 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">
@@ -49,202 +53,212 @@ 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;
+@XmlType(
+  name = "pdbentry",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "property" })
+@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
+public class Pdbentry
+{
 
-    /**
-     * Gets the value of the property property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the property property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getProperty().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link Pdbentry.Property }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the property property.
-     */
-    public List getProperty() {
-        if (property == null) {
-            property = new ArrayList();
-        }
-        return this.property;
-    }
+  protected List property;
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
+  @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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the property property.
+   */
+  public List getProperty()
+  {
+    if (property == null)
+    {
+      property = new ArrayList();
     }
+    return this.property;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String 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 type property.
+     * Gets the value of the name property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getType() {
-        return type;
+    public String getName()
+    {
+      return name;
     }
 
     /**
-     * Sets the value of the type property.
+     * Sets the value of the name property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
-
-    /**
-     * Gets the value of the file property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getFile() {
-        return file;
+    public void setName(String value)
+    {
+      this.name = value;
     }
 
     /**
-     * Sets the value of the file property.
+     * Gets the value of the value property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
      */
-    public void setFile(String value) {
-        this.file = 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="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>
-     * 
    
+     * Sets the value of the value property.
      * 
+     * @param value
+     *          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 d63c051..7807e1e 100644
--- a/src/jalview/xml/binding/jalview/Property.java
+++ b/src/jalview/xml/binding/jalview/Property.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,16 @@ 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 +38,59 @@ 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 3b9e3f5..09a68df 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,11 +16,16 @@ 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>
@@ -55,325 +59,333 @@ 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;
+  @XmlElement(name = "DBRef")
+  protected List dbRef;
+
+  /**
+   * dataset sequence id for this sequence. Will be created as union of
+   * sequences.
+   * 
+   */
+  @XmlAttribute(name = "dsseqid")
+  protected String dsseqid;
+
+  /**
+   * Biotype of the sequence (if known)
+   * 
+   */
+  @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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the dbRef property.
+   */
+  public List getDBRef()
+  {
+    if (dbRef == null)
+    {
+      dbRef = new ArrayList();
+    }
+    return this.dbRef;
+  }
+
+  /**
+   * dataset sequence id for this sequence. Will be created as union of
+   * sequences.
+   * 
+   * @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 }
+   * 
+   * @see #getDsseqid()
+   */
+  public void setDsseqid(String value)
+  {
+    this.dsseqid = value;
+  }
+
+  /**
+   * Biotype of the sequence (if known)
+   * 
+   * @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 }
+   * 
+   * @see #getBiotype()
+   */
+  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;
+
     /**
-     * dataset sequence id for this sequence. Will be
-     * 								created as union of sequences.
+     * true for gene locus mapping, source=species, version=assembly,
+     * accession=chromosome
      * 
      */
-    @XmlAttribute(name = "dsseqid")
-    protected String dsseqid;
+    @XmlAttribute(name = "locus")
+    protected Boolean locus;
+
     /**
-     * Biotype of the sequence (if known)
+     * true for the representative accession for databases where multiple
+     * accessions map to the same entry (eg. Uniprot)
      * 
      */
-    @XmlAttribute(name = "biotype")
-    protected String biotype;
+    @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 }
      * 
-     * @return
-     *     The value of the dbRef property.
      */
-    public List getDBRef() {
-        if (dbRef == null) {
-            dbRef = new ArrayList();
-        }
-        return this.dbRef;
+    public void setSource(String value)
+    {
+      this.source = value;
     }
 
     /**
-     * dataset sequence id for this sequence. Will be
-     * 								created as union of sequences.
+     * 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 }
-     *     
-     * @see #getDsseqid()
+     *          allowed object is {@link String }
+     * 
      */
-    public void setDsseqid(String value) {
-        this.dsseqid = value;
+    public void setVersion(String value)
+    {
+      this.version = value;
     }
 
     /**
-     * Biotype of the sequence (if known)
+     * 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 }
-     *     
-     * @see #getBiotype()
+     *          allowed object is {@link String }
+     * 
      */
-    public void setBiotype(String value) {
-        this.biotype = value;
+    public void setAccessionId(String value)
+    {
+      this.accessionId = value;
     }
 
+    /**
+     * true for gene locus mapping, source=species, version=assembly,
+     * accession=chromosome
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public boolean isLocus()
+    {
+      if (locus == null)
+      {
+        return false;
+      }
+      else
+      {
+        return locus;
+      }
+    }
 
     /**
-     * 
    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>
-     * 
    
+     * @see #isLocus()
+     */
+    public void setLocus(Boolean value)
+    {
+      this.locus = value;
+    }
+
+    /**
+     * true for the representative accession for databases where multiple
+     * accessions map to the same entry (eg. Uniprot)
      * 
+     * @return possible object is {@link Boolean }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "mapping"
-    })
-    public static class DBRef {
-
-        @XmlElement(name = "Mapping")
-        protected Mapping mapping;
-        @XmlAttribute(name = "source")
-        protected String source;
-        @XmlAttribute(name = "version")
-        protected String version;
-        @XmlAttribute(name = "accessionId")
-        protected String accessionId;
-        /**
-         * true for gene locus mapping, source=species,
-         * 											version=assembly, accession=chromosome
-         * 
-         */
-        @XmlAttribute(name = "locus")
-        protected Boolean locus;
-        /**
-         * true for the representative accession for
-         * 											databases where multiple accessions map to the same entry
-         * 											(eg. Uniprot)
-         * 
-         */
-        @XmlAttribute(name = "canonical")
-        protected Boolean canonical;
-
-        /**
-         * Gets the value of the mapping property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link Mapping }
-         *     
-         */
-        public Mapping getMapping() {
-            return mapping;
-        }
-
-        /**
-         * Sets the value of the mapping property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Mapping }
-         *     
-         */
-        public void setMapping(Mapping value) {
-            this.mapping = value;
-        }
-
-        /**
-         * Gets the value of the source property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getSource() {
-            return source;
-        }
-
-        /**
-         * Sets the value of the source property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setSource(String value) {
-            this.source = value;
-        }
-
-        /**
-         * Gets the value of the version property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getVersion() {
-            return version;
-        }
-
-        /**
-         * Sets the value of the version property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setVersion(String value) {
-            this.version = value;
-        }
-
-        /**
-         * Gets the value of the accessionId property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getAccessionId() {
-            return accessionId;
-        }
-
-        /**
-         * Sets the value of the accessionId property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setAccessionId(String value) {
-            this.accessionId = value;
-        }
-
-        /**
-         * true for gene locus mapping, source=species,
-         * 											version=assembly, accession=chromosome
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isLocus() {
-            if (locus == null) {
-                return false;
-            } else {
-                return locus;
-            }
-        }
-
-        /**
-         * Sets the value of the locus property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isLocus()
-         */
-        public void setLocus(Boolean value) {
-            this.locus = value;
-        }
-
-        /**
-         * true for the representative accession for
-         * 											databases where multiple accessions map to the same entry
-         * 											(eg. Uniprot)
-         * 
-         * @return
-         *     possible object is
-         *     {@link Boolean }
-         *     
-         */
-        public boolean isCanonical() {
-            if (canonical == null) {
-                return false;
-            } else {
-                return canonical;
-            }
-        }
-
-        /**
-         * Sets the value of the canonical property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Boolean }
-         *     
-         * @see #isCanonical()
-         */
-        public void setCanonical(Boolean value) {
-            this.canonical = value;
-        }
+    public boolean isCanonical()
+    {
+      if (canonical == null)
+      {
+        return false;
+      }
+      else
+      {
+        return canonical;
+      }
+    }
 
+    /**
+     * Sets the value of the canonical property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     * @see #isCanonical()
+     */
+    public void setCanonical(Boolean value)
+    {
+      this.canonical = value;
     }
 
+  }
+
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index 8629a7e..46c7007 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,11 +16,16 @@ 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>
@@ -53,327 +57,354 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "sequence",
-    "annotation",
-    "sequenceSetProperties",
-    "alcodonFrame",
-    "matrix"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame",
+      "matrix" })
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet {
+public class SequenceSet
+{
 
