From: James Procter Date: Mon, 22 May 2023 08:52:01 +0000 (+0100) Subject: JAL-1551 spotless X-Git-Tag: Release_2_11_3_0~14^2~3^2^2~19^2^2 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=fdde9a078d7bdb46ed9fb7fe115ea83c84a19c81;p=jalview.git JAL-1551 spotless --- diff --git a/src/jalview/analysis/AlignmentSorter.java b/src/jalview/analysis/AlignmentSorter.java index 0f3edfd..b02d49c 100755 --- a/src/jalview/analysis/AlignmentSorter.java +++ b/src/jalview/analysis/AlignmentSorter.java @@ -548,7 +548,9 @@ public class AlignmentSorter if ((left == null) && (right == null)) { - if (!(node instanceof SequenceNode && ((SequenceNode)node).isPlaceholder()) && (node.element() != null)) + if (!(node instanceof SequenceNode + && ((SequenceNode) node).isPlaceholder()) + && (node.element() != null)) { if (node.element() instanceof SequenceI) { diff --git a/src/jalview/analysis/AlignmentUtils.java b/src/jalview/analysis/AlignmentUtils.java index 0906872..201f88b 100644 --- a/src/jalview/analysis/AlignmentUtils.java +++ b/src/jalview/analysis/AlignmentUtils.java @@ -184,10 +184,10 @@ public class AlignmentUtils // TODO use Character.toLowerCase to avoid creating String objects? char[] upstream = new String(ds .getSequence(s.getStart() - 1 - ustream_ds, s.getStart() - 1)) - .toLowerCase(Locale.ROOT).toCharArray(); + .toLowerCase(Locale.ROOT).toCharArray(); char[] downstream = new String( ds.getSequence(s_end - 1, s_end + dstream_ds)) - .toLowerCase(Locale.ROOT).toCharArray(); + .toLowerCase(Locale.ROOT).toCharArray(); char[] coreseq = s.getSequence(); char[] nseq = new char[offset + upstream.length + downstream.length + coreseq.length]; @@ -1471,19 +1471,20 @@ public class AlignmentUtils */ final Iterable matchedAlignmentAnnotations = al .findAnnotations(seq, dsann.getCalcId(), dsann.label); - boolean found=false; + boolean found = false; if (matchedAlignmentAnnotations != null) { - for (AlignmentAnnotation matched:matchedAlignmentAnnotations) + for (AlignmentAnnotation matched : matchedAlignmentAnnotations) { if (dsann.description.equals(matched.description)) { - found=true; + found = true; break; } } } - if (!found) { + if (!found) + { result.add(dsann); if (labelForCalcId != null) { diff --git a/src/jalview/analysis/AnnotationSorter.java b/src/jalview/analysis/AnnotationSorter.java index 0f0cf68..1f2e78f 100644 --- a/src/jalview/analysis/AnnotationSorter.java +++ b/src/jalview/analysis/AnnotationSorter.java @@ -157,12 +157,13 @@ public class AnnotationSorter return showAutocalcAbove ? 1 : -1; } int computedOrder = compareSequences(o1, o2); - if (computedOrder==0) { + if (computedOrder == 0) + { computedOrder = compareLabels(o1, o2); } - if (computedOrder==0) + if (computedOrder == 0) { - computedOrder = compareDescriptions(o1,o2); + computedOrder = compareDescriptions(o1, o2); } return computedOrder; } @@ -365,18 +366,19 @@ public class AnnotationSorter } String label1 = o1.label; String label2 = o2.label; - return compareString(label1,label2); + return compareString(label1, label2); } /** - * Non-case-sensitive comparison of annotation descriptions. Returns zero if either - * argument is null. + * Non-case-sensitive comparison of annotation descriptions. Returns zero if + * either argument is null. * * @param o1 * @param o2 * @return */ - private int compareDescriptions(AlignmentAnnotation o1, AlignmentAnnotation o2) + private int compareDescriptions(AlignmentAnnotation o1, + AlignmentAnnotation o2) { if (o1 == null || o2 == null) { @@ -384,8 +386,9 @@ public class AnnotationSorter } String label1 = o1.description; String label2 = o2.description; - return compareString(label1,label2); + return compareString(label1, label2); } + private int compareString(String label1, String label2) { if (label1 == null && label2 == null) diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java index dd56424..6260067 100644 --- a/src/jalview/analysis/TreeModel.java +++ b/src/jalview/analysis/TreeModel.java @@ -80,7 +80,7 @@ public class TreeModel public TreeModel(SequenceI[] seqs, AlignmentView odata, NewickFile treefile) { - this(seqs, treefile.getTree(), treefile.HasDistances(), + this(seqs, treefile.getTree(), treefile.HasDistances(), treefile.HasBootstrap(), treefile.HasRootDistance()); seqData = odata; @@ -94,7 +94,7 @@ public class TreeModel */ public TreeModel(TreeBuilder tree) { - this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(), + this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(), tree.hasBootstrap(), tree.hasRootDistance()); seqData = tree.getOriginalData(); } @@ -141,7 +141,7 @@ public class TreeModel while (i < leaves.size()) { // TODO - decide if we get rid of the polymorphism here ? - j = (SequenceNode)leaves.elementAt(i++); + j = (SequenceNode) leaves.elementAt(i++); realnam = j.getName(); nam = null; @@ -311,8 +311,7 @@ public class TreeModel * * @return Vector of leaf nodes on binary tree */ - Vector findLeaves(BinaryNode nd, - Vector leaves) + Vector findLeaves(BinaryNode nd, Vector leaves) { if (nd == null) { diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java index 8c3e39a..f965ff4 100755 --- a/src/jalview/appletgui/TreeCanvas.java +++ b/src/jalview/appletgui/TreeCanvas.java @@ -131,7 +131,7 @@ public class TreeCanvas extends Panel { BinaryNode lf = leaves.elementAt(i); - if (lf instanceof SequenceNode && ((SequenceNode)lf).isPlaceholder()) + if (lf instanceof SequenceNode && ((SequenceNode) lf).isPlaceholder()) { has_placeholders = true; } @@ -211,9 +211,10 @@ public class TreeCanvas extends Panel g.drawString(nodeLabel, xstart + 2, ypos - 2); } - String name = (markPlaceholders && node instanceof SequenceNode && ((SequenceNode) node).isPlaceholder()) - ? (PLACEHOLDER + node.getName()) - : node.getName(); + String name = (markPlaceholders && node instanceof SequenceNode + && ((SequenceNode) node).isPlaceholder()) + ? (PLACEHOLDER + node.getName()) + : node.getName(); FontMetrics fm = g.getFontMetrics(font); int charWidth = fm.stringWidth(name) + 3; int charHeight = fm.getHeight(); @@ -385,8 +386,8 @@ public class TreeCanvas extends Panel } else { - pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, - offx, offy); + pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width, offx, + offy); pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width, offx, offy); } diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java index f4c8854..6b33fea 100755 --- a/src/jalview/bin/Cache.java +++ b/src/jalview/bin/Cache.java @@ -1436,11 +1436,10 @@ public class Cache if (customProxySet && // we have a username but no password for the scheme being // requested - (protocol.equalsIgnoreCase("http") - && (httpUser != null - && httpUser.length() > 0 - && (httpPassword == null - || httpPassword.length == 0))) + (protocol.equalsIgnoreCase("http") + && (httpUser != null && httpUser.length() > 0 + && (httpPassword == null + || httpPassword.length == 0))) || (protocol.equalsIgnoreCase("https") && (httpsUser != null && httpsUser.length() > 0 diff --git a/src/jalview/datamodel/Alignment.java b/src/jalview/datamodel/Alignment.java index 517a6dd..4d3d578 100755 --- a/src/jalview/datamodel/Alignment.java +++ b/src/jalview/datamodel/Alignment.java @@ -2050,14 +2050,14 @@ public class Alignment implements AlignmentI, AutoCloseable public ContactMatrixI getContactMatrixFor(AlignmentAnnotation _aa) { ContactMatrixI cm = cmholder.getContactMatrixFor(_aa); - if (cm==null && _aa.groupRef!=null) + if (cm == null && _aa.groupRef != null) { cm = _aa.groupRef.getContactMatrixFor(_aa); } - if (cm==null && _aa.sequenceRef!=null) + if (cm == null && _aa.sequenceRef != null) { cm = _aa.sequenceRef.getContactMatrixFor(_aa); - if (cm==null) + if (cm == null) { // TODO fix up this logic and unify with getContactListFor cm = _aa.sequenceRef.getDatasetSequence().getContactMatrixFor(_aa); @@ -2080,10 +2080,12 @@ public class Alignment implements AlignmentI, AutoCloseable if (spos >= _aa.sequenceRef.getStart() && spos <= 1 + _aa.sequenceRef.getEnd()) { - cl = _aa.sequenceRef.getContactListFor(_aa, spos-_aa.sequenceRef.getStart()); + cl = _aa.sequenceRef.getContactListFor(_aa, + spos - _aa.sequenceRef.getStart()); if (cl == null && _aa.sequenceRef.getDatasetSequence() != null) { - _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, spos-_aa.sequenceRef.getStart()); + _aa.sequenceRef.getDatasetSequence().getContactListFor(_aa, + spos - _aa.sequenceRef.getStart()); } } } diff --git a/src/jalview/datamodel/AlignmentAnnotation.java b/src/jalview/datamodel/AlignmentAnnotation.java index 4861dfd..b5987f4 100755 --- a/src/jalview/datamodel/AlignmentAnnotation.java +++ b/src/jalview/datamodel/AlignmentAnnotation.java @@ -568,12 +568,12 @@ public class AlignmentAnnotation : annotations[index + offset].displayCharacter == null || annotations[index + offset].displayCharacter - .length() == 0 - ? annotations[index - + offset].secondaryStructure - : annotations[index - + offset].displayCharacter - .charAt(0)); + .length() == 0 + ? annotations[index + + offset].secondaryStructure + : annotations[index + + offset].displayCharacter + .charAt(0)); } @Override diff --git a/src/jalview/datamodel/ColumnSelection.java b/src/jalview/datamodel/ColumnSelection.java index 6ee324f..3c2d166 100644 --- a/src/jalview/datamodel/ColumnSelection.java +++ b/src/jalview/datamodel/ColumnSelection.java @@ -586,8 +586,8 @@ public class ColumnSelection int cpos = ann_row.sequenceRef.findPosition(column) - 1; ContactListI clist = ann_row.sequenceRef .getContactListFor(ann_row, cpos); - for (int row = column + 8, - rowEnd = clist.getContactHeight(); row < rowEnd; row++) + for (int row = column + 8, rowEnd = clist + .getContactHeight(); row < rowEnd; row++) { if (filterParams .getThresholdType() == AnnotationFilterParameter.ThresholdType.ABOVE_THRESHOLD diff --git a/src/jalview/datamodel/ContactMatrixI.java b/src/jalview/datamodel/ContactMatrixI.java index 3510ed1..1d7391b 100644 --- a/src/jalview/datamodel/ContactMatrixI.java +++ b/src/jalview/datamodel/ContactMatrixI.java @@ -33,41 +33,51 @@ public interface ContactMatrixI int getWidth(); int getHeight(); - - default boolean hasGroups() { + + default boolean hasGroups() + { return false; } - default BitSet getGroupsFor(int column) { - BitSet colbitset = new BitSet(); + + default BitSet getGroupsFor(int column) + { + BitSet colbitset = new BitSet(); colbitset.set(column); return colbitset; } - default List getGroups() { + default List getGroups() + { return Arrays.asList(); } - default boolean hasTree() { + default boolean hasTree() + { return false; } /** * Newick representation of clustered matrix + * * @return null unless hasTree is true */ - default String getNewick() { + default String getNewick() + { return null; } - default String getTreeMethod() { + default String getTreeMethod() + { return null; } - default boolean hasCutHeight() { + default boolean hasCutHeight() + { return false; } - default double getCutHeight() { + default double getCutHeight() + { return 0; } @@ -75,5 +85,8 @@ public interface ContactMatrixI void setColorForGroup(BitSet bs, Color color); - default Color getColourForGroup(BitSet bs) { return Color.white;}; + default Color getColourForGroup(BitSet bs) + { + return Color.white; + }; } diff --git a/src/jalview/datamodel/ContactRange.java b/src/jalview/datamodel/ContactRange.java index 5de8b04..fe66aa5 100644 --- a/src/jalview/datamodel/ContactRange.java +++ b/src/jalview/datamodel/ContactRange.java @@ -1,6 +1,5 @@ package jalview.datamodel; - /** * bean for max/min positions for a given range * @@ -31,8 +30,8 @@ public class ContactRange * @param maxPos * @param max */ - public void update(int from_column, int to_column, int minPos, - double min, int maxPos, double max, double mean) + public void update(int from_column, int to_column, int minPos, double min, + int maxPos, double max, double mean) { this.from_column = from_column; this.to_column = to_column; diff --git a/src/jalview/datamodel/SeqDistanceContactMatrix.java b/src/jalview/datamodel/SeqDistanceContactMatrix.java index e37a5b2..a915bb0 100644 --- a/src/jalview/datamodel/SeqDistanceContactMatrix.java +++ b/src/jalview/datamodel/SeqDistanceContactMatrix.java @@ -124,40 +124,47 @@ public class SeqDistanceContactMatrix implements ContactMatrixI { return width; } - private List groups=null; + + private List groups = null; + @Override public void updateGroups(List colGroups) { groups = colGroups; } + @Override public boolean hasGroups() { - return groups!