-    @XmlElement(name = "Sequence")
-    protected List sequence;
-    @XmlElement(name = "Annotation")
-    protected List annotation;
-    protected List sequenceSetProperties;
-    @XmlElement(name = "AlcodonFrame")
-    protected List alcodonFrame;
-    /**
-     * Matrices referred to by this set of sequences.
-     * 
-     */
-    @XmlElement(name = "Matrix")
-    protected List matrix;
-    @XmlAttribute(name = "gapChar", required = true)
-    protected String gapChar;
-    /**
-     * reference to set where jalview will gather the
-     * 						dataset sequences for all sequences in the set.
-     * 
-     */
-    @XmlAttribute(name = "datasetId")
-    protected String datasetId;
+  @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 }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the sequence property.
-     */
-    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;
+
+  /**
+   * Matrices referred to by this set of sequences.
+   * 
+   */
+  @XmlElement(name = "Matrix")
+  protected List matrix;
+
+  @XmlAttribute(name = "gapChar", required = true)
+  protected String gapChar;
+
+  /**
+   * reference to set where jalview will gather the dataset sequences for all
+   * sequences in the set.
+   * 
+   */
+  @XmlAttribute(name = "datasetId")
+  protected String datasetId;
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the sequence property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getSequence().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link Sequence }
+   * 
    
+   * 
+   * 
+   * @return The value of the sequence property.
+   */
+  public List getSequence()
+  {
+    if (sequence == null)
+    {
+      sequence = new ArrayList();
     }
+    return this.sequence;
+  }
 
-    /**
-     * Gets the value of the annotation property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the annotation property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getAnnotation().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link Annotation }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the annotation property.
-     */
-    public List getAnnotation() {
-        if (annotation == null) {
-            annotation = new ArrayList();
-        }
-        return this.annotation;
+  /**
+   * Gets the value of the annotation property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the annotation property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getAnnotation().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link Annotation
+   * }
+   * 
    
+   * 
+   * 
+   * @return The value of the annotation property.
+   */
+  public List getAnnotation()
+  {
+    if (annotation == null)
+    {
+      annotation = new ArrayList();
     }
+    return this.annotation;
+  }
 
-    /**
-     * Gets the value of the sequenceSetProperties property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the sequenceSetProperties property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getSequenceSetProperties().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link SequenceSet.SequenceSetProperties }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the sequenceSetProperties property.
-     */
-    public List getSequenceSetProperties() {
-        if (sequenceSetProperties == null) {
-            sequenceSetProperties = new ArrayList();
-        }
-        return this.sequenceSetProperties;
+  /**
+   * Gets the value of the sequenceSetProperties property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the sequenceSetProperties property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getSequenceSetProperties().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list
+   * {@link SequenceSet.SequenceSetProperties }
+   * 
    
+   * 
+   * 
+   * @return The value of the sequenceSetProperties property.
+   */
+  public List getSequenceSetProperties()
+  {
+    if (sequenceSetProperties == null)
+    {
+      sequenceSetProperties = new ArrayList();
     }
+    return this.sequenceSetProperties;
+  }
 
-    /**
-     * Gets the value of the alcodonFrame property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the alcodonFrame property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getAlcodonFrame().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link AlcodonFrame }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the alcodonFrame property.
-     */
-    public List getAlcodonFrame() {
-        if (alcodonFrame == null) {
-            alcodonFrame = new ArrayList();
-        }
-        return this.alcodonFrame;
+  /**
+   * Gets the value of the alcodonFrame property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the alcodonFrame property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getAlcodonFrame().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list
+   * {@link AlcodonFrame }
+   * 
    
+   * 
+   * 
+   * @return The value of the alcodonFrame property.
+   */
+  public List getAlcodonFrame()
+  {
+    if (alcodonFrame == null)
+    {
+      alcodonFrame = new ArrayList();
     }
+    return this.alcodonFrame;
+  }
 
-    /**
-     * Matrices referred to by this set of sequences.
-     * 
-     * Gets the value of the matrix property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the matrix property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getMatrix().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link MatrixType }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the matrix property.
-     */
-    public List getMatrix() {
-        if (matrix == null) {
-            matrix = new ArrayList();
-        }
-        return this.matrix;
+  /**
+   * Matrices referred to by this set of sequences.
+   * 
+   * Gets the value of the matrix property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the matrix property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getMatrix().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link MatrixType
+   * }
+   * 
    
+   * 
+   * 
+   * @return The value of the matrix property.
+   */
+  public List getMatrix()
+  {
+    if (matrix == null)
+    {
+      matrix = new ArrayList();
     }
+    return this.matrix;
+  }
+
+  /**
+   * 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;
+  }
+
+  /**
+   * reference to set where jalview will gather the dataset sequences for all
+   * sequences in the set.
+   * 
+   * @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 }
+   * 
+   * @see #getDatasetId()
+   */
+  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;
-    }
-
-    /**
-     * reference to set where jalview will gather the
-     * 						dataset sequences for all sequences in the set.
+     *          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 }
-     *     
-     * @see #getDatasetId()
      */
-    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 590ea6d..703d9f0 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,11 +13,16 @@ 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 +42,111 @@ 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 345ede6..fd5a31a 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -5,20 +5,24 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Whether filter has a threshold, and if so is it
- * 				above or below
+ * Whether filter has a threshold, and if so is it above or below
+ * 
+ * 
    
+ * 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">
@@ -32,18 +36,19 @@ 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 bd17cc2..621339a 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,11 +14,16 @@ 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">
@@ -37,79 +41,85 @@ 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 }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the tree property.
-     */
-    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 }
+   * 
    
+   * 
+   * 
+   * @return The value of the tree property.
+   */
+  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 }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the sequenceSet property.
-     */
-    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
+   * }
+   * 
    
+   * 
+   * 
+   * @return The value of the sequenceSet property.
+   */
+  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 78833f6..4489516 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -5,7 +5,6 @@
 // Generated on: 2024.07.25 at 04:43:38 PM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -18,11 +17,16 @@ 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">
@@ -43,201 +47,197 @@ 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 {
-
-    /**
-     * A Jalview Web Service Parameter Set container
-     * 						version number.
-     * 						Version 1 created for storing Jaba user presets.
-     * 
-     */
-    @XmlElement(name = "Version", namespace = "")
-    protected String version;
-    /**
-     * Short description - as utf8 encoded text. This is
-     * 						usually displayed
-     * 						in the body of an HTML capable tooltip, so HTML tags may be embedded
-     * 						using standard UTF8 encoding.
-     * 
-     */
-    @XmlElement(namespace = "")
-    protected String description;
-    /**
-     * URL for which the parameter set is valid. Jalview will use it to
-     * 						match up parameter sets to service instances that can parse the
-     * 						parameter set payload.
-     * 
-     */
-    @XmlElement(namespace = "", required = true)
-    @XmlSchemaType(name = "anyURI")
-    protected List serviceURL;
-    /**
-     * UTF8 encoded string to be processed into a specific web services'
-     * 						parameter set. Note - newlines may be important to the structure
-     * 						of this file.
-     * 
-     */
-    @XmlElement(namespace = "", required = true)
-    protected String parameters;
-    /**
-     * The short name for the parameter set. This will be shown amongst the
-     * 					other presets for the web service.
-     * 
-     */
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
-
-    /**
-     * A Jalview Web Service Parameter Set container
-     * 						version number.
-     * 						Version 1 created for storing Jaba user presets.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getVersion() {
-        return version;
-    }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getVersion()
-     */
-    public void setVersion(String value) {
-        this.version = value;
-    }
-
-    /**
-     * Short description - as utf8 encoded text. This is
-     * 						usually displayed
-     * 						in the body of an HTML capable tooltip, so HTML tags may be embedded
-     * 						using standard UTF8 encoding.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getDescription()
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * URL for which the parameter set is valid. Jalview will use it to
-     * 						match up parameter sets to service instances that can parse the
-     * 						parameter set payload.
-     * 
-     * Gets the value of the serviceURL property.
-     * 
-     * 
    This accessor method returns a reference to the live list,
-     * not a snapshot. Therefore any modification you make to the
-     * returned list will be present inside the JAXB object.
-     * This is why there is not a set method for the serviceURL property.
    
-     * 
-     * 
    
-     * For example, to add a new item, do as follows:
-     * 
    
-     * 
    -     * getServiceURL().add(newItem);
-     * 
    
-     * 
-     * 
-     * 
    
-     * Objects of the following type(s) are allowed in the list
-     * {@link String }
-     * 
    
-     * 
-     * 
-     * @return
-     *     The value of the serviceURL property.
-     */
-    public List getServiceURL() {
-        if (serviceURL == null) {
-            serviceURL = new ArrayList();
-        }
-        return this.serviceURL;
-    }
-
-    /**
-     * UTF8 encoded string to be processed into a specific web services'
-     * 						parameter set. Note - newlines may be important to the structure
-     * 						of this file.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getParameters() {
-        return parameters;
-    }
-
-    /**
-     * Sets the value of the parameters property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getParameters()
-     */
-    public void setParameters(String value) {
-        this.parameters = value;
-    }
-
-    /**
-     * The short name for the parameter set. This will be shown amongst the
-     * 					other presets for the web service.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     * @see #getName()
-     */
-    public void setName(String value) {
-        this.name = value;
+    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
+public class WebServiceParameterSet
+{
+
+  /**
+   * A Jalview Web Service Parameter Set container version number. Version 1
+   * created for storing Jaba user presets.
+   * 
+   */
+  @XmlElement(name = "Version", namespace = "")
+  protected String version;
+
+  /**
+   * Short description - as utf8 encoded text. This is usually displayed in the
+   * body of an HTML capable tooltip, so HTML tags may be embedded using
+   * standard UTF8 encoding.
+   * 
+   */
+  @XmlElement(namespace = "")
+  protected String description;
+
+  /**
+   * URL for which the parameter set is valid. Jalview will use it to match up
+   * parameter sets to service instances that can parse the parameter set
+   * payload.
+   * 
+   */
+  @XmlElement(namespace = "", required = true)
+  @XmlSchemaType(name = "anyURI")
+  protected List serviceURL;
+
+  /**
+   * UTF8 encoded string to be processed into a specific web services' parameter
+   * set. Note - newlines may be important to the structure of this file.
+   * 
+   */
+  @XmlElement(namespace = "", required = true)
+  protected String parameters;
+
+  /**
+   * The short name for the parameter set. This will be shown amongst the other
+   * presets for the web service.
+   * 
+   */
+  @XmlAttribute(name = "name", required = true)
+  protected String name;
+
+  /**
+   * A Jalview Web Service Parameter Set container version number. Version 1
+   * created for storing Jaba user presets.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getVersion()
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Short description - as utf8 encoded text. This is usually displayed in the
+   * body of an HTML capable tooltip, so HTML tags may be embedded using
+   * standard UTF8 encoding.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getDescription()
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * URL for which the parameter set is valid. Jalview will use it to match up
+   * parameter sets to service instances that can parse the parameter set
+   * payload.
+   * 
+   * Gets the value of the serviceURL property.
+   * 
+   * 
    
+   * This accessor method returns a reference to the live list, not a snapshot.
+   * Therefore any modification you make to the returned list will be present
+   * inside the JAXB object. This is why there is not a set method
+   * for the serviceURL property.
+   * 
    
+   * 
+   * 
    
+   * For example, to add a new item, do as follows:
+   * 
    
+   * 
+   * 
    +   * getServiceURL().add(newItem);
+   * 
    
+   * 
+   * 
+   * 
    
+   * Objects of the following type(s) are allowed in the list {@link String }
+   * 
    
+   * 
+   * 
+   * @return The value of the serviceURL property.
+   */
+  public List getServiceURL()
+  {
+    if (serviceURL == null)
+    {
+      serviceURL = new ArrayList();
     }
+    return this.serviceURL;
+  }
+
+  /**
+   * UTF8 encoded string to be processed into a specific web services' parameter
+   * set. Note - newlines may be important to the structure of this file.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getParameters()
+  {
+    return parameters;
+  }
+
+  /**
+   * Sets the value of the parameters property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getParameters()
+   */
+  public void setParameters(String value)
+  {
+    this.parameters = value;
+  }
+
+  /**
+   * The short name for the parameter set. This will be shown amongst the other
+   * presets for the web service.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   * @see #getName()
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index cdebe06..d2cfb8b 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: 2024.07.25 at 04:43:38 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/test/jalview/analysis/AlignSeqTest.java b/test/jalview/analysis/AlignSeqTest.java
index 03bdd0b..1f94601 100644
--- a/test/jalview/analysis/AlignSeqTest.java
+++ b/test/jalview/analysis/AlignSeqTest.java
@@ -76,16 +76,18 @@ public class AlignSeqTest
     String s = "aArRnNzZxX *.-?";
     assertArrayEquals(expected, as.indexEncode(s));
   }
-  @Test(groups= {"Functional"})
+
+  @Test(groups = { "Functional" })
   public void testGlobalAlignment()
   {
-    String seq1="CAGCTAGCG",seq2="CCATACGA";
-    Sequence sq1=new Sequence("s1",seq1),sq2=new Sequence("s2",seq2);
+    String seq1 = "CAGCTAGCG", seq2 = "CCATACGA";
+    Sequence sq1 = new Sequence("s1", seq1), sq2 = new Sequence("s2", seq2);
     // AlignSeq doesn't report the unaligned regions at either end of sequences
-    //String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
+    // String alseq1="-CAGCTAGCG-",alseq2="CCA--TA-CGA";
     // so we check we have the aligned segment correct only
-    String alseq1="CAGCTAGCG",alseq2="CA--TA-CG";
-    AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1,sq2,AlignSeq.DNA);
-    assertEquals(as.getAStr1()+"\n"+as.getAStr2(),alseq1+"\n"+alseq2);
+    String alseq1 = "CAGCTAGCG", alseq2 = "CA--TA-CG";
+    AlignSeq as = AlignSeq.doGlobalNWAlignment(sq1, sq2, AlignSeq.DNA);
+    assertEquals(as.getAStr1() + "\n" + as.getAStr2(),
+            alseq1 + "\n" + alseq2);
   }
 }
diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java
index 1cf9a80..fc2a577 100644
--- a/test/jalview/analysis/AlignmentUtilsTests.java
+++ b/test/jalview/analysis/AlignmentUtilsTests.java
@@ -83,25 +83,29 @@ public class AlignmentUtilsTests
   {
     JvOptionPane.setInteractiveMode(false);
     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
-    
-    AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure",
-            new Annotation[] {});
-    AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred",
+
+    AlignmentAnnotation ann1 = new AlignmentAnnotation(
+            "Secondary Structure", "Secondary Structure",
             new Annotation[] {});
+    AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+            "jnetpred", new Annotation[] {});
     AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
             new Annotation[] {});
     AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
             new Annotation[] {});
-    
-    AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] {ann1, ann3, ann4};
 
-    AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] {ann2, ann3, ann4};
-    
-    AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] {ann3, ann4};
-    
+    AlignmentAnnotation[] anns1 = new AlignmentAnnotation[] { ann1, ann3,
+        ann4 };
+
+    AlignmentAnnotation[] anns2 = new AlignmentAnnotation[] { ann2, ann3,
+        ann4 };
+
+    AlignmentAnnotation[] anns3 = new AlignmentAnnotation[] { ann3, ann4 };
+
     AlignmentAnnotation[] anns4 = new AlignmentAnnotation[0];
-    
-    AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] {ann1, ann2, ann3, ann4};
+
+    AlignmentAnnotation[] anns5 = new AlignmentAnnotation[] { ann1, ann2,
+        ann3, ann4 };
   }
 
   @Test(groups = { "Functional" })
@@ -2775,139 +2779,179 @@ public class AlignmentUtilsTests
                     && al.getAlignmentAnnotation().length == 2);
 
   }
-    
-    @Test(groups = "Functional", dataProvider = "SecondaryStructureAnnotations")
-    public void testSecondaryStructurePresentAndSources(AlignmentAnnotation[] annotations, boolean expectedSSPresent, ArrayList expectedSSSources) {
-        Assert.assertEquals(expectedSSPresent, AlignmentUtils.isSecondaryStructurePresent(annotations));
-    }
 
-    @DataProvider(name = "SecondaryStructureAnnotations")
-    public static Object[][] provideSecondaryStructureAnnotations() {
-        AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{});
-        AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{});
-        AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
-        AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp", new Annotation[]{});
-
-        List ssSources1 = new ArrayList<>(Arrays.asList("3D Structures"));
-        List ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
-        List ssSources3 = new ArrayList<>(Arrays.asList("3D Structures", "JPred"));
-        List ssSources4 = new ArrayList<>();
-
-        return new Object[][]{
-            {new AlignmentAnnotation[]{ann1, ann3, ann4}, true, ssSources1},
-            {new AlignmentAnnotation[]{ann2, ann3, ann4}, true, ssSources2},
-            {new AlignmentAnnotation[]{ann3, ann4}, false, ssSources4},
-            {new AlignmentAnnotation[]{}, false, ssSources4},
-            {new AlignmentAnnotation[]{ann1, ann2, ann3, ann4}, true, ssSources3}
-        };
-    }
-    
-    @Test(dataProvider = "SecondaryStructureAnnotationColours")
-    public void testSecondaryStructureAnnotationColour(char symbol, Color expectedColor) {
-        Color actualColor = AlignmentUtils.getSecondaryStructureAnnotationColour(symbol);
-        Assert.assertEquals(actualColor, expectedColor);
-    }
+  @Test(
+    groups = "Functional",
+    dataProvider = "SecondaryStructureAnnotations")
+  public void testSecondaryStructurePresentAndSources(
+          AlignmentAnnotation[] annotations, boolean expectedSSPresent,
+          ArrayList expectedSSSources)
+  {
+    Assert.assertEquals(expectedSSPresent,
+            AlignmentUtils.isSecondaryStructurePresent(annotations));
+  }
 