=null; + return groups != null; } + @Override public List getGroups() { return groups; - } + } - HashMap colorMap = new HashMap<>(); - @Override + HashMap colorMap = new HashMap<>(); + + @Override public Color getColourForGroup(BitSet bs) { - if (bs==null) { + if (bs == null) + { return Color.white; } - Color groupCol=colorMap.get(bs); - if (groupCol==null) + Color groupCol = colorMap.get(bs); + if (groupCol == null) { return Color.white; } return groupCol; } - @Override - public void setColorForGroup(BitSet bs,Color color) + + @Override + public void setColorForGroup(BitSet bs, Color color) { - colorMap.put(bs,color); + colorMap.put(bs, color); } } diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java index 52a6066..7462bc8 100755 --- a/src/jalview/gui/AnnotationLabels.java +++ b/src/jalview/gui/AnnotationLabels.java @@ -422,13 +422,14 @@ public class AnnotationLabels extends JPanel consclipbrd.addActionListener(this); pop.add(consclipbrd); } - if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP + if (aa[selectedRow].graph == AlignmentAnnotation.CONTACT_MAP && PAEContactMatrix.PAEMATRIX .equals(aa[selectedRow].getCalcId())) { final PAEContactMatrix cm = (PAEContactMatrix) av .getContactMatrix(aa[selectedRow]); - if (cm!=null && cm.getNewick()!=null && cm.getNewick().length()>0) + if (cm != null && cm.getNewick() != null + && cm.getNewick().length() > 0) { item = new JMenuItem("Show Tree for Matrix"); item.addActionListener(new ActionListener() @@ -438,7 +439,7 @@ public class AnnotationLabels extends JPanel public void actionPerformed(ActionEvent e) { - ap.alignFrame.showContactMapTree(aa[selectedRow],cm); + ap.alignFrame.showContactMapTree(aa[selectedRow], cm); } }); @@ -1123,7 +1124,8 @@ public class AnnotationLabels extends JPanel } olY = y; // look ahead to next annotation - for (nexAA=i+1; nexAA leaves = tree.findLeaves(highlightNode); - if (tp.isColumnWise()) { - markColumnsFor(getAssociatedPanels(), leaves, Color.red); - } else { - for (int i = 0; i < leaves.size(); i++) + if (tp.isColumnWise()) { - SequenceI seq = (SequenceI) leaves.elementAt(i).element(); - treeSelectionChanged(seq); + markColumnsFor(getAssociatedPanels(), leaves, Color.red); } + else + { + for (int i = 0; i < leaves.size(); i++) + { + SequenceI seq = (SequenceI) leaves.elementAt(i).element(); + treeSelectionChanged(seq); + } } av.sendSelection(); } @@ -998,7 +1001,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { AlignmentPanel[] aps = getAssociatedPanels(); List colGroups = new ArrayList<>(); - Map colors=new HashMap(); + Map colors = new HashMap(); for (int i = 0; i < groups.size(); i++) { Color col = new Color((int) (Math.random() * 255), @@ -1006,10 +1009,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, setColor(groups.get(i), col.brighter()); Vector l = tree.findLeaves(groups.get(i)); - if (!tp.isColumnWise()) { + if (!tp.isColumnWise()) + { createSeqGroupFor(aps, l, col); - } else { - BitSet gp=createColumnGroupFor(l,col); + } + else + { + BitSet gp = createColumnGroupFor(l, col); colGroups.add(gp); colors.put(gp, col); @@ -1018,12 +1024,13 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, if (tp.isColumnWise()) { AlignmentAnnotation aa = tp.getAssocAnnotation(); - if (aa!=null) { + if (aa != null) + { ContactMatrixI cm = av.getContactMatrix(aa); - if (cm!=null) + if (cm != null) { cm.updateGroups(colGroups); - for (BitSet gp:colors.keySet()) + for (BitSet gp : colors.keySet()) { cm.setColorForGroup(gp, colors.get(gp)); } @@ -1058,46 +1065,50 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, { return false; } - if (av==null||av.getAlignment()==null) + if (av == null || av.getAlignment() == null) { // alignment is closed return false; } ColumnSelection cs = av.getColumnSelection(); - + HiddenColumns hc = av.getAlignment().getHiddenColumns(); int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) : colm; if (!av.hasHiddenColumns()) { - return cs.contains(offp-1); + return cs.contains(offp - 1); } - if (hc.isVisible(offp-1)) + if (hc.isVisible(offp - 1)) { - return cs.contains(offp-1); -// return cs.contains(hc.absoluteToVisibleColumn(offp)); + return cs.contains(offp - 1); + // return cs.contains(hc.absoluteToVisibleColumn(offp)); } return false; } - - private BitSet createColumnGroupFor(Vector l, - Color col) + + private BitSet createColumnGroupFor(Vector l, Color col) { - BitSet gp=new BitSet(); - for (BinaryNode bn:l) + BitSet gp = new BitSet(); + for (BinaryNode bn : l) { - int colm=-1; - if (bn.element()!=null && bn.element()instanceof Integer) - { colm = (Integer)bn.element(); - } else { - // parse out from nodename - try { - colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1)); - } catch (Exception e) + int colm = -1; + if (bn.element() != null && bn.element() instanceof Integer) { - continue; + colm = (Integer) bn.element(); } + else + { + // parse out from nodename + try + { + colm = Integer.parseInt( + bn.getName().substring(bn.getName().indexOf("c") + 1)); + } catch (Exception e) + { + continue; + } } gp.set(colm); } @@ -1108,17 +1119,19 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, Color col) { SequenceI rseq = tp.assocAnnotation.sequenceRef; - if (av==null||av.getAlignment()==null) + if (av == null || av.getAlignment() == null) { // alignment is closed return; } - for (BinaryNode bn:l) + for (BinaryNode bn : l) { - int colm=-1; - try { - colm = Integer.parseInt(bn.getName().substring(bn.getName().indexOf("c")+1)); + int colm = -1; + try + { + colm = Integer.parseInt( + bn.getName().substring(bn.getName().indexOf("c") + 1)); } catch (Exception e) { continue; @@ -1126,19 +1139,22 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable, ColumnSelection cs = av.getColumnSelection(); HiddenColumns hc = av.getAlignment().getHiddenColumns(); { - int offp = (rseq!=null) ? rseq.findIndex(rseq.getStart()+colm) : colm; - - if (!av.hasHiddenColumns() || hc.isVisible(offp-1)) - { - if (cs.contains(offp-1)) + int offp = (rseq != null) ? rseq.findIndex(rseq.getStart() + colm) + : colm; + + if (!av.hasHiddenColumns() || hc.isVisible(offp - 1)) + { + if (cs.contains(offp - 1)) { - cs.removeElement(offp-1); - } else { - cs.addElement(offp-1); + cs.removeElement(offp - 1); + } + else + { + cs.addElement(offp - 1); } } } - } + } } public void createSeqGroupFor(AlignmentPanel[] aps, Vector l, diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java index 30e4305..0e1fd42 100755 --- a/src/jalview/gui/TreePanel.java +++ b/src/jalview/gui/TreePanel.java @@ -136,20 +136,24 @@ public class TreePanel extends GTreePanel AlignmentAnnotation aa, String title) { super(); - columnWise=true; + columnWise = true; assocAnnotation = aa; this.setFrameIcon(null); this.treeTitle = title; initTreePanel(alignPanel, null, null, fin, null); } - - boolean columnWise=false; - AlignmentAnnotation assocAnnotation=null; + + boolean columnWise = false; + + AlignmentAnnotation assocAnnotation = null; + public boolean isColumnWise() { return columnWise; } - public AlignmentAnnotation getAssocAnnotation() { + + public AlignmentAnnotation getAssocAnnotation() + { return assocAnnotation; } diff --git a/src/jalview/gui/WebserviceInfo.java b/src/jalview/gui/WebserviceInfo.java index 4aac062..7eeee9a 100644 --- a/src/jalview/gui/WebserviceInfo.java +++ b/src/jalview/gui/WebserviceInfo.java @@ -626,8 +626,8 @@ public class WebserviceInfo extends GWebserviceInfo true, false); ((JEditorPane) ((JScrollPane) jobPanes.get(which)).getViewport() .getComponent(0)) - .setText(ensureHtmlTagged( - txt + getHtmlFragment(text, false, true))); + .setText(ensureHtmlTagged( + txt + getHtmlFragment(text, false, true))); } else { diff --git a/src/jalview/io/BackupFiles.java b/src/jalview/io/BackupFiles.java index bec584f..c67c307 100644 --- a/src/jalview/io/BackupFiles.java +++ b/src/jalview/io/BackupFiles.java @@ -234,7 +234,8 @@ public class BackupFiles classInit(); if (file.getParentFile() == null) { - // filename probably in pwd represented with no parent -- fix it before it's a problem + // filename probably in pwd represented with no parent -- fix it before + // it's a problem file = file.getAbsoluteFile(); } this.file = file; diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index d3a6ba9..8d3283d 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -343,8 +343,8 @@ public class FileParse } String encoding = _conn.getContentEncoding(); String contentType = _conn.getContentType(); - boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType) || contentType.endsWith("gzip") - || "gzip".equals(encoding); + boolean isgzipped = "application/x-gzip".equalsIgnoreCase(contentType) + || contentType.endsWith("gzip") || "gzip".equals(encoding); Exception e = null; InputStream inputStream = _conn.getInputStream(); if (isgzipped) diff --git a/src/jalview/io/PContactPredictionFile.java b/src/jalview/io/PContactPredictionFile.java index 3df9804..164d7cc 100644 --- a/src/jalview/io/PContactPredictionFile.java +++ b/src/jalview/io/PContactPredictionFile.java @@ -47,8 +47,8 @@ public class PContactPredictionFile extends AlignFile { protected static final String CONTACT_PREDICTION = "CONTACT_PREDICTION"; - public PContactPredictionFile(String inFile, DataSourceType fileSourceType) - throws IOException + public PContactPredictionFile(String inFile, + DataSourceType fileSourceType) throws IOException { super(inFile, fileSourceType); @@ -109,19 +109,23 @@ public class PContactPredictionFile extends AlignFile if (cm == null) { - cm = new ContactMatrix(true) { + cm = new ContactMatrix(true) + { @Override public String getType() { return CONTACT_PREDICTION; } + @Override public int getHeight() { // TODO Auto-generated method stub - // return maximum contact height + // return maximum contact height return 0; - }@Override + } + + @Override public int getWidth() { // TODO Auto-generated method stub @@ -140,15 +144,15 @@ public class PContactPredictionFile extends AlignFile } catch (Exception x) { error = true; - errormessage = "Couldn't process line: " - + x.getLocalizedMessage() + "\n" + line; + errormessage = "Couldn't process line: " + x.getLocalizedMessage() + + "\n" + line; return; } cm.addContact(left, right, (float) strength); } } // TODO COMPLETE - throw(new Error("Not Implemented yet.")); + throw (new Error("Not Implemented yet.")); } @Override diff --git a/src/jalview/io/StockholmFile.java b/src/jalview/io/StockholmFile.java index eeadcbf..28f062f 100644 --- a/src/jalview/io/StockholmFile.java +++ b/src/jalview/io/StockholmFile.java @@ -218,8 +218,9 @@ public class StockholmFile extends AlignFile r = new Regex("# STOCKHOLM ([\\d\\.]+)"); if (!r.search(nextLine())) { - throw new IOException(MessageManager - .getString("exception.stockholm_invalid_format") +" ("+r+")"); + throw new IOException( + MessageManager.getString("exception.stockholm_invalid_format") + + " (" + r + ")"); } else { @@ -1052,11 +1053,11 @@ public class StockholmFile extends AlignFile while (i < slen && (seq = s[i]) != null) { - if (seq.getDescription()!