-    @DataProvider(name = "SecondaryStructureAnnotationColours")
-    public static Object[][] provideSecondaryStructureAnnotationColours() {
-        return new Object[][]{
-            {'C', Color.gray},
-            {'E', Color.green},
-            {'H', Color.red},
-            {'-', Color.gray}
-        };
-    }
-    
-    @Test(dataProvider = "SSAnnotationPresence")
-    public void testIsSSAnnotationPresent(Map> annotations, boolean expectedPresence) {
-        boolean actualPresence = AlignmentUtils.isSSAnnotationPresent(annotations);
-        Assert.assertEquals(actualPresence, expectedPresence);
-    }
+  @DataProvider(name = "SecondaryStructureAnnotations")
+  public static Object[][] provideSecondaryStructureAnnotations()
+  {
+    AlignmentAnnotation ann1 = new AlignmentAnnotation(
+            "Secondary Structure", "Secondary Structure",
+            new Annotation[] {});
+    AlignmentAnnotation ann2 = new AlignmentAnnotation("jnetpred",
+            "jnetpred", new Annotation[] {});
+    AlignmentAnnotation ann3 = new AlignmentAnnotation("Temp", "Temp",
+            new Annotation[] {});
+    AlignmentAnnotation ann4 = new AlignmentAnnotation("Temp", "Temp",
+            new Annotation[] {});
 
-    @DataProvider(name = "SSAnnotationPresence")
-    public static Object[][] provideSSAnnotationPresence() {
-        Map> annotations1 = new HashMap<>();
-        SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
-        List annotationsList1 = new ArrayList<>();
-        annotationsList1.add(new AlignmentAnnotation("Secondary Structure", "Secondary Structure", new Annotation[]{}));
-        annotations1.put(seq1, annotationsList1); // Annotation present secondary structure for seq1
-
-        Map> annotations2 = new HashMap<>();
-        SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
-        List annotationsList2 = new ArrayList<>();
-        annotationsList2.add(new AlignmentAnnotation("Other Annotation", "Other Annotation", new Annotation[]{}));
-        annotations2.put(seq2, annotationsList2); // Annotation not related to any of secondary structure for seq2
-
-        Map> annotations3 = new HashMap<>();
-        // Empty annotation map
-        
-        Map> annotations4 = new HashMap<>();
-        SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
-        List annotationsList4 = new ArrayList<>();
-        annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred", new Annotation[]{}));
-        annotations4.put(seq4, annotationsList4); // Annotation present from JPred for seq4
-
-
-        return new Object[][]{
-            {annotations1, true}, // Annotations present secondary structure present
-            {annotations2, false}, // No annotations related to any of the secondary structure present
-            {annotations3, false},  // Empty annotation map
-            {annotations4, true}, // Annotations present from JPred secondary structure present
-        };
-    }
-    
-    @Test
-    public void testGetSSSourceFromAnnotationDescription(AlignmentAnnotation[] annotations, String expectedSSSource) {
-        List actualSSSource = AlignmentUtils.extractSSSourceInAlignmentAnnotation(annotations);
-        Assert.assertEquals(actualSSSource, expectedSSSource);
-    }
-    
-    @DataProvider(name = "SSSourceFromAnnotationDescription")
-    public static Object[][] provideSSSourceFromAnnotationDescription() {
-        Map> annotations1 = new HashMap<>();
-        SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
-        List annotationsList1 = new ArrayList<>();
-        annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output", new Annotation[]{}));
-        annotations1.put(seq1, annotationsList1); // Annotation present from JPred for seq1
-
-        Map> annotations2 = new HashMap<>();
-        SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
-        List annotationsList2 = new ArrayList<>();
-        annotationsList2.add(new AlignmentAnnotation("Secondary Structure", 
-                "Secondary Structure for af-q43517-f1A", new Annotation[]{}));
-        annotations2.put(seq2, annotationsList2); // Annotation present secondary structure from Alphafold for seq2
-
-        Map> annotations3 = new HashMap<>();
-        // Empty annotation map
-        
-        Map> annotations4 = new HashMap<>();
-        SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
-        List annotationsList4 = new ArrayList<>();
-        annotationsList4.add(new AlignmentAnnotation("Secondary Structure", 
-                "Secondary Structure for 4zhpA", new Annotation[]{}));
-        annotations4.put(seq4, annotationsList4); // Annotation present secondary structure from pdb for seq4
-        
-        Map> annotations5 = new HashMap<>();
-        SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
-        List annotationsList5 = new ArrayList<>();
-        annotationsList5.add(new AlignmentAnnotation("Secondary Structure", 
-                "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P", 
-                new Annotation[]{}));
-        annotations5.put(seq5, annotationsList5); // Annotation present secondary structure from Swiss model for seq5
-        
-
-        //JPred Output - JPred
-        //Secondary Structure for af-q43517-f1A - Alphafold
-        //Secondary Structure for 4zhpA - Experimental
-        //Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P - Swiss Model
-        
-        return new Object[][]{
-            {annotations1, "JPred"}, 
-            {annotations2, "Alphafold"}, 
-            {annotations3, null},  
-            {annotations4, "PDB"},
-            {annotations5, "Swiss Model"}
-        };
-    }   
+    List ssSources1 = new ArrayList<>(
+            Arrays.asList("3D Structures"));
+    List ssSources2 = new ArrayList<>(Arrays.asList("JPred"));
+    List ssSources3 = new ArrayList<>(
+            Arrays.asList("3D Structures", "JPred"));
+    List ssSources4 = new ArrayList<>();
+
+    return new Object[][] {
+        { new AlignmentAnnotation[]
+        { ann1, ann3, ann4 }, true, ssSources1 },
+        { new AlignmentAnnotation[]
+        { ann2, ann3, ann4 }, true, ssSources2 },
+        { new AlignmentAnnotation[]
+        { ann3, ann4 }, false, ssSources4 },
+        { new AlignmentAnnotation[] {}, false, ssSources4 },
+        { new AlignmentAnnotation[]
+        { ann1, ann2, ann3, ann4 }, true, ssSources3 } };
+  }
+
+  @Test(dataProvider = "SecondaryStructureAnnotationColours")
+  public void testSecondaryStructureAnnotationColour(char symbol,
+          Color expectedColor)
+  {
+    Color actualColor = AlignmentUtils
+            .getSecondaryStructureAnnotationColour(symbol);
+    Assert.assertEquals(actualColor, expectedColor);
+  }
+
+  @DataProvider(name = "SecondaryStructureAnnotationColours")
+  public static Object[][] provideSecondaryStructureAnnotationColours()
+  {
+    return new Object[][] { { 'C', Color.gray }, { 'E', Color.green },
+        { 'H', Color.red },
+        { '-', Color.gray } };
+  }
+
+  @Test(dataProvider = "SSAnnotationPresence")
+  public void testIsSSAnnotationPresent(
+          Map> annotations,
+          boolean expectedPresence)
+  {
+    boolean actualPresence = AlignmentUtils
+            .isSSAnnotationPresent(annotations);
+    Assert.assertEquals(actualPresence, expectedPresence);
+  }
+
+  @DataProvider(name = "SSAnnotationPresence")
+  public static Object[][] provideSSAnnotationPresence()
+  {
+    Map> annotations1 = new HashMap<>();
+    SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+    List annotationsList1 = new ArrayList<>();
+    annotationsList1.add(new AlignmentAnnotation("Secondary Structure",
+            "Secondary Structure", new Annotation[] {}));
+    annotations1.put(seq1, annotationsList1); // Annotation present secondary
+                                              // structure for seq1
+
+    Map> annotations2 = new HashMap<>();
+    SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+    List annotationsList2 = new ArrayList<>();
+    annotationsList2.add(new AlignmentAnnotation("Other Annotation",
+            "Other Annotation", new Annotation[] {}));
+    annotations2.put(seq2, annotationsList2); // Annotation not related to any
+                                              // of secondary structure for seq2
+
+    Map> annotations3 = new HashMap<>();
+    // Empty annotation map
+
+    Map> annotations4 = new HashMap<>();
+    SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+    List annotationsList4 = new ArrayList<>();
+    annotationsList4.add(new AlignmentAnnotation("jnetpred", "jnetpred",
+            new Annotation[] {}));
+    annotations4.put(seq4, annotationsList4); // Annotation present from JPred
+                                              // for seq4
+
+    return new Object[][] { { annotations1, true }, // Annotations present
+                                                    // secondary structure
+                                                    // present
+        { annotations2, false }, // No annotations related to any of the
+                                 // secondary structure present
+        { annotations3, false }, // Empty annotation map
+        { annotations4, true }, // Annotations present from JPred secondary
+                                // structure present
+    };
+  }
+
+  @Test
+  public void testGetSSSourceFromAnnotationDescription(
+          AlignmentAnnotation[] annotations, String expectedSSSource)
+  {
+    List actualSSSource = AlignmentUtils
+            .extractSSSourceInAlignmentAnnotation(annotations);
+    Assert.assertEquals(actualSSSource, expectedSSSource);
+  }
+
+  @DataProvider(name = "SSSourceFromAnnotationDescription")
+  public static Object[][] provideSSSourceFromAnnotationDescription()
+  {
+    Map> annotations1 = new HashMap<>();
+    SequenceI seq1 = new Sequence("Seq1", "ASD---ASD---ASD", 37, 45);
+    List annotationsList1 = new ArrayList<>();
+    annotationsList1.add(new AlignmentAnnotation("jnetpred", "JPred Output",
+            new Annotation[] {}));
+    annotations1.put(seq1, annotationsList1); // Annotation present from JPred
+                                              // for seq1
+
+    Map> annotations2 = new HashMap<>();
+    SequenceI seq2 = new Sequence("Seq2", "ASD---ASD------", 37, 42);
+    List annotationsList2 = new ArrayList<>();
+    annotationsList2.add(new AlignmentAnnotation("Secondary Structure",
+            "Secondary Structure for af-q43517-f1A", new Annotation[] {}));
+    annotations2.put(seq2, annotationsList2); // Annotation present secondary
+                                              // structure from Alphafold for
+                                              // seq2
+
+    Map> annotations3 = new HashMap<>();
+    // Empty annotation map
+
+    Map> annotations4 = new HashMap<>();
+    SequenceI seq4 = new Sequence("Seq4", "ASD---ASD---AS-", 37, 44);
+    List annotationsList4 = new ArrayList<>();
+    annotationsList4.add(new AlignmentAnnotation("Secondary Structure",
+            "Secondary Structure for 4zhpA", new Annotation[] {}));
+    annotations4.put(seq4, annotationsList4); // Annotation present secondary
+                                              // structure from pdb for seq4
+
+    Map> annotations5 = new HashMap<>();
+    SequenceI seq5 = new Sequence("Seq5", "ASD---ASD---AS-", 37, 44);
+    List annotationsList5 = new ArrayList<>();
+    annotationsList5.add(new AlignmentAnnotation("Secondary Structure",
+            "Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P",
+            new Annotation[] {}));
+    annotations5.put(seq5, annotationsList5); // Annotation present secondary
+                                              // structure from Swiss model for
+                                              // seq5
+
+    // JPred Output - JPred
+    // Secondary Structure for af-q43517-f1A - Alphafold
+    // Secondary Structure for 4zhpA - Experimental
+    // Secondary Structure for p09911_54-147__3a7wzn.1.p3502557454997462030P -
+    // Swiss Model
+
+    return new Object[][] { { annotations1, "JPred" },
+        { annotations2, "Alphafold" },
+        { annotations3, null },
+        { annotations4, "PDB" },
+        { annotations5, "Swiss Model" } };
+  }
 