=null) + if (seq.getDescription() != null) { // out.append("#=GR "); - out.append(new Format("%-" + maxid + "s").form( - "#=GS " + printId(seq, jvSuffix) + " DE " + seq.getDescription())); + out.append(new Format("%-" + maxid + "s").form("#=GS " + + printId(seq, jvSuffix) + " DE " + seq.getDescription())); out.append(newline); } diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java index c0d1774..1ac7bab 100644 --- a/src/jalview/io/vamsas/Tree.java +++ b/src/jalview/io/vamsas/Tree.java @@ -394,8 +394,7 @@ public class Tree extends DatastoreItem { if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder()) { - Object assocseq = ((BinaryNode) tnode) - .element(); + Object assocseq = ((BinaryNode) tnode).element(); if (assocseq instanceof SequenceI) { Vobject vobj = this.getjv2vObj(assocseq); diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index ddf2afd..913dffe 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -1523,7 +1523,7 @@ public class Jalview2XML ov.getCanvas().getResidueColour().getRGB()); overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB()); view.setOverview(overview); - } + } if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) { view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(), @@ -2304,22 +2304,24 @@ public class Jalview2XML line.setColour(annotation.getThreshold().colour.getRGB()); an.setThresholdLine(line); } - if (annotation.graph==AlignmentAnnotation.CONTACT_MAP) + if (annotation.graph == AlignmentAnnotation.CONTACT_MAP) { - if (annotation.sequenceRef.getContactMaps()!=null) + if (annotation.sequenceRef.getContactMaps() != null) { - ContactMatrixI cm = annotation.sequenceRef.getContactMatrixFor(annotation); - if (cm!=null) + ContactMatrixI cm = annotation.sequenceRef + .getContactMatrixFor(annotation); + if (cm != null) { MatrixType xmlmat = new MatrixType(); xmlmat.setType(cm.getType()); xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); - // consider using an opaque to/from -> allow instance to control its representation ? + // consider using an opaque to/from -> allow instance to control + // its representation ? xmlmat.setElements(ContactMatrix.contactToFloatString(cm)); if (cm.hasGroups()) { - for (BitSet gp: cm.getGroups()) + for (BitSet gp : cm.getGroups()) { BigInteger val = new BigInteger(gp.toByteArray()); xmlmat.getGroups().add(val.toString()); @@ -2335,7 +2337,7 @@ public class Jalview2XML { xmlmat.setCutHeight(cm.getCutHeight()); } - + // set/get properties an.getContactmatrix().add(xmlmat); } @@ -3948,7 +3950,8 @@ public class Jalview2XML jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { - for (jalview.xml.binding.jalview.Property prop : annotation.getProperty()) + for (jalview.xml.binding.jalview.Property prop : annotation + .getProperty()) { jaa.setProperty(prop.getName(), prop.getValue()); } @@ -3975,29 +3978,37 @@ public class Jalview2XML PAEContactMatrix newpae = new PAEContactMatrix( jaa.sequenceRef, elements); - List newgroups=new ArrayList(); - if (xmlmat.getGroups().size()>0) + List newgroups = new ArrayList(); + if (xmlmat.getGroups().size() > 0) { - for (String sgroup:xmlmat.getGroups()) + for (String sgroup : xmlmat.getGroups()) { - try { + try + { BigInteger group = new BigInteger(sgroup); newgroups.add(BitSet.valueOf(group.toByteArray())); } catch (NumberFormatException nfe) { - Console.error("Problem parsing groups for a contact matrix (\""+sgroup+"\"",nfe); + Console.error( + "Problem parsing groups for a contact matrix (\"" + + sgroup + "\"", + nfe); } } } - String nwk=xmlmat.getNewick().size()>0 ? xmlmat.getNewick().get(0):null; - if (xmlmat.getNewick().size()>1) + String nwk = xmlmat.getNewick().size() > 0 + ? xmlmat.getNewick().get(0) + : null; + if (xmlmat.getNewick().size() > 1) { Console.log.info( "Ignoring additional clusterings for contact matrix"); } - + String treeMethod = xmlmat.getTreeMethod(); - double thresh = xmlmat.getCutHeight()!=null ? xmlmat.getCutHeight() : 0; + double thresh = xmlmat.getCutHeight() != null + ? xmlmat.getCutHeight() + : 0; newpae.restoreGroups(newgroups, treeMethod, nwk, thresh); jaa.sequenceRef.addContactListFor(jaa, newpae); } @@ -4246,8 +4257,8 @@ public class Jalview2XML */ protected void loadOverview(Viewport view, String version, AlignFrame af) { - if (!isVersionStringLaterThan("2.11.3", - version) && view.getOverview()==null) + if (!isVersionStringLaterThan("2.11.3", version) + && view.getOverview() == null) { return; } @@ -4394,8 +4405,8 @@ public class Jalview2XML { if (tree.isColumnWise()) { - AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds.get(tree - .getColumnReference()); + AlignmentAnnotation aa = (AlignmentAnnotation) annotationIds + .get(tree.getColumnReference()); if (aa == null) { Console.warn( @@ -4953,10 +4964,11 @@ public class Jalview2XML viewport.setIncrement(safeInt(view.getConsThreshold())); viewport.setShowJVSuffix(safeBoolean(view.isShowFullId())); viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds())); - viewport.setFont(new Font(view.getFontName(), - safeInt(view.getFontStyle()), safeInt(view.getFontSize())), - (view.getCharWidth()!=null) ? false : true); - if (view.getCharWidth()!=null) + viewport.setFont( + new Font(view.getFontName(), safeInt(view.getFontStyle()), + safeInt(view.getFontSize())), + (view.getCharWidth() != null) ? false : true); + if (view.getCharWidth() != null) { viewport.setCharWidth(view.getCharWidth()); viewport.setCharHeight(view.getCharHeight()); @@ -5283,7 +5295,7 @@ public class Jalview2XML + annotationId); return null; } - // belt-and-braces create a threshold line if the + // belt-and-braces create a threshold line if the // colourscheme needs one but the matchedAnnotation doesn't have one if (safeInt(viewAnnColour.getAboveThreshold()) != 0 && matchedAnnotation.getThreshold() == null) diff --git a/src/jalview/renderer/AnnotationRendererFactory.java b/src/jalview/renderer/AnnotationRendererFactory.java index db2eb7a..85d22c9 100644 --- a/src/jalview/renderer/AnnotationRendererFactory.java +++ b/src/jalview/renderer/AnnotationRendererFactory.java @@ -7,8 +7,7 @@ import jalview.ws.datamodel.alphafold.PAEContactMatrix; import java.util.IdentityHashMap; -public class AnnotationRendererFactory implements - AnnotationRendererFactoryI +public class AnnotationRendererFactory implements AnnotationRendererFactoryI { private static AnnotationRendererFactoryI factory = null; @@ -40,8 +39,9 @@ public class AnnotationRendererFactory implements { return ContactMapRenderer.newPAERenderer(); } - // TODO add potential for configuring renderer directly from the annotation row and/or viewmodel - + // TODO add potential for configuring renderer directly from the + // annotation row and/or viewmodel + } return null; } diff --git a/src/jalview/renderer/ContactMapRenderer.java b/src/jalview/renderer/ContactMapRenderer.java index e54f471..cbc4af9 100644 --- a/src/jalview/renderer/ContactMapRenderer.java +++ b/src/jalview/renderer/ContactMapRenderer.java @@ -25,6 +25,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI { /** * bean holding colours for shading + * * @author jprocter * */ @@ -34,10 +35,12 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI * shown when no data available from map */ Color no_data; + /** * shown for region not currently visible - should normally not see this */ Color hidden; + /** * linear shading scheme min/max */ @@ -66,6 +69,7 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI /** * build an EBI-AlphaFold style renderer of PAE matrices + * * @return */ public static ContactMapRenderer newPAERenderer() @@ -146,7 +150,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI x++; continue; } - Color gpcol = (cm==null) ? Color.white: cm.getColourForGroup(cm.getGroupsFor(column)); + Color gpcol = (cm == null) ? Color.white + : cm.getColourForGroup(cm.getGroupsFor(column)); // feature still in development - highlight or omit regions hidden in // the alignment - currently marks them as red rows boolean maskHiddenCols = false; @@ -216,14 +221,17 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI { col = shade.hidden; } - if (gpcol!=null && gpcol!=Color.white) { + if (gpcol != null && gpcol != Color.white) + { // todo - could overlay group as a transparent rectangle ? - col = new Color((int)(((float)(col.getRed()+gpcol.getRed()))/2f), - (int)(((float)(col.getGreen()+gpcol.getGreen()))/2f), - (int)(((float)(col.getBlue()+gpcol.getBlue()))/2f)); + col = new Color( + (int) (((float) (col.getRed() + gpcol.getRed())) / 2f), + (int) (((float) (col.getGreen() + gpcol.getGreen())) + / 2f), + (int) (((float) (col.getBlue() + gpcol.getBlue())) / 2f)); } g.setColor(col); - + if (cgeom.pixels_step > 1) { g.fillRect(x * charWidth, ht, charWidth, 1 + cgeom.pixels_step); @@ -240,8 +248,8 @@ public abstract class ContactMapRenderer implements AnnotationRowRendererI Color shadeFor(float min, float max, float value) { - return jalview.util.ColorUtils.getGraduatedColour(value, 0, shade.minColor, - max, shade.maxColor); + return jalview.util.ColorUtils.getGraduatedColour(value, 0, + shade.minColor, max, shade.maxColor); } public Color getColorForRange(float min, float max, ContactListI cl, diff --git a/src/jalview/renderer/OverviewResColourFinder.java b/src/jalview/renderer/OverviewResColourFinder.java index ef4d04b..4cbb1ba 100644 --- a/src/jalview/renderer/OverviewResColourFinder.java +++ b/src/jalview/renderer/OverviewResColourFinder.java @@ -48,6 +48,7 @@ public class OverviewResColourFinder extends ResidueColourFinder /** * Constructor without colour settings (used by applet) + * * @deprecated */ @Deprecated diff --git a/src/jalview/renderer/api/AnnotationRowRendererI.java b/src/jalview/renderer/api/AnnotationRowRendererI.java index bedbad5..0907228 100644 --- a/src/jalview/renderer/api/AnnotationRowRendererI.java +++ b/src/jalview/renderer/api/AnnotationRowRendererI.java @@ -13,9 +13,8 @@ public interface AnnotationRowRendererI void renderRow(Graphics g, int charWidth, int charHeight, boolean hasHiddenColumns, AlignViewportI av, - HiddenColumns hiddenColumns, - ColumnSelection columnSelection, AlignmentAnnotation row, - Annotation[] row_annotations, int startRes, int endRes, - float graphMin, float graphMax, int y); + HiddenColumns hiddenColumns, ColumnSelection columnSelection, + AlignmentAnnotation row, Annotation[] row_annotations, + int startRes, int endRes, float graphMin, float graphMax, int y); } diff --git a/src/jalview/renderer/seqfeatures/FeatureRenderer.java b/src/jalview/renderer/seqfeatures/FeatureRenderer.java index e66b7d5..2d16fcd 100644 --- a/src/jalview/renderer/seqfeatures/FeatureRenderer.java +++ b/src/jalview/renderer/seqfeatures/FeatureRenderer.java @@ -543,7 +543,7 @@ public class FeatureRenderer extends FeatureRendererModel */ List overlaps = seq.findFeatures(column, column, type); - for (int i = overlaps.size() - 1 ; i >= 0 ; i--) + for (int i = overlaps.size() - 1; i >= 0; i--) { SequenceFeature sequenceFeature = overlaps.get(i); if (!featureGroupNotShown(sequenceFeature)) diff --git a/src/jalview/viewmodel/AlignmentViewport.java b/src/jalview/viewmodel/AlignmentViewport.java index 36b0851..a8c93cf 100644 --- a/src/jalview/viewmodel/AlignmentViewport.java +++ b/src/jalview/viewmodel/AlignmentViewport.java @@ -2956,7 +2956,6 @@ public abstract class AlignmentViewport return alignment.getContactMatrixFor(alignmentAnnotation); } - /** * get the consensus sequence as displayed under the PID consensus annotation * row. diff --git a/src/jalview/xml/binding/embl/EntrySetType.java b/src/jalview/xml/binding/embl/EntrySetType.java index 0479a34..43689d3 100644 --- a/src/jalview/xml/binding/embl/EntrySetType.java +++ b/src/jalview/xml/binding/embl/EntrySetType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:45 PM GMT // - package jalview.xml.binding.embl; import java.util.ArrayList; @@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for EntrySetType complex type. + *

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

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

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

  * <complexType name="EntrySetType">
@@ -36,41 +37,42 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntrySetType", propOrder = {
-    "entry"
-})
-public class EntrySetType {
+@XmlType(name = "EntrySetType", propOrder = { "entry" })
+public class EntrySetType
+{
 
-    @XmlElement(required = true)
-    protected List entry;
+  @XmlElement(required = true)
+  protected List entry;
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getEntry().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link EntryType } + * + * + */ + public List getEntry() + { + if (entry == null) + { + entry = new ArrayList(); } + return this.entry; + } } diff --git a/src/jalview/xml/binding/embl/EntryType.java b/src/jalview/xml/binding/embl/EntryType.java index 6336ef1..bc3e556 100644 --- a/src/jalview/xml/binding/embl/EntryType.java +++ b/src/jalview/xml/binding/embl/EntryType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:45 PM GMT // - package jalview.xml.binding.embl; import java.math.BigInteger; @@ -20,11 +19,13 @@ import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlType; import javax.xml.datatype.XMLGregorianCalendar; - /** - *

Java class for EntryType complex type. + *

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

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

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

  * <complexType name="EntryType">
@@ -225,669 +226,1666 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "EntryType", propOrder = {
-    "secondaryAccession",
-    "projectAccession",
-    "description",
-    "comment",
-    "keyword",
-    "reference",
-    "xref",
-    "feature",
-    "assembly",
-    "contig",
-    "sequence"
-})
-public class EntryType {
-
-    protected List secondaryAccession;
-    protected List projectAccession;
+@XmlType(
+  name = "EntryType",
+  propOrder =
+  { "secondaryAccession", "projectAccession", "description", "comment",
+      "keyword", "reference", "xref", "feature", "assembly", "contig",
+      "sequence" })
+public class EntryType
+{
+
+  protected List secondaryAccession;
+
+  protected List projectAccession;
+
+  @XmlElement(required = true)
+  protected String description;
+
+  protected String comment;
+
+  protected List keyword;
+
+  protected List reference;
+
+  protected List xref;
+
+  protected List feature;
+
+  protected EntryType.Assembly assembly;
+
+  protected EntryType.Contig contig;
+
+  protected String sequence;
+
+  @XmlAttribute(name = "accession", required = true)
+  protected String accession;
+
+  @XmlAttribute(name = "version", required = true)
+  protected BigInteger version;
+
+  @XmlAttribute(name = "entryVersion")
+  protected BigInteger entryVersion;
+
+  @XmlAttribute(name = "dataClass", required = true)
+  protected String dataClass;
+
+  @XmlAttribute(name = "taxonomicDivision", required = true)
+  protected String taxonomicDivision;
+
+  @XmlAttribute(name = "moleculeType", required = true)
+  protected String moleculeType;
+
+  @XmlAttribute(name = "sequenceLength", required = true)
+  protected BigInteger sequenceLength;
+
+  @XmlAttribute(name = "topology", required = true)
+  protected String topology;
+
+  @XmlAttribute(name = "firstPublic")
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar firstPublic;
+
+  @XmlAttribute(name = "firstPublicRelease")
+  protected BigInteger firstPublicRelease;
+
+  @XmlAttribute(name = "lastUpdated")
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar lastUpdated;
+
+  @XmlAttribute(name = "lastUpdatedRelease")
+  protected BigInteger lastUpdatedRelease;
+
+  /**
+   * Gets the value of the secondaryAccession property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getProjectAccession() + { + if (projectAccession == null) + { + projectAccession = new ArrayList(); + } + return this.projectAccession; + } + + /** + * Gets the value of the description property. + * + * @return possible object is {@link String } + * + */ + public String getDescription() + { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDescription(String value) + { + this.description = value; + } + + /** + * Gets the value of the comment property. + * + * @return possible object is {@link String } + * + */ + public String getComment() + { + return comment; + } + + /** + * Sets the value of the comment property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setComment(String value) + { + this.comment = value; + } + + /** + * Gets the value of the keyword property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link EntryType.Feature } + * + * + */ + public List getFeature() + { + if (feature == null) + { + feature = new ArrayList(); + } + return this.feature; + } + + /** + * Gets the value of the assembly property. + * + * @return possible object is {@link EntryType.Assembly } + * + */ + public EntryType.Assembly getAssembly() + { + return assembly; + } + + /** + * Sets the value of the assembly property. + * + * @param value + * allowed object is {@link EntryType.Assembly } + * + */ + public void setAssembly(EntryType.Assembly value) + { + this.assembly = value; + } + + /** + * Gets the value of the contig property. + * + * @return possible object is {@link EntryType.Contig } + * + */ + public EntryType.Contig getContig() + { + return contig; + } + + /** + * Sets the value of the contig property. + * + * @param value + * allowed object is {@link EntryType.Contig } + * + */ + public void setContig(EntryType.Contig value) + { + this.contig = value; + } + + /** + * Gets the value of the sequence property. + * + * @return possible object is {@link String } + * + */ + public String getSequence() + { + return sequence; + } + + /** + * Sets the value of the sequence property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setSequence(String value) + { + this.sequence = value; + } + + /** + * Gets the value of the accession property. + * + * @return possible object is {@link String } + * + */ + public String getAccession() + { + return accession; + } + + /** + * Sets the value of the accession property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setAccession(String value) + { + this.accession = value; + } + + /** + * Gets the value of the version property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getVersion() + { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setVersion(BigInteger value) + { + this.version = value; + } + + /** + * Gets the value of the entryVersion property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getEntryVersion() + { + return entryVersion; + } + + /** + * Sets the value of the entryVersion property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setEntryVersion(BigInteger value) + { + this.entryVersion = value; + } + + /** + * Gets the value of the dataClass property. + * + * @return possible object is {@link String } + * + */ + public String getDataClass() + { + return dataClass; + } + + /** + * Sets the value of the dataClass property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDataClass(String value) + { + this.dataClass = value; + } + + /** + * Gets the value of the taxonomicDivision property. + * + * @return possible object is {@link String } + * + */ + public String getTaxonomicDivision() + { + return taxonomicDivision; + } + + /** + * Sets the value of the taxonomicDivision property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTaxonomicDivision(String value) + { + this.taxonomicDivision = value; + } + + /** + * Gets the value of the moleculeType property. + * + * @return possible object is {@link String } + * + */ + public String getMoleculeType() + { + return moleculeType; + } + + /** + * Sets the value of the moleculeType property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setMoleculeType(String value) + { + this.moleculeType = value; + } + + /** + * Gets the value of the sequenceLength property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getSequenceLength() + { + return sequenceLength; + } + + /** + * Sets the value of the sequenceLength property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setSequenceLength(BigInteger value) + { + this.sequenceLength = value; + } + + /** + * Gets the value of the topology property. + * + * @return possible object is {@link String } + * + */ + public String getTopology() + { + return topology; + } + + /** + * Sets the value of the topology property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTopology(String value) + { + this.topology = value; + } + + /** + * Gets the value of the firstPublic property. + * + * @return possible object is {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getFirstPublic() + { + return firstPublic; + } + + /** + * Sets the value of the firstPublic property. + * + * @param value + * allowed object is {@link XMLGregorianCalendar } + * + */ + public void setFirstPublic(XMLGregorianCalendar value) + { + this.firstPublic = value; + } + + /** + * Gets the value of the firstPublicRelease property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getFirstPublicRelease() + { + return firstPublicRelease; + } + + /** + * Sets the value of the firstPublicRelease property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setFirstPublicRelease(BigInteger value) + { + this.firstPublicRelease = value; + } + + /** + * Gets the value of the lastUpdated property. + * + * @return possible object is {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getLastUpdated() + { + return lastUpdated; + } + + /** + * Sets the value of the lastUpdated property. + * + * @param value + * allowed object is {@link XMLGregorianCalendar } + * + */ + public void setLastUpdated(XMLGregorianCalendar value) + { + this.lastUpdated = value; + } + + /** + * Gets the value of the lastUpdatedRelease property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getLastUpdatedRelease() + { + return lastUpdatedRelease; + } + + /** + * Sets the value of the lastUpdatedRelease property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setLastUpdatedRelease(BigInteger value) + { + this.lastUpdatedRelease = value; + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="range" maxOccurs="unbounded">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                 <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "range" }) + public static class Assembly + { + @XmlElement(required = true) - protected String description; - protected String comment; - protected List keyword; - protected List reference; - protected List xref; - protected List feature; - protected EntryType.Assembly assembly; - protected EntryType.Contig contig; - protected String sequence; - @XmlAttribute(name = "accession", required = true) - protected String accession; - @XmlAttribute(name = "version", required = true) - protected BigInteger version; - @XmlAttribute(name = "entryVersion") - protected BigInteger entryVersion; - @XmlAttribute(name = "dataClass", required = true) - protected String dataClass; - @XmlAttribute(name = "taxonomicDivision", required = true) - protected String taxonomicDivision; - @XmlAttribute(name = "moleculeType", required = true) - protected String moleculeType; - @XmlAttribute(name = "sequenceLength", required = true) - protected BigInteger sequenceLength; - @XmlAttribute(name = "topology", required = true) - protected String topology; - @XmlAttribute(name = "firstPublic") - @XmlSchemaType(name = "date") - protected XMLGregorianCalendar firstPublic; - @XmlAttribute(name = "firstPublicRelease") - protected BigInteger firstPublicRelease; - @XmlAttribute(name = "lastUpdated") - @XmlSchemaType(name = "date") - protected XMLGregorianCalendar lastUpdated; - @XmlAttribute(name = "lastUpdatedRelease") - protected BigInteger lastUpdatedRelease; + protected List range; /** - * Gets the value of the secondaryAccession property. + * Gets the value of the range property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getSecondaryAccession().add(newItem);
+     * getRange().add(newItem);
      * 
* * *