 }
diff --git a/test/jalview/analysis/scoremodels/ScoreModelsTest.java b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
index d0a8047..f82a18a 100644
--- a/test/jalview/analysis/scoremodels/ScoreModelsTest.java
+++ b/test/jalview/analysis/scoremodels/ScoreModelsTest.java
@@ -83,7 +83,7 @@ public class ScoreModelsTest
     assertFalse(sm instanceof PairwiseScoreModelI);
     assertTrue(sm instanceof DistanceScoreModel);
     assertEquals(sm.getName(), "Sequence Feature Similarity");
-    
+
     sm = models.next();
     assertFalse(sm instanceof SimilarityScoreModel);
     assertFalse(sm instanceof PairwiseScoreModelI);
diff --git a/test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java b/test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java
index f32be37..03dcdc7 100644
--- a/test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java
+++ b/test/jalview/analysis/scoremodels/SecondaryStructureDistanceModelTest.java
@@ -48,7 +48,7 @@ import org.testng.annotations.Test;
 // This class tests methods in Class SecondaryStructureDistanceModel 
 public class SecondaryStructureDistanceModelTest
 {
-  
+
   /**
    * Verify computed distances of sequences with gap
    */
@@ -62,7 +62,7 @@ public class SecondaryStructureDistanceModelTest
     ScoreModelI sm = new SecondaryStructureDistanceModel();
     sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
             af.alignPanel);
-    
+
     /*
      * feature distance model always normalises by region width
      * gap-gap is always included (but scores zero)
@@ -73,27 +73,28 @@ public class SecondaryStructureDistanceModelTest
      * include gaps
      * score = 0 + 0 + 1 + 0 = 1/4
      */
-    SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+    SimilarityParamsI params = new SimilarityParams(false, true, true,
+            true);
     params.setSecondaryStructureSource("3D Structures");
     MatrixI distances = sm.findDistances(view, params);
     assertEquals(distances.getValue(0, 0), 1d);
     assertEquals(distances.getValue(1, 1), 1d);
-    assertEquals(distances.getValue(0, 1), 0d); 
+    assertEquals(distances.getValue(0, 1), 0d);
     assertEquals(distances.getValue(1, 0), 0d);
-    
+
     /*
      * exclude gaps
      * score = 0 + 0 + 0 + 0 = 0/4
      */
-    
-    SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+    SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+            true);
     params2.setSecondaryStructureSource("3D Structures");
     MatrixI distances2 = sm.findDistances(view, params2);
-    assertEquals(distances2.getValue(0, 1), 0d); 
+    assertEquals(distances2.getValue(0, 1), 0d);
     assertEquals(distances2.getValue(1, 0), 0d);
   }
-  
-  
+
   /**
    * Verify computed distances of sequences with gap
    */
@@ -107,7 +108,7 @@ public class SecondaryStructureDistanceModelTest
     ScoreModelI sm = new SecondaryStructureDistanceModel();
     sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
             af.alignPanel);
-    
+
     /*
      * feature distance model always normalises by region width
      * gap-gap is always included (but scores zero)
@@ -118,27 +119,28 @@ public class SecondaryStructureDistanceModelTest
      * include gaps
      * score = 0 + 0 + 2 + 2 = 2/4
      */
-    SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+    SimilarityParamsI params = new SimilarityParams(false, true, true,
+            true);
     params.setSecondaryStructureSource("3D Structures");
     MatrixI distances = sm.findDistances(view, params);
     assertEquals(distances.getValue(0, 0), 1d);
     assertEquals(distances.getValue(1, 1), 1d);
-    assertEquals(distances.getValue(0, 1), 0d); 
+    assertEquals(distances.getValue(0, 1), 0d);
     assertEquals(distances.getValue(1, 0), 0d);
-    
+
     /*
      * exclude gaps
      * score = 0 + 0 + 2 + 2 = 2/4
      */
-    
-    SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+    SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+            true);
     params2.setSecondaryStructureSource("3D Structures");
     MatrixI distances2 = sm.findDistances(view, params2);
-    assertEquals(distances2.getValue(0, 1), 0d); 
+    assertEquals(distances2.getValue(0, 1), 0d);
     assertEquals(distances2.getValue(1, 0), 0d);
   }
 