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

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

- * For example, to add a new item, do as follows: + * The following schema fragment specifies the expected content contained + * within this class. + * *

-     *    getProjectAccession().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
* * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * */ - public List getProjectAccession() { - if (projectAccession == null) { - projectAccession = new ArrayList(); + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Range + { + + @XmlAttribute(name = "begin", required = true) + protected BigInteger begin; + + @XmlAttribute(name = "end", required = true) + protected BigInteger end; + + @XmlAttribute(name = "primaryBegin") + protected BigInteger primaryBegin; + + @XmlAttribute(name = "primaryEnd") + protected BigInteger primaryEnd; + + @XmlAttribute(name = "accession", required = true) + protected String accession; + + @XmlAttribute(name = "version", required = true) + protected BigInteger version; + + @XmlAttribute(name = "complement") + protected Boolean complement; + + /** + * Gets the value of the begin property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getBegin() + { + return begin; + } + + /** + * Sets the value of the begin property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setBegin(BigInteger value) + { + this.begin = value; + } + + /** + * Gets the value of the end property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getEnd() + { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setEnd(BigInteger value) + { + this.end = value; + } + + /** + * Gets the value of the primaryBegin property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPrimaryBegin() + { + return primaryBegin; + } + + /** + * Sets the value of the primaryBegin property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setPrimaryBegin(BigInteger value) + { + this.primaryBegin = value; + } + + /** + * Gets the value of the primaryEnd property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPrimaryEnd() + { + return primaryEnd; + } + + /** + * Sets the value of the primaryEnd property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setPrimaryEnd(BigInteger value) + { + this.primaryEnd = value; + } + + /** + * Gets the value of the accession property. + * + * @return possible object is {@link String } + * + */ + public String getAccession() + { + return accession; + } + + /** + * Sets the value of the accession property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setAccession(String value) + { + this.accession = value; + } + + /** + * Gets the value of the version property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getVersion() + { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setVersion(BigInteger value) + { + this.version = value; + } + + /** + * Gets the value of the complement property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isComplement() + { + if (complement == null) + { + return false; } - return this.projectAccession; - } - - /** - * Gets the value of the description property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDescription() { - return description; - } - - /** - * Sets the value of the description property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDescription(String value) { - this.description = value; - } + else + { + return complement; + } + } + + /** + * Sets the value of the complement property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setComplement(Boolean value) + { + this.complement = value; + } - /** - * Gets the value of the comment property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getComment() { - return comment; } - /** - * Sets the value of the comment property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setComment(String value) { - this.comment = value; - } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <choice maxOccurs="unbounded" minOccurs="0">
+   *           <element name="range">
+   *             <complexType>
+   *               <complexContent>
+   *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                   <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 </restriction>
+   *               </complexContent>
+   *             </complexType>
+   *           </element>
+   *           <element name="gap">
+   *             <complexType>
+   *               <complexContent>
+   *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *                   <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 </restriction>
+   *               </complexContent>
+   *             </complexType>
+   *           </element>
+   *         </choice>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "rangeOrGap" }) + public static class Contig + { + + @XmlElements({ + @XmlElement(name = "range", type = EntryType.Contig.Range.class), + @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) }) + protected List rangeOrGap; /** - * Gets the value of the keyword property. + * Gets the value of the rangeOrGap property. * *

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

* For example, to add a new item, do as follows: - *

-     *    getKeyword().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: *

-     *    getReference().add(newItem);
+     * getRangeOrGap().add(newItem);
      * 
* * *

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

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

- * For example, to add a new item, do as follows: + * The following schema fragment specifies the expected content contained + * within this class. + * *

-     *    getXref().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
* * - *

- * Objects of the following type(s) are allowed in the list - * {@link XrefType } - * - * */ - public List getXref() { - if (xref == null) { - xref = new ArrayList(); + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Gap + { + + @XmlAttribute(name = "begin", required = true) + protected BigInteger begin; + + @XmlAttribute(name = "end", required = true) + protected BigInteger end; + + @XmlAttribute(name = "length", required = true) + protected BigInteger length; + + @XmlAttribute(name = "unknownLength") + protected Boolean unknownLength; + + /** + * Gets the value of the begin property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getBegin() + { + return begin; + } + + /** + * Sets the value of the begin property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setBegin(BigInteger value) + { + this.begin = value; + } + + /** + * Gets the value of the end property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getEnd() + { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setEnd(BigInteger value) + { + this.end = value; + } + + /** + * Gets the value of the length property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getLength() + { + return length; + } + + /** + * Sets the value of the length property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setLength(BigInteger value) + { + this.length = value; + } + + /** + * Gets the value of the unknownLength property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isUnknownLength() + { + if (unknownLength == null) + { + return false; + } + else + { + return unknownLength; } - return this.xref; + } + + /** + * Sets the value of the unknownLength property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setUnknownLength(Boolean value) + { + this.unknownLength = value; + } + } /** - * Gets the value of the feature property. - * *

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

- * For example, to add a new item, do as follows: + * The following schema fragment specifies the expected content contained + * within this class. + * *

-     *    getFeature().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
* * - *

- * Objects of the following type(s) are allowed in the list - * {@link EntryType.Feature } - * - * */ - public List getFeature() { - if (feature == null) { - feature = new ArrayList(); + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Range + { + + @XmlAttribute(name = "begin", required = true) + protected BigInteger begin; + + @XmlAttribute(name = "end", required = true) + protected BigInteger end; + + @XmlAttribute(name = "primaryBegin") + protected BigInteger primaryBegin; + + @XmlAttribute(name = "primaryEnd") + protected BigInteger primaryEnd; + + @XmlAttribute(name = "accession", required = true) + protected String accession; + + @XmlAttribute(name = "version", required = true) + protected BigInteger version; + + @XmlAttribute(name = "complement") + protected Boolean complement; + + /** + * Gets the value of the begin property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getBegin() + { + return begin; + } + + /** + * Sets the value of the begin property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setBegin(BigInteger value) + { + this.begin = value; + } + + /** + * Gets the value of the end property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getEnd() + { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setEnd(BigInteger value) + { + this.end = value; + } + + /** + * Gets the value of the primaryBegin property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPrimaryBegin() + { + return primaryBegin; + } + + /** + * Sets the value of the primaryBegin property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setPrimaryBegin(BigInteger value) + { + this.primaryBegin = value; + } + + /** + * Gets the value of the primaryEnd property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPrimaryEnd() + { + return primaryEnd; + } + + /** + * Sets the value of the primaryEnd property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setPrimaryEnd(BigInteger value) + { + this.primaryEnd = value; + } + + /** + * Gets the value of the accession property. + * + * @return possible object is {@link String } + * + */ + public String getAccession() + { + return accession; + } + + /** + * Sets the value of the accession property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setAccession(String value) + { + this.accession = value; + } + + /** + * Gets the value of the version property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getVersion() + { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setVersion(BigInteger value) + { + this.version = value; + } + + /** + * Gets the value of the complement property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isComplement() + { + if (complement == null) + { + return false; } - return this.feature; - } + else + { + return complement; + } + } + + /** + * Sets the value of the complement property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setComplement(Boolean value) + { + this.complement = value; + } - /** - * Gets the value of the assembly property. - * - * @return - * possible object is - * {@link EntryType.Assembly } - * - */ - public EntryType.Assembly getAssembly() { - return assembly; } - /** - * Sets the value of the assembly property. - * - * @param value - * allowed object is - * {@link EntryType.Assembly } - * - */ - public void setAssembly(EntryType.Assembly value) { - this.assembly = value; - } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="taxon" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="lineage" minOccurs="0">
+   *                     <complexType>
+   *                       <complexContent>
+   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                           <sequence>
+   *                             <element name="taxon" maxOccurs="unbounded">
+   *                               <complexType>
+   *                                 <complexContent>
+   *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                                     <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                                   </restriction>
+   *                                 </complexContent>
+   *                               </complexType>
+   *                             </element>
+   *                           </sequence>
+   *                         </restriction>
+   *                       </complexContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *                 </sequence>
+   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "taxon", "xref", "qualifier" }) + public static class Feature + { + + protected EntryType.Feature.FeatureTaxon taxon; - /** - * Gets the value of the contig property. - * - * @return - * possible object is - * {@link EntryType.Contig } - * - */ - public EntryType.Contig getContig() { - return contig; - } + protected List xref; - /** - * Sets the value of the contig property. - * - * @param value - * allowed object is - * {@link EntryType.Contig } - * - */ - public void setContig(EntryType.Contig value) { - this.contig = value; - } + protected List qualifier; - /** - * Gets the value of the sequence property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getSequence() { - return sequence; - } + @XmlAttribute(name = "name", required = true) + protected String name; - /** - * Sets the value of the sequence property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setSequence(String value) { - this.sequence = value; - } + @XmlAttribute(name = "location", required = true) + protected String location; /** - * Gets the value of the accession property. + * Gets the value of the taxon property. + * + * @return possible object is {@link EntryType.Feature.FeatureTaxon } * - * @return - * possible object is - * {@link String } - * */ - public String getAccession() { - return accession; + public EntryType.Feature.FeatureTaxon getTaxon() + { + return taxon; } /** - * Sets the value of the accession property. + * Sets the value of the taxon property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setAccession(String value) { - this.accession = value; - } - - /** - * Gets the value of the version property. + * allowed object is {@link EntryType.Feature.FeatureTaxon } * - * @return - * possible object is - * {@link BigInteger } - * */ - public BigInteger getVersion() { - return version; + public void setTaxon(EntryType.Feature.FeatureTaxon value) + { + this.taxon = value; } /** - * Sets the value of the version property. + * Gets the value of the xref property. * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setVersion(BigInteger value) { - this.version = value; - } - - /** - * Gets the value of the entryVersion property. + *

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

+ * For example, to add a new item, do as follows: * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setEntryVersion(BigInteger value) { - this.entryVersion = value; - } - - /** - * Gets the value of the dataClass property. + *

+     * getXref().add(newItem);
+     * 
* - * @return - * possible object is - * {@link String } - * - */ - public String getDataClass() { - return dataClass; - } - - /** - * Sets the value of the dataClass property. * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDataClass(String value) { - this.dataClass = value; - } - - /** - * Gets the value of the taxonomicDivision property. + *

+ * Objects of the following type(s) are allowed in the list {@link XrefType + * } * - * @return - * possible object is - * {@link String } - * - */ - public String getTaxonomicDivision() { - return taxonomicDivision; - } - - /** - * Sets the value of the taxonomicDivision property. * - * @param value - * allowed object is - * {@link String } - * */ - public void setTaxonomicDivision(String value) { - this.taxonomicDivision = value; + public List getXref() + { + if (xref == null) + { + xref = new ArrayList(); + } + return this.xref; } /** - * Gets the value of the moleculeType property. + * Gets the value of the qualifier property. * - * @return - * possible object is - * {@link String } - * - */ - public String getMoleculeType() { - return moleculeType; - } - - /** - * Sets the value of the moleculeType property. + *

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

+ * For example, to add a new item, do as follows: * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getSequenceLength() { - return sequenceLength; - } - - /** - * Sets the value of the sequenceLength property. + *

+     * getQualifier().add(newItem);
+     * 
* - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setSequenceLength(BigInteger value) { - this.sequenceLength = value; - } - - /** - * Gets the value of the topology property. * - * @return - * possible object is - * {@link String } - * - */ - public String getTopology() { - return topology; - } - - /** - * Sets the value of the topology property. + *

+ * Objects of the following type(s) are allowed in the list + * {@link EntryType.Feature.Qualifier } * - * @param value - * allowed object is - * {@link String } - * - */ - public void setTopology(String value) { - this.topology = value; - } - - /** - * Gets the value of the firstPublic property. * - * @return - * possible object is - * {@link XMLGregorianCalendar } - * */ - public XMLGregorianCalendar getFirstPublic() { - return firstPublic; + public List getQualifier() + { + if (qualifier == null) + { + qualifier = new ArrayList(); + } + return this.qualifier; } /** - * Sets the value of the firstPublic property. + * Gets the value of the name property. * - * @param value - * allowed object is - * {@link XMLGregorianCalendar } - * - */ - public void setFirstPublic(XMLGregorianCalendar value) { - this.firstPublic = value; - } - - /** - * Gets the value of the firstPublicRelease property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link BigInteger } - * */ - public BigInteger getFirstPublicRelease() { - return firstPublicRelease; + public String getName() + { + return name; } /** - * Sets the value of the firstPublicRelease property. + * Sets the value of the name property. * * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setFirstPublicRelease(BigInteger value) { - this.firstPublicRelease = value; - } - - /** - * Gets the value of the lastUpdated property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link XMLGregorianCalendar } - * */ - public XMLGregorianCalendar getLastUpdated() { - return lastUpdated; + public void setName(String value) + { + this.name = value; } /** - * Sets the value of the lastUpdated property. + * Gets the value of the location property. * - * @param value - * allowed object is - * {@link XMLGregorianCalendar } - * - */ - public void setLastUpdated(XMLGregorianCalendar value) { - this.lastUpdated = value; - } - - /** - * Gets the value of the lastUpdatedRelease property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link BigInteger } - * */ - public BigInteger getLastUpdatedRelease() { - return lastUpdatedRelease; + public String getLocation() + { + return location; } /** - * Sets the value of the lastUpdatedRelease property. + * Sets the value of the location property. * * @param value - * allowed object is - * {@link BigInteger } - * + * allowed object is {@link String } + * */ - public void setLastUpdatedRelease(BigInteger value) { - this.lastUpdatedRelease = value; + public void setLocation(String value) + { + this.location = value; } - /** - *

Java class for anonymous complex type. + *

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

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

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

      * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       <sequence>
-     *         <element name="range" maxOccurs="unbounded">
+     *         <element name="lineage" minOccurs="0">
      *           <complexType>
      *             <complexContent>
      *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                 <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <sequence>
+     *                   <element name="taxon" maxOccurs="unbounded">
+     *                     <complexType>
+     *                       <complexContent>
+     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </restriction>
+     *                       </complexContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
      *               </restriction>
      *             </complexContent>
      *           </complexType>
      *         </element>
      *       </sequence>
+     *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -896,366 +1894,198 @@ public class EntryType {
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "range"
-    })
-    public static class Assembly {
+    @XmlType(name = "", propOrder = { "lineage" })
+    public static class FeatureTaxon
+    {
+
+      protected EntryType.Feature.FeatureTaxon.Lineage lineage;
+
+      @XmlAttribute(name = "scientificName", required = true)
+      protected String scientificName;
+
+      @XmlAttribute(name = "commonName")
+      protected String commonName;
+
+      @XmlAttribute(name = "taxId")
+      protected BigInteger taxId;
+
+      /**
+       * Gets the value of the lineage property.
+       * 
+       * @return possible object is
+       *         {@link EntryType.Feature.FeatureTaxon.Lineage }
+       * 
+       */
+      public EntryType.Feature.FeatureTaxon.Lineage getLineage()
+      {
+        return lineage;
+      }
+
+      /**
+       * Sets the value of the lineage property.
+       * 
+       * @param value
+       *          allowed object is
+       *          {@link EntryType.Feature.FeatureTaxon.Lineage }
+       * 
+       */
+      public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value)
+      {
+        this.lineage = value;
+      }
+
+      /**
+       * Gets the value of the scientificName property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getScientificName()
+      {
+        return scientificName;
+      }
+
+      /**
+       * Sets the value of the scientificName property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setScientificName(String value)
+      {
+        this.scientificName = value;
+      }
+
+      /**
+       * Gets the value of the commonName property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getCommonName()
+      {
+        return commonName;
+      }
+
+      /**
+       * Sets the value of the commonName property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setCommonName(String value)
+      {
+        this.commonName = value;
+      }
+
+      /**
+       * Gets the value of the taxId property.
+       * 
+       * @return possible object is {@link BigInteger }
+       * 
+       */
+      public BigInteger getTaxId()
+      {
+        return taxId;
+      }
+
+      /**
+       * Sets the value of the taxId property.
+       * 
+       * @param value
+       *          allowed object is {@link BigInteger }
+       * 
+       */
+      public void setTaxId(BigInteger value)
+      {
+        this.taxId = value;
+      }
+
+      /**
+       * 

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

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

+       * <complexType>
+       *   <complexContent>
+       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       <sequence>
+       *         <element name="taxon" maxOccurs="unbounded">
+       *           <complexType>
+       *             <complexContent>
+       *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *               </restriction>
+       *             </complexContent>
+       *           </complexType>
+       *         </element>
+       *       </sequence>
+       *     </restriction>
+       *   </complexContent>
+       * </complexType>
+       * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "taxon" }) + public static class Lineage + { @XmlElement(required = true) - protected List range; + protected List taxon; /** - * Gets the value of the range property. + * Gets the value of the taxon property. * *

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

* For example, to add a new item, do as follows: + * *

-         *    getRange().add(newItem);
+         * getTaxon().add(newItem);
          * 
* * *

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

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
+ * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon } * * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Range { - - @XmlAttribute(name = "begin", required = true) - protected BigInteger begin; - @XmlAttribute(name = "end", required = true) - protected BigInteger end; - @XmlAttribute(name = "primaryBegin") - protected BigInteger primaryBegin; - @XmlAttribute(name = "primaryEnd") - protected BigInteger primaryEnd; - @XmlAttribute(name = "accession", required = true) - protected String accession; - @XmlAttribute(name = "version", required = true) - protected BigInteger version; - @XmlAttribute(name = "complement") - protected Boolean complement; - - /** - * Gets the value of the begin property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getBegin() { - return begin; - } - - /** - * Sets the value of the begin property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setBegin(BigInteger value) { - this.begin = value; - } - - /** - * Gets the value of the end property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getEnd() { - return end; - } - - /** - * Sets the value of the end property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setEnd(BigInteger value) { - this.end = value; - } - - /** - * Gets the value of the primaryBegin property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPrimaryBegin() { - return primaryBegin; - } - - /** - * Sets the value of the primaryBegin property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPrimaryBegin(BigInteger value) { - this.primaryBegin = value; - } - - /** - * Gets the value of the primaryEnd property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPrimaryEnd() { - return primaryEnd; - } - - /** - * Sets the value of the primaryEnd property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPrimaryEnd(BigInteger value) { - this.primaryEnd = value; - } - - /** - * Gets the value of the accession property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getAccession() { - return accession; - } - - /** - * Sets the value of the accession property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setAccession(String value) { - this.accession = value; - } - - /** - * Gets the value of the version property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getVersion() { - return version; - } - - /** - * Sets the value of the version property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setVersion(BigInteger value) { - this.version = value; - } - - /** - * Gets the value of the complement property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isComplement() { - if (complement == null) { - return false; - } else { - return complement; - } - } - - /** - * Sets the value of the complement property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setComplement(Boolean value) { - this.complement = value; - } - + public List getTaxon() + { + if (taxon == null) + { + taxon = new ArrayList(); + } + return this.taxon; } - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <choice maxOccurs="unbounded" minOccurs="0">
-     *           <element name="range">
-     *             <complexType>
-     *               <complexContent>
-     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                   <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 </restriction>
-     *               </complexContent>
-     *             </complexType>
-     *           </element>
-     *           <element name="gap">
-     *             <complexType>
-     *               <complexContent>
-     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *                   <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 </restriction>
-     *               </complexContent>
-     *             </complexType>
-     *           </element>
-     *         </choice>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "rangeOrGap" - }) - public static class Contig { - - @XmlElements({ - @XmlElement(name = "range", type = EntryType.Contig.Range.class), - @XmlElement(name = "gap", type = EntryType.Contig.Gap.class) - }) - protected List rangeOrGap; - /** - * Gets the value of the rangeOrGap property. - * *

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

- * For example, to add a new item, do as follows: - *

-         *    getRangeOrGap().add(newItem);
-         * 
- * - * - *

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

Java class for anonymous complex type. - * - *

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

          * <complexType>
          *   <complexContent>
          *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
          *     </restriction>
          *   </complexContent>
          * </complexType>
@@ -1265,397 +2095,57 @@ public class EntryType {
          */
         @XmlAccessorType(XmlAccessType.FIELD)
         @XmlType(name = "")
-        public static class Gap {
-
-            @XmlAttribute(name = "begin", required = true)
-            protected BigInteger begin;
-            @XmlAttribute(name = "end", required = true)
-            protected BigInteger end;
-            @XmlAttribute(name = "length", required = true)
-            protected BigInteger length;
-            @XmlAttribute(name = "unknownLength")
-            protected Boolean unknownLength;
-
-            /**
-             * Gets the value of the begin property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getBegin() {
-                return begin;
-            }
-
-            /**
-             * Sets the value of the begin property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setBegin(BigInteger value) {
-                this.begin = value;
-            }
-
-            /**
-             * Gets the value of the end property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getEnd() {
-                return end;
-            }
-
-            /**
-             * Sets the value of the end property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setEnd(BigInteger value) {
-                this.end = value;
-            }
-
-            /**
-             * Gets the value of the length property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link BigInteger }
-             *     
-             */
-            public BigInteger getLength() {
-                return length;
-            }
-
-            /**
-             * Sets the value of the length property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link BigInteger }
-             *     
-             */
-            public void setLength(BigInteger value) {
-                this.length = value;
-            }
-
-            /**
-             * Gets the value of the unknownLength property.
-             * 
-             * @return
-             *     possible object is
-             *     {@link Boolean }
-             *     
-             */
-            public boolean isUnknownLength() {
-                if (unknownLength == null) {
-                    return false;
-                } else {
-                    return unknownLength;
-                }
-            }
-
-            /**
-             * Sets the value of the unknownLength property.
-             * 
-             * @param value
-             *     allowed object is
-             *     {@link Boolean }
-             *     
-             */
-            public void setUnknownLength(Boolean value) {
-                this.unknownLength = value;
-            }
+        public static class Taxon
+        {
+
+          @XmlAttribute(name = "scientificName", required = true)
+          protected String scientificName;
+
+          /**
+           * Gets the value of the scientificName property.
+           * 
+           * @return possible object is {@link String }
+           * 
+           */
+          public String getScientificName()
+          {
+            return scientificName;
+          }
+
+          /**
+           * Sets the value of the scientificName property.
+           * 
+           * @param value
+           *          allowed object is {@link String }
+           * 
+           */
+          public void setScientificName(String value)
+          {
+            this.scientificName = value;
+          }
 