-  
   /**
    * Verify computed distances of sequences with gap
    */
@@ -152,7 +154,7 @@ public class SecondaryStructureDistanceModelTest
     ScoreModelI sm = new SecondaryStructureDistanceModel();
     sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
             af.alignPanel);
-    
+
     /*
      * feature distance model always normalises by region width
      * gap-gap is always included (but scores zero)
@@ -163,28 +165,28 @@ public class SecondaryStructureDistanceModelTest
      * include gaps
      * score = 0 + 0 + 2 + 2 = 2/4
      */
-    SimilarityParamsI params = new SimilarityParams(false, true, true, true);
+    SimilarityParamsI params = new SimilarityParams(false, true, true,
+            true);
     params.setSecondaryStructureSource("3D Structures");
     MatrixI distances = sm.findDistances(view, params);
     assertEquals(distances.getValue(0, 0), 1d);
     assertEquals(distances.getValue(1, 1), 1d);
-    assertEquals(distances.getValue(0, 1), 0d); 
+    assertEquals(distances.getValue(0, 1), 0d);
     assertEquals(distances.getValue(1, 0), 0d);
-    
+
     /*
      * exclude gaps
      * score = 0 + 0 + 2 + 2 = 2/4
      */
-    
-    SimilarityParamsI params2 = new SimilarityParams(false, true, false, true);
+
+    SimilarityParamsI params2 = new SimilarityParams(false, true, false,
+            true);
     params2.setSecondaryStructureSource("3D Structures");
     MatrixI distances2 = sm.findDistances(view, params2);
-    assertEquals(distances2.getValue(0, 1), 0d); 
+    assertEquals(distances2.getValue(0, 1), 0d);
     assertEquals(distances2.getValue(1, 0), 0d);
   }
 
-
-  
   /**
    * 
        * Set up
@@ -214,18 +216,17 @@ public class SecondaryStructureDistanceModelTest
             new SequenceFeature("metal", null, 1, 4, 0f, null));
     s2.addSequenceFeature(
             new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-    
-    
+
     /*
      * Set up secondary structure annotations
      */
-    Annotation ssE = new Annotation("","",'E',0);
-    Annotation ssH = new Annotation("","",'H',0);
-    Annotation ssC = new Annotation(".","",' ',0);
-    
+    Annotation ssE = new Annotation("", "", 'E', 0);
+    Annotation ssH = new Annotation("", "", 'H', 0);
+    Annotation ssC = new Annotation(".", "", ' ', 0);
+
     Annotation[] anns1;
     Annotation[] anns2;
-    
+
     /* All secondary structure annotations are similar for each column
      * Set up
     *   column      1 2 3 4 
@@ -235,13 +236,14 @@ public class SecondaryStructureDistanceModelTest
     *        seq s2 F S J L
     *        	 ss E H S E
     */
-    if(similar == "All Similar") {
-    
-    	anns1 = new Annotation[] { ssE, ssH, ssC, ssE};
-    	anns2 = new Annotation[] { ssE, ssH, ssC, ssE};
-    
+    if (similar == "All Similar")
+    {
+
+      anns1 = new Annotation[] { ssE, ssH, ssC, ssE };
+      anns2 = new Annotation[] { ssE, ssH, ssC, ssE };
+
     }
-    
+
     /* All secondary structure annotations are dissimilar for each column
      * Set up
      *   column      1 2 3 4 
@@ -251,13 +253,14 @@ public class SecondaryStructureDistanceModelTest
      *        seq s2 F S J L
      *        	  ss H E E C
      */
-    else if(similar == "Not Similar") {
-        
-    	anns1 = new Annotation[] { ssE, ssE, ssC, ssE};
-    	anns2 = new Annotation[] { ssH, ssH, ssE, ssC};
-    
+    else if (similar == "Not Similar")
+    {
+
+      anns1 = new Annotation[] { ssE, ssE, ssC, ssE };
+      anns2 = new Annotation[] { ssH, ssH, ssE, ssC };
+
     }
-    
+
     /* All secondary structure annotations are dissimilar for each column
      * Set up
      *   column      1 2 3 4 
@@ -267,13 +270,14 @@ public class SecondaryStructureDistanceModelTest
      *        seq s2 F S J L
      *            ss H E E C
      */
-    else if(similar == "With Coil") {
-        
-      anns1 = new Annotation[] { ssE, ssE, null, ssE};
-      anns2 = new Annotation[] { ssH, ssH, ssE, null};
-    
+    else if (similar == "With Coil")
+    {
+
+      anns1 = new Annotation[] { ssE, ssE, null, ssE };
+      anns2 = new Annotation[] { ssH, ssH, ssE, null };
+
     }
-    
+
     /*  Set up
      *   column      1 2 3 4 
      *        seq s1 F R K S
@@ -282,28 +286,27 @@ public class SecondaryStructureDistanceModelTest
      *        seq s2 F S J L
      *        	  ss H E E C
      */
-    else {
-    	
-    	anns1 = new Annotation[] { ssH, ssE, ssC, ssE};
-    	anns2 = new Annotation[] { ssH, ssE, ssE, ssC};
+    else
+    {
+
+      anns1 = new Annotation[] { ssH, ssE, ssC, ssE };
+      anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
     }
-    
-    
-    AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure", anns1);
-    AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure", anns2);
-    
+
+    AlignmentAnnotation ann1 = new AlignmentAnnotation(
+            "Secondary Structure", "Secondary Structure", anns1);
+    AlignmentAnnotation ann2 = new AlignmentAnnotation(
+            "Secondary Structure", "Secondary Structure", anns2);
+
     s1.addAlignmentAnnotation(ann1);
-    s2.addAlignmentAnnotation(ann2);    
-    
+    s2.addAlignmentAnnotation(ann2);
+
     AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
     AlignFrame af = new AlignFrame(al, 300, 300);
     af.setShowSeqFeatures(true);
     af.getFeatureRenderer().findAllFeatures(true);
     return af;
   }
-  
 
   /**
    * 
    @@ -320,7 +323,7 @@ public class SecondaryStructureDistanceModelTest
    */
   protected AlignFrame setupAlignmentViewWithGap()
   {
-    
+
     SequenceI s1 = new Sequence("s1", "FR S");
     SequenceI s2 = new Sequence("s2", "FSJL");
 
@@ -334,39 +337,39 @@ public class SecondaryStructureDistanceModelTest
             new SequenceFeature("metal", null, 1, 4, 0f, null));
     s2.addSequenceFeature(
             new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-    
-    
-    Annotation ssE = new Annotation("","",'E',0);
-    Annotation ssH = new Annotation("","",'H',0);
-    Annotation ssC = new Annotation(".","",' ',0);
-    
+
+    Annotation ssE = new Annotation("", "", 'E', 0);
+    Annotation ssH = new Annotation("", "", 'H', 0);
+    Annotation ssC = new Annotation(".", "", ' ', 0);
+
     Annotation[] anns1;
     Annotation[] anns2;
-    	
-    anns1 = new Annotation[] { ssH, ssE, ssC};
-    anns2 = new Annotation[] { ssH, ssE, ssE, ssC};    
-    
-    AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure", anns1);
-    AlignmentAnnotation ann2 = new AlignmentAnnotation("Secondary Structure",
-            "Secondary Structure", anns2);
-    
+
+    anns1 = new Annotation[] { ssH, ssE, ssC };
+    anns2 = new Annotation[] { ssH, ssE, ssE, ssC };
+
+    AlignmentAnnotation ann1 = new AlignmentAnnotation(
+            "Secondary Structure", "Secondary Structure", anns1);
+    AlignmentAnnotation ann2 = new AlignmentAnnotation(
+            "Secondary Structure", "Secondary Structure", anns2);
+
     s1.addAlignmentAnnotation(ann1);
-    s2.addAlignmentAnnotation(ann2);    
-        
+    s2.addAlignmentAnnotation(ann2);
+
     AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
     AlignFrame af = new AlignFrame(al, 300, 300);
     af.setShowSeqFeatures(true);
     af.getFeatureRenderer().findAllFeatures(true);
-    
+
     return af;
   }
-  
-  protected AlignFrame setupAlignmentViewWithoutSS(String type) {
-    
+
+  protected AlignFrame setupAlignmentViewWithoutSS(String type)
+  {
+
     SequenceI s1 = new Sequence("s1", "FR S");
     SequenceI s2 = new Sequence("s2", "FSJL");
-    
+
     s1.addSequenceFeature(
             new SequenceFeature("chain", null, 1, 3, 0f, null));
     s1.addSequenceFeature(
@@ -377,60 +380,61 @@ public class SecondaryStructureDistanceModelTest
             new SequenceFeature("metal", null, 1, 4, 0f, null));
     s2.addSequenceFeature(
             new SequenceFeature("Pfam", null, 1, 4, 0f, null));
-    
-    if(!type.equals("both")) {    
-      Annotation ssE = new Annotation("","",'E',0);
-      Annotation ssH = new Annotation("","",'H',0);
-      Annotation ssC = new Annotation(".","",' ',0);
-      
+
+    if (!type.equals("both"))
+    {
+      Annotation ssE = new Annotation("", "", 'E', 0);
+      Annotation ssH = new Annotation("", "", 'H', 0);
+      Annotation ssC = new Annotation(".", "", ' ', 0);
+
       Annotation[] anns1;
-        
-      anns1 = new Annotation[] { ssH, ssE, ssC};
-          
-      AlignmentAnnotation ann1 = new AlignmentAnnotation("Secondary Structure",
-              "Secondary Structure", anns1);    
-  
-      s1.addAlignmentAnnotation(ann1);    
+
+      anns1 = new Annotation[] { ssH, ssE, ssC };
+
+      AlignmentAnnotation ann1 = new AlignmentAnnotation(
+              "Secondary Structure", "Secondary Structure", anns1);
+
+      s1.addAlignmentAnnotation(ann1);
     }
-    
+
     AlignmentI al = new Alignment(new SequenceI[] { s1, s2 });
     AlignFrame af = new AlignFrame(al, 300, 300);
     af.setShowSeqFeatures(true);
     af.getFeatureRenderer().findAllFeatures(true);
     return af;
   }
-  
-  
+
   @DataProvider(name = "testData")
-  public Object[][] testData() {
-      return new Object[][] {
-              {"All Similar", 1d, 1d, 0d, 0d / 4},
-              {"Partially Similar", 1d, 1d, 0d, 0d},
-              {"Not Similar", 1d, 1d, 0d, 0d},
-              {"With Coil", 1d, 1d, 0d, 0d},
-      };
+  public Object[][] testData()
+  {
+    return new Object[][] { { "All Similar", 1d, 1d, 0d, 0d / 4 },
+        { "Partially Similar", 1d, 1d, 0d, 0d },
+        { "Not Similar", 1d, 1d, 0d, 0d },
+        { "With Coil", 1d, 1d, 0d, 0d }, };
   }
 