         }
 
-
-        /**
-         * 

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Range { - - @XmlAttribute(name = "begin", required = true) - protected BigInteger begin; - @XmlAttribute(name = "end", required = true) - protected BigInteger end; - @XmlAttribute(name = "primaryBegin") - protected BigInteger primaryBegin; - @XmlAttribute(name = "primaryEnd") - protected BigInteger primaryEnd; - @XmlAttribute(name = "accession", required = true) - protected String accession; - @XmlAttribute(name = "version", required = true) - protected BigInteger version; - @XmlAttribute(name = "complement") - protected Boolean complement; - - /** - * Gets the value of the begin property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getBegin() { - return begin; - } - - /** - * Sets the value of the begin property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setBegin(BigInteger value) { - this.begin = value; - } - - /** - * Gets the value of the end property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getEnd() { - return end; - } - - /** - * Sets the value of the end property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setEnd(BigInteger value) { - this.end = value; - } - - /** - * Gets the value of the primaryBegin property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPrimaryBegin() { - return primaryBegin; - } - - /** - * Sets the value of the primaryBegin property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPrimaryBegin(BigInteger value) { - this.primaryBegin = value; - } - - /** - * Gets the value of the primaryEnd property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPrimaryEnd() { - return primaryEnd; - } - - /** - * Sets the value of the primaryEnd property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPrimaryEnd(BigInteger value) { - this.primaryEnd = value; - } - - /** - * Gets the value of the accession property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getAccession() { - return accession; - } - - /** - * Sets the value of the accession property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setAccession(String value) { - this.accession = value; - } - - /** - * Gets the value of the version property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getVersion() { - return version; - } - - /** - * Sets the value of the version property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setVersion(BigInteger value) { - this.version = value; - } - - /** - * Gets the value of the complement property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isComplement() { - if (complement == null) { - return false; - } else { - return complement; - } - } - - /** - * Sets the value of the complement property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setComplement(Boolean value) { - this.complement = value; - } - - } + } } - /** - *

Java class for anonymous complex type. + *

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

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

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

      * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       <sequence>
-     *         <element name="taxon" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="lineage" minOccurs="0">
-     *                     <complexType>
-     *                       <complexContent>
-     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           <sequence>
-     *                             <element name="taxon" maxOccurs="unbounded">
-     *                               <complexType>
-     *                                 <complexContent>
-     *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                                     <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                                   </restriction>
-     *                                 </complexContent>
-     *                               </complexType>
-     *                             </element>
-     *                           </sequence>
-     *                         </restriction>
-     *                       </complexContent>
-     *                     </complexType>
-     *                   </element>
-     *                 </sequence>
-     *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-     *                 </sequence>
-     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
+     *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
      *       </sequence>
      *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -1664,1017 +2154,578 @@ public class EntryType {
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "taxon",
-        "xref",
-        "qualifier"
-    })
-    public static class Feature {
-
-        protected EntryType.Feature.FeatureTaxon taxon;
-        protected List xref;
-        protected List qualifier;
-        @XmlAttribute(name = "name", required = true)
-        protected String name;
-        @XmlAttribute(name = "location", required = true)
-        protected String location;
+    @XmlType(name = "", propOrder = { "value" })
+    public static class Qualifier
+    {
+
+      protected String value;
+
+      @XmlAttribute(name = "name", required = true)
+      protected String name;
+
+      /**
+       * Gets the value of the value property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getValue()
+      {
+        return value;
+      }
+
+      /**
+       * Sets the value of the value property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setValue(String value)
+      {
+        this.value = value;
+      }
+
+      /**
+       * Gets the value of the name property.
+       * 
+       * @return possible object is {@link String }
+       * 
+       */
+      public String getName()
+      {
+        return name;
+      }
+
+      /**
+       * Sets the value of the name property.
+       * 
+       * @param value
+       *          allowed object is {@link String }
+       * 
+       */
+      public void setName(String value)
+      {
+        this.name = value;
+      }
 
-        /**
-         * Gets the value of the taxon property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link EntryType.Feature.FeatureTaxon }
-         *     
-         */
-        public EntryType.Feature.FeatureTaxon getTaxon() {
-            return taxon;
-        }
+    }
 
-        /**
-         * Sets the value of the taxon property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link EntryType.Feature.FeatureTaxon }
-         *     
-         */
-        public void setTaxon(EntryType.Feature.FeatureTaxon value) {
-            this.taxon = value;
-        }
+  }
+
+  /**
+   * 

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
+   *         <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+   *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="type" use="required">
+   *         <simpleType>
+   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             <enumeration value="submission"/>
+   *             <enumeration value="book"/>
+   *             <enumeration value="article"/>
+   *             <enumeration value="patent"/>
+   *             <enumeration value="thesis"/>
+   *             <enumeration value="unpublished"/>
+   *           </restriction>
+   *         </simpleType>
+   *       </attribute>
+   *       <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "title", "author", "applicant", "consortium", "submissionDate", + "journal", "year", "volume", "issue", "firstPage", "lastPage", + "comment", "referenceLocation", "xref" }) + public static class Reference + { + + protected String title; + + protected List author; + + protected List applicant; + + protected String consortium; - /** - * Gets the value of the xref property. - * - *

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

- * For example, to add a new item, do as follows: - *

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

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

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

- * For example, to add a new item, do as follows: - *

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

- * Objects of the following type(s) are allowed in the list - * {@link EntryType.Feature.Qualifier } - * - * - */ - public List getQualifier() { - if (qualifier == null) { - qualifier = new ArrayList(); - } - return this.qualifier; - } + protected String journal; - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } + protected String year; - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } + protected String volume; - /** - * Gets the value of the location property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getLocation() { - return location; - } + protected String issue; - /** - * Sets the value of the location property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setLocation(String value) { - this.location = value; - } + protected String firstPage; + protected String lastPage; - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="lineage" minOccurs="0">
-         *           <complexType>
-         *             <complexContent>
-         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 <sequence>
-         *                   <element name="taxon" maxOccurs="unbounded">
-         *                     <complexType>
-         *                       <complexContent>
-         *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                         </restriction>
-         *                       </complexContent>
-         *                     </complexType>
-         *                   </element>
-         *                 </sequence>
-         *               </restriction>
-         *             </complexContent>
-         *           </complexType>
-         *         </element>
-         *       </sequence>
-         *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "lineage" - }) - public static class FeatureTaxon { - - protected EntryType.Feature.FeatureTaxon.Lineage lineage; - @XmlAttribute(name = "scientificName", required = true) - protected String scientificName; - @XmlAttribute(name = "commonName") - protected String commonName; - @XmlAttribute(name = "taxId") - protected BigInteger taxId; - - /** - * Gets the value of the lineage property. - * - * @return - * possible object is - * {@link EntryType.Feature.FeatureTaxon.Lineage } - * - */ - public EntryType.Feature.FeatureTaxon.Lineage getLineage() { - return lineage; - } - - /** - * Sets the value of the lineage property. - * - * @param value - * allowed object is - * {@link EntryType.Feature.FeatureTaxon.Lineage } - * - */ - public void setLineage(EntryType.Feature.FeatureTaxon.Lineage value) { - this.lineage = value; - } - - /** - * Gets the value of the scientificName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getScientificName() { - return scientificName; - } - - /** - * Sets the value of the scientificName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setScientificName(String value) { - this.scientificName = value; - } - - /** - * Gets the value of the commonName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getCommonName() { - return commonName; - } - - /** - * Sets the value of the commonName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setCommonName(String value) { - this.commonName = value; - } - - /** - * Gets the value of the taxId property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getTaxId() { - return taxId; - } - - /** - * Sets the value of the taxId property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setTaxId(BigInteger value) { - this.taxId = value; - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-             * <complexType>
-             *   <complexContent>
-             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       <sequence>
-             *         <element name="taxon" maxOccurs="unbounded">
-             *           <complexType>
-             *             <complexContent>
-             *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *               </restriction>
-             *             </complexContent>
-             *           </complexType>
-             *         </element>
-             *       </sequence>
-             *     </restriction>
-             *   </complexContent>
-             * </complexType>
-             * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "taxon" - }) - public static class Lineage { - - @XmlElement(required = true) - protected List taxon; - - /** - * Gets the value of the taxon property. - * - *

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

- * For example, to add a new item, do as follows: - *

-                 *    getTaxon().add(newItem);
-                 * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon } - * - * - */ - public List getTaxon() { - if (taxon == null) { - taxon = new ArrayList(); - } - return this.taxon; - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-                 * <complexType>
-                 *   <complexContent>
-                 *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-                 *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-                 *     </restriction>
-                 *   </complexContent>
-                 * </complexType>
-                 * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Taxon { - - @XmlAttribute(name = "scientificName", required = true) - protected String scientificName; - - /** - * Gets the value of the scientificName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getScientificName() { - return scientificName; - } - - /** - * Sets the value of the scientificName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setScientificName(String value) { - this.scientificName = value; - } - - } - - } + protected String comment; - } + protected String referenceLocation; + protected List xref; - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-         *       </sequence>
-         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "value" - }) - public static class Qualifier { - - protected String value; - @XmlAttribute(name = "name", required = true) - protected String name; - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } + @XmlAttribute(name = "type", required = true) + protected String type; - } + @XmlAttribute(name = "number", required = true) + protected BigInteger number; + + @XmlAttribute(name = "location") + protected String location; + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; } + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } /** - *

Java class for anonymous complex type. + * Gets the value of the author property. * - *

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

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

+ * For example, to add a new item, do as follows: * *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "title", - "author", - "applicant", - "consortium", - "submissionDate", - "journal", - "year", - "volume", - "issue", - "firstPage", - "lastPage", - "comment", - "referenceLocation", - "xref" - }) - public static class Reference { - - protected String title; - protected List author; - protected List applicant; - protected String consortium; - @XmlSchemaType(name = "date") - protected XMLGregorianCalendar submissionDate; - protected String journal; - protected String year; - protected String volume; - protected String issue; - protected String firstPage; - protected String lastPage; - protected String comment; - protected String referenceLocation; - protected List xref; - @XmlAttribute(name = "type", required = true) - protected String type; - @XmlAttribute(name = "number", required = true) - protected BigInteger number; - @XmlAttribute(name = "location") - protected String location; - - /** - * Gets the value of the title property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTitle() { - return title; - } - - /** - * Sets the value of the title property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setTitle(String value) { - this.title = value; - } + public List getAuthor() + { + if (author == null) + { + author = new ArrayList(); + } + return this.author; + } - /** - * Gets the value of the author property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getAuthor().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getApplicant().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getApplicant() { - if (applicant == null) { - applicant = new ArrayList(); - } - return this.applicant; - } - - /** - * Gets the value of the consortium property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getConsortium() { - return consortium; - } + /** + * Gets the value of the applicant property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getApplicant() + { + if (applicant == null) + { + applicant = new ArrayList(); + } + return this.applicant; + } - /** - * Sets the value of the consortium property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setConsortium(String value) { - this.consortium = value; - } + /** + * Gets the value of the consortium property. + * + * @return possible object is {@link String } + * + */ + public String getConsortium() + { + return consortium; + } - /** - * Gets the value of the submissionDate property. - * - * @return - * possible object is - * {@link XMLGregorianCalendar } - * - */ - public XMLGregorianCalendar getSubmissionDate() { - return submissionDate; - } + /** + * Sets the value of the consortium property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setConsortium(String value) + { + this.consortium = value; + } - /** - * Sets the value of the submissionDate property. - * - * @param value - * allowed object is - * {@link XMLGregorianCalendar } - * - */ - public void setSubmissionDate(XMLGregorianCalendar value) { - this.submissionDate = value; - } + /** + * Gets the value of the submissionDate property. + * + * @return possible object is {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getSubmissionDate() + { + return submissionDate; + } - /** - * Gets the value of the journal property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getJournal() { - return journal; - } + /** + * Sets the value of the submissionDate property. + * + * @param value + * allowed object is {@link XMLGregorianCalendar } + * + */ + public void setSubmissionDate(XMLGregorianCalendar value) + { + this.submissionDate = value; + } - /** - * Sets the value of the journal property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setJournal(String value) { - this.journal = value; - } + /** + * Gets the value of the journal property. + * + * @return possible object is {@link String } + * + */ + public String getJournal() + { + return journal; + } - /** - * Gets the value of the year property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getYear() { - return year; - } + /** + * Sets the value of the journal property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setJournal(String value) + { + this.journal = value; + } - /** - * Sets the value of the year property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setYear(String value) { - this.year = value; - } + /** + * Gets the value of the year property. + * + * @return possible object is {@link String } + * + */ + public String getYear() + { + return year; + } - /** - * Gets the value of the volume property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getVolume() { - return volume; - } + /** + * Sets the value of the year property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setYear(String value) + { + this.year = value; + } - /** - * Sets the value of the volume property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setVolume(String value) { - this.volume = value; - } + /** + * Gets the value of the volume property. + * + * @return possible object is {@link String } + * + */ + public String getVolume() + { + return volume; + } - /** - * Gets the value of the issue property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getIssue() { - return issue; - } + /** + * Sets the value of the volume property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setVolume(String value) + { + this.volume = value; + } - /** - * Sets the value of the issue property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setIssue(String value) { - this.issue = value; - } + /** + * Gets the value of the issue property. + * + * @return possible object is {@link String } + * + */ + public String getIssue() + { + return issue; + } - /** - * Gets the value of the firstPage property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getFirstPage() { - return firstPage; - } + /** + * Sets the value of the issue property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setIssue(String value) + { + this.issue = value; + } - /** - * Sets the value of the firstPage property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setFirstPage(String value) { - this.firstPage = value; - } + /** + * Gets the value of the firstPage property. + * + * @return possible object is {@link String } + * + */ + public String getFirstPage() + { + return firstPage; + } - /** - * Gets the value of the lastPage property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getLastPage() { - return lastPage; - } + /** + * Sets the value of the firstPage property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setFirstPage(String value) + { + this.firstPage = value; + } - /** - * Sets the value of the lastPage property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setLastPage(String value) { - this.lastPage = value; - } + /** + * Gets the value of the lastPage property. + * + * @return possible object is {@link String } + * + */ + public String getLastPage() + { + return lastPage; + } - /** - * Gets the value of the comment property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getComment() { - return comment; - } + /** + * Sets the value of the lastPage property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setLastPage(String value) + { + this.lastPage = value; + } - /** - * Sets the value of the comment property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setComment(String value) { - this.comment = value; - } + /** + * Gets the value of the comment property. + * + * @return possible object is {@link String } + * + */ + public String getComment() + { + return comment; + } - /** - * Gets the value of the referenceLocation property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getReferenceLocation() { - return referenceLocation; - } + /** + * Sets the value of the comment property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setComment(String value) + { + this.comment = value; + } - /** - * Sets the value of the referenceLocation property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setReferenceLocation(String value) { - this.referenceLocation = value; - } + /** + * Gets the value of the referenceLocation property. + * + * @return possible object is {@link String } + * + */ + public String getReferenceLocation() + { + return referenceLocation; + } - /** - * Gets the value of the xref property. - * - *

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

- * For example, to add a new item, do as follows: - *

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

- * Objects of the following type(s) are allowed in the list - * {@link XrefType } - * - * - */ - public List getXref() { - if (xref == null) { - xref = new ArrayList(); - } - return this.xref; - } + /** + * Sets the value of the referenceLocation property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setReferenceLocation(String value) + { + this.referenceLocation = value; + } - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } + /** + * Gets the value of the xref property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link XrefType + * } + * + * + */ + public List getXref() + { + if (xref == null) + { + xref = new ArrayList(); + } + return this.xref; + } - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } - /** - * Gets the value of the number property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getNumber() { - return number; - } + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } - /** - * Sets the value of the number property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setNumber(BigInteger value) { - this.number = value; - } + /** + * Gets the value of the number property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getNumber() + { + return number; + } - /** - * Gets the value of the location property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getLocation() { - return location; - } + /** + * Sets the value of the number property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setNumber(BigInteger value) + { + this.number = value; + } - /** - * Sets the value of the location property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setLocation(String value) { - this.location = value; - } + /** + * Gets the value of the location property. + * + * @return possible object is {@link String } + * + */ + public String getLocation() + { + return location; + } + /** + * Sets the value of the location property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setLocation(String value) + { + this.location = value; } + } + } diff --git a/src/jalview/xml/binding/embl/ObjectFactory.java b/src/jalview/xml/binding/embl/ObjectFactory.java index e1a917a..2fef24a 100644 --- a/src/jalview/xml/binding/embl/ObjectFactory.java +++ b/src/jalview/xml/binding/embl/ObjectFactory.java @@ -5,155 +5,167 @@ // Generated on: 2023.03.17 at 05:31:45 PM GMT // - package jalview.xml.binding.embl; import javax.xml.bind.annotation.XmlRegistry; - /** - * This object contains factory methods for each - * Java content interface and Java element interface - * generated in the jalview.xml.binding.embl package. - *

An ObjectFactory allows you to programatically - * construct new instances of the Java representation - * for XML content. The Java representation of XML - * content can consist of schema derived interfaces - * and classes representing the binding of schema - * type definitions, element declarations and model - * groups. Factory methods for each of these are - * provided in this class. + * This object contains factory methods for each Java content interface and Java + * element interface generated in the jalview.xml.binding.embl package. + *

+ * An ObjectFactory allows you to programatically construct new instances of the + * Java representation for XML content. The Java representation of XML content + * can consist of schema derived interfaces and classes representing the binding + * of schema type definitions, element declarations and model groups. Factory + * methods for each of these are provided in this class. * */ @XmlRegistry -public class ObjectFactory { - - - /** - * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.embl - * - */ - public ObjectFactory() { - } - - /** - * Create an instance of {@link EntryType } - * - */ - public EntryType createEntryType() { - return new EntryType(); - } - - /** - * Create an instance of {@link EntryType.Contig } - * - */ - public EntryType.Contig createEntryTypeContig() { - return new EntryType.Contig(); - } - - /** - * Create an instance of {@link EntryType.Assembly } - * - */ - public EntryType.Assembly createEntryTypeAssembly() { - return new EntryType.Assembly(); - } - - /** - * Create an instance of {@link EntryType.Feature } - * - */ - public EntryType.Feature createEntryTypeFeature() { - return new EntryType.Feature(); - } - - /** - * Create an instance of {@link EntryType.Feature.FeatureTaxon } - * - */ - public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() { - return new EntryType.Feature.FeatureTaxon(); - } - - /** - * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage } - * - */ - public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() { - return new EntryType.Feature.FeatureTaxon.Lineage(); - } - - /** - * Create an instance of {@link ROOT } - * - */ - public ROOT createROOT() { - return new ROOT(); - } - - /** - * Create an instance of {@link EntrySetType } - * - */ - public EntrySetType createEntrySetType() { - return new EntrySetType(); - } - - /** - * Create an instance of {@link XrefType } - * - */ - public XrefType createXrefType() { - return new XrefType(); - } - - /** - * Create an instance of {@link EntryType.Reference } - * - */ - public EntryType.Reference createEntryTypeReference() { - return new EntryType.Reference(); - } - - /** - * Create an instance of {@link EntryType.Contig.Range } - * - */ - public EntryType.Contig.Range createEntryTypeContigRange() { - return new EntryType.Contig.Range(); - } - - /** - * Create an instance of {@link EntryType.Contig.Gap } - * - */ - public EntryType.Contig.Gap createEntryTypeContigGap() { - return new EntryType.Contig.Gap(); - } - - /** - * Create an instance of {@link EntryType.Assembly.Range } - * - */ - public EntryType.Assembly.Range createEntryTypeAssemblyRange() { - return new EntryType.Assembly.Range(); - } - - /** - * Create an instance of {@link EntryType.Feature.Qualifier } - * - */ - public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() { - return new EntryType.Feature.Qualifier(); - } - - /** - * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon } - * - */ - public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() { - return new EntryType.Feature.FeatureTaxon.Lineage.Taxon(); - } +public class ObjectFactory +{ + + /** + * Create a new ObjectFactory that can be used to create new instances of + * schema derived classes for package: jalview.xml.binding.embl + * + */ + public ObjectFactory() + { + } + + /** + * Create an instance of {@link EntryType } + * + */ + public EntryType createEntryType() + { + return new EntryType(); + } + + /** + * Create an instance of {@link EntryType.Contig } + * + */ + public EntryType.Contig createEntryTypeContig() + { + return new EntryType.Contig(); + } + + /** + * Create an instance of {@link EntryType.Assembly } + * + */ + public EntryType.Assembly createEntryTypeAssembly() + { + return new EntryType.Assembly(); + } + + /** + * Create an instance of {@link EntryType.Feature } + * + */ + public EntryType.Feature createEntryTypeFeature() + { + return new EntryType.Feature(); + } + + /** + * Create an instance of {@link EntryType.Feature.FeatureTaxon } + * + */ + public EntryType.Feature.FeatureTaxon createEntryTypeFeatureFeatureTaxon() + { + return new EntryType.Feature.FeatureTaxon(); + } + + /** + * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage } + * + */ + public EntryType.Feature.FeatureTaxon.Lineage createEntryTypeFeatureFeatureTaxonLineage() + { + return new EntryType.Feature.FeatureTaxon.Lineage(); + } + + /** + * Create an instance of {@link ROOT } + * + */ + public ROOT createROOT() + { + return new ROOT(); + } + + /** + * Create an instance of {@link EntrySetType } + * + */ + public EntrySetType createEntrySetType() + { + return new EntrySetType(); + } + + /** + * Create an instance of {@link XrefType } + * + */ + public XrefType createXrefType() + { + return new XrefType(); + } + + /** + * Create an instance of {@link EntryType.Reference } + * + */ + public EntryType.Reference createEntryTypeReference() + { + return new EntryType.Reference(); + } + + /** + * Create an instance of {@link EntryType.Contig.Range } + * + */ + public EntryType.Contig.Range createEntryTypeContigRange() + { + return new EntryType.Contig.Range(); + } + + /** + * Create an instance of {@link EntryType.Contig.Gap } + * + */ + public EntryType.Contig.Gap createEntryTypeContigGap() + { + return new EntryType.Contig.Gap(); + } + + /** + * Create an instance of {@link EntryType.Assembly.Range } + * + */ + public EntryType.Assembly.Range createEntryTypeAssemblyRange() + { + return new EntryType.Assembly.Range(); + } + + /** + * Create an instance of {@link EntryType.Feature.Qualifier } + * + */ + public EntryType.Feature.Qualifier createEntryTypeFeatureQualifier() + { + return new EntryType.Feature.Qualifier(); + } + + /** + * Create an instance of {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon } + * + */ + public EntryType.Feature.FeatureTaxon.Lineage.Taxon createEntryTypeFeatureFeatureTaxonLineageTaxon() + { + return new EntryType.Feature.FeatureTaxon.Lineage.Taxon(); + } } diff --git a/src/jalview/xml/binding/embl/ROOT.java b/src/jalview/xml/binding/embl/ROOT.java index 958cdbc..f35812e 100644 --- a/src/jalview/xml/binding/embl/ROOT.java +++ b/src/jalview/xml/binding/embl/ROOT.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:45 PM GMT // - package jalview.xml.binding.embl; import javax.xml.bind.annotation.XmlAccessType; @@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -35,62 +36,59 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "entrySet",
-    "entry"
-})
+@XmlType(name = "", propOrder = { "entrySet", "entry" })
 @XmlRootElement(name = "ROOT")