   @Test(dataProvider = "testData")
-  public void testFindDistances(String scenario, double expectedValue00, double expectedValue11,
-                                 double expectedValue01, double expectedValue10) {
-      AlignFrame af = setupAlignmentView(scenario);
-      AlignViewport viewport = af.getViewport();
-      AlignmentView view = viewport.getAlignmentView(false);
-
-      ScoreModelI sm = new SecondaryStructureDistanceModel();
-      sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
-              af.alignPanel);
-
-      SimilarityParamsI params = new SimilarityParams(false, true, true, true);
-      params.setSecondaryStructureSource("3D Structures");
-      MatrixI distances = sm.findDistances(view, params);
-
-      assertEquals(distances.getValue(0, 0), expectedValue00);
-      assertEquals(distances.getValue(1, 1), expectedValue11);
-      assertEquals(distances.getValue(0, 1), expectedValue01);
-      assertEquals(distances.getValue(1, 0), expectedValue10);
+  public void testFindDistances(String scenario, double expectedValue00,
+          double expectedValue11, double expectedValue01,
+          double expectedValue10)
+  {
+    AlignFrame af = setupAlignmentView(scenario);
+    AlignViewport viewport = af.getViewport();
+    AlignmentView view = viewport.getAlignmentView(false);
+
+    ScoreModelI sm = new SecondaryStructureDistanceModel();
+    sm = ScoreModels.getInstance().getScoreModel(sm.getName(),
+            af.alignPanel);
+
+    SimilarityParamsI params = new SimilarityParams(false, true, true,
+            true);
+    params.setSecondaryStructureSource("3D Structures");
+    MatrixI distances = sm.findDistances(view, params);
+
+    assertEquals(distances.getValue(0, 0), expectedValue00);
+    assertEquals(distances.getValue(1, 1), expectedValue11);
+    assertEquals(distances.getValue(0, 1), expectedValue01);
+    assertEquals(distances.getValue(1, 0), expectedValue10);
   }
 
-  
 }
diff --git a/test/jalview/commands/EditCommandTest.java b/test/jalview/commands/EditCommandTest.java
index 1255c58..2e36111 100644
--- a/test/jalview/commands/EditCommandTest.java
+++ b/test/jalview/commands/EditCommandTest.java
@@ -1182,12 +1182,14 @@ public class EditCommandTest
     assertEquals(10, sf.getBegin());
     assertEquals(11, sf.getEnd());
   }
+
   private SequenceI mkDs(SequenceI as)
   {
     SequenceI ds = as.createDatasetSequence();
     ds.setSequence(ds.getSequenceAsString().toUpperCase(Locale.ROOT));
     return ds;
   }
+
   /**
    * Test that mimics 'remove all gapped columns' action. This generates a
    * series Delete Gap edits that each act on all sequences that share a gapped
@@ -1210,35 +1212,38 @@ public class EditCommandTest
      * and check we are preserving data - if the calls below fail, something has broken the Jalview dataset derivation process
      */
     assertEquals("ABCDEF", seq1.getDatasetSequence().getSequenceAsString());
-    assertEquals(original1,seq1.getSequenceAsString());
-    SequenceI seq2 = new Sequence("sq2",original2);
+    assertEquals(original1, seq1.getSequenceAsString());
+    SequenceI seq2 = new Sequence("sq2", original2);
     SequenceI ds2 = mkDs(seq2);
     SequenceI seq3 = new Sequence("sq3", original3);
     SequenceI ds3 = mkDs(seq3);
-    List sqs = Arrays.asList( seq1, seq2, seq3 );
+    List sqs = Arrays.asList(seq1, seq2, seq3);
     Alignment al = new Alignment(sqs.toArray(new SequenceI[0]));
-    EditCommand lefj = new JustifyLeftOrRightCommand("Left J", true, sqs, 1, 7, al);
+    EditCommand lefj = new JustifyLeftOrRightCommand("Left J", true, sqs, 1,
+            7, al);
     String exp = "-ABcD---EF";
     // check without case conservation
-    assertEquals(exp.toUpperCase(Locale.ROOT),seq1.getSequenceAsString().toUpperCase(Locale.ROOT));
+    assertEquals(exp.toUpperCase(Locale.ROOT),
+            seq1.getSequenceAsString().toUpperCase(Locale.ROOT));
     // check case
-    assertEquals(exp,seq1.getSequenceAsString());
+    assertEquals(exp, seq1.getSequenceAsString());
     // and other seqs
-    assertEquals("-GHiJ---",seq2.getSequenceAsString());
-    assertEquals("-MNoP---Q",seq3.getSequenceAsString());
-    lefj.undoCommand(new AlignmentI[] { al});
-    assertEquals(original3,seq3.getSequenceAsString());
-    assertEquals(original1,seq1.getSequenceAsString());
-    assertEquals(original2,seq2.getSequenceAsString());
-    
-    EditCommand righj = new JustifyLeftOrRightCommand("Right J", false, sqs, 2, 7, al);
-    assertEquals("----ABcDEF",seq1.getSequenceAsString());
-    assertEquals("-G---HiJ",seq2.getSequenceAsString());
-    assertEquals("-M---NoPQ",seq3.getSequenceAsString());
-    righj.undoCommand(new AlignmentI[] { al});
-    assertEquals(original3,seq3.getSequenceAsString());
-    assertEquals(original1,seq1.getSequenceAsString());
-    assertEquals(original2,seq2.getSequenceAsString());
-        
+    assertEquals("-GHiJ---", seq2.getSequenceAsString());
+    assertEquals("-MNoP---Q", seq3.getSequenceAsString());
+    lefj.undoCommand(new AlignmentI[] { al });
+    assertEquals(original3, seq3.getSequenceAsString());
+    assertEquals(original1, seq1.getSequenceAsString());
+    assertEquals(original2, seq2.getSequenceAsString());
+
+    EditCommand righj = new JustifyLeftOrRightCommand("Right J", false, sqs,
+            2, 7, al);
+    assertEquals("----ABcDEF", seq1.getSequenceAsString());
+    assertEquals("-G---HiJ", seq2.getSequenceAsString());
+    assertEquals("-M---NoPQ", seq3.getSequenceAsString());
+    righj.undoCommand(new AlignmentI[] { al });
+    assertEquals(original3, seq3.getSequenceAsString());
+    assertEquals(original1, seq1.getSequenceAsString());
+    assertEquals(original2, seq2.getSequenceAsString());
+
   }
 }
diff --git a/test/jalview/gui/AssociatePDBFileTest.java b/test/jalview/gui/AssociatePDBFileTest.java
index 0e6791b..c1b5b6e 100644
--- a/test/jalview/gui/AssociatePDBFileTest.java
+++ b/test/jalview/gui/AssociatePDBFileTest.java
@@ -20,7 +20,6 @@
  */
 package jalview.gui;
 
-
 import java.awt.Color;
 import java.io.File;
 import java.util.Iterator;
@@ -92,18 +91,14 @@ public class AssociatePDBFileTest
             + "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
             + "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
             + "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
-            + "DQWNVEVY\n"
-            + ">1GAQ|B/1-98\n"
+            + "DQWNVEVY\n" + ">1GAQ|B/1-98\n"
             + "ATYNVKLITPEGEVELQVPDDVYILDQAEEDGIDLPYSCRAGSCSSCAGKVVSGSVDQSDQSYLDDGQIADG\n"
-            + "WVLTCHAYPTSDVVIETHKEEELTGA\n"
-            + ">1GAQ|C/19-314\n"
+            + "WVLTCHAYPTSDVVIETHKEEELTGA\n" + ">1GAQ|C/19-314\n"
             + "ESKKQEEGVVTNLYKPKEPYVGRCLLNTKITGDDAPGETWHMVFSTEGKIPYREGQSIGVIADGVDKNGKPH\n"
             + "KVRLYSIASSAIGDFGDSKTVSLCVKRLIYTNDAGEIVKGVCSNFLCDLQPGDNVQITGPVGKEMLMPKDPN\n"
             + "ATIIMLATGTGIAPFRSFLWKMFFEKHDDYKFNGLGWLFLGVPTSSSLLYKEEFGKMKERAPENFRVDYAVS\n"
             + "REQTNAAGERMYIQTRMAEYKEELWELLKKDNTYVYMCGLKGMEKGIDDIMVSLAEKDGIDWFDYKKQLKRG\n"
-            + "DQWNVEVY\n"
-            ,
-            DataSourceType.PASTE);
+            + "DQWNVEVY\n", DataSourceType.PASTE);
 
     /*
      * wait for Consensus thread to complete
@@ -128,15 +123,15 @@ public class AssociatePDBFileTest
   @Test(groups = "Functional")
   public void testAssociatePDBFile()
   {
-    String assoc_file="examples/1gaq.txt";
-    for (SequenceI toassoc:af.getViewport().getAlignment().getSequences())
+    String assoc_file = "examples/1gaq.txt";
+    for (SequenceI toassoc : af.getViewport().getAlignment().getSequences())
     {
-      PDBEntry pe = new AssociatePdbFileWithSeq()
-              .associatePdbWithSeq(assoc_file,
-                      DataSourceType.FILE, toassoc, false,
-                      Desktop.instance);
+      PDBEntry pe = new AssociatePdbFileWithSeq().associatePdbWithSeq(
+              assoc_file, DataSourceType.FILE, toassoc, false,
+              Desktop.instance);
       Assert.assertNotNull(pe);
-      Assert.assertNotEquals(toassoc.getDatasetSequence().getAnnotation().length,0);
+      Assert.assertNotEquals(
+              toassoc.getDatasetSequence().getAnnotation().length, 0);
     }
   }
 }
diff --git a/test/jalview/gui/CalculationChooserTest.java b/test/jalview/gui/CalculationChooserTest.java
index ac02c03..e6316f3 100644
--- a/test/jalview/gui/CalculationChooserTest.java
+++ b/test/jalview/gui/CalculationChooserTest.java
@@ -55,29 +55,33 @@ public class CalculationChooserTest
      * peptide models for PCA
      */
     List filtered = CalculationChooser
-            .getApplicableScoreModels(false, true, true,false);
+            .getApplicableScoreModels(false, true, true, false);
     assertEquals(filtered.size(), 5);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
     assertEquals(filtered.get(2).getName(), "PID");
     assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
-    assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
+    assertEquals(filtered.get(4).getName(),
+            "Secondary Structure Similarity");
 
     /*
      * peptide models for Tree are the same
      */
-    filtered = CalculationChooser.getApplicableScoreModels(false, false, true,false);
+    filtered = CalculationChooser.getApplicableScoreModels(false, false,
+            true, false);
     assertEquals(filtered.size(), 5);
     assertSame(filtered.get(0), blosum62);
     assertSame(filtered.get(1), pam250);
     assertEquals(filtered.get(2).getName(), "PID");
     assertEquals(filtered.get(3).getName(), "Sequence Feature Similarity");
-    assertEquals(filtered.get(4).getName(), "Secondary Structure Similarity");
+    assertEquals(filtered.get(4).getName(),
+            "Secondary Structure Similarity");
 
     /*
      * nucleotide models for PCA
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true,
+            false, false);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -86,7 +90,8 @@ public class CalculationChooserTest
     /*
      * nucleotide models for Tree are the same
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, false, false,false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, false,
+            false, false);
     assertEquals(filtered.size(), 3);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
@@ -101,30 +106,37 @@ public class CalculationChooserTest
     /*
      * nucleotide models for Tree are unchanged
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, false, true,false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, false,
+            true, false);
     assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
     assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
-    assertEquals(filtered.get(3).getName(), "Secondary Structure Similarity");
+    assertEquals(filtered.get(3).getName(),
+            "Secondary Structure Similarity");
 
     /*
      * nucleotide models for PCA add BLOSUM62 as last option
      */
-    filtered = CalculationChooser.getApplicableScoreModels(true, true, false,false);
+    filtered = CalculationChooser.getApplicableScoreModels(true, true,
+            false, false);
     assertEquals(filtered.size(), 4);
     assertSame(filtered.get(0), dna);
     assertEquals(filtered.get(1).getName(), "PID");
     assertEquals(filtered.get(2).getName(), "Sequence Feature Similarity");
     assertSame(filtered.get(3), blosum62);
-    
-    filtered = CalculationChooser.getApplicableScoreModels(true, true, false,true);
+
+    filtered = CalculationChooser.getApplicableScoreModels(true, true,
+            false, true);
     assertEquals(filtered.size(), 1); // DNA matrix for DNA pasimap
-    for (int i=0; i<=8;i++)
+    for (int i = 0; i <= 8; i++)
     {
-      boolean isDna = (i & 1) != 0,isPca = (i & 2) != 0,isSS = (i & 4) != 0;
-     
-      assertEquals(CalculationChooser.getApplicableScoreModels(isDna,isPca,isSS,true).size(), (isDna) ? 1: 2);
+      boolean isDna = (i & 1) != 0, isPca = (i & 2) != 0,
+              isSS = (i & 4) != 0;
+
+      assertEquals(CalculationChooser
+              .getApplicableScoreModels(isDna, isPca, isSS, true).size(),
+              (isDna) ? 1 : 2);
     }
   }
 }
diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java
index 8b2fa74..ca90d8a 100644
--- a/test/jalview/project/Jalview2xmlTests.java
+++ b/test/jalview/project/Jalview2xmlTests.java
@@ -250,9 +250,8 @@ 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))
@@ -271,9 +270,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase
     assertTrue(__rcs.isSeqAssociated(),
             "Group Annotation colourscheme wasn't sequence associated");
 
-    for (int p = 0,
-            pSize = af.getViewport().getAlignment().getWidth(); p < pSize
-                    && (!diffseqcols || !diffgseqcols); p++)
+    for (int p = 0, pSize = af.getViewport().getAlignment()
+            .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++)
     {
       if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null,
               0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null,
diff --git a/test/jalview/renderer/ResidueShaderTest.java b/test/jalview/renderer/ResidueShaderTest.java
index 9ff93e1..a198d3c 100644
--- a/test/jalview/renderer/ResidueShaderTest.java
+++ b/test/jalview/renderer/ResidueShaderTest.java
@@ -345,7 +345,7 @@ public class ResidueShaderTest
                   SecondaryStructureCount secondaryStructureCount)
           {
             // TODO Auto-generated method stub
-            
+
           }
 
           @Override
diff --git a/test/jalview/schemes/ClustalxColourSchemeTest.java b/test/jalview/schemes/ClustalxColourSchemeTest.java
index d476d6e..983f94c 100644
--- a/test/jalview/schemes/ClustalxColourSchemeTest.java
+++ b/test/jalview/schemes/ClustalxColourSchemeTest.java
@@ -151,6 +151,7 @@ public class ClustalxColourSchemeTest
     // viewport
     // assertEquals(cs.findColour('C', 0, al.getSequenceAt(0)), clustalPink);
   }
+
   @Test
   public void testDocString()
   {
-- 
1.7.10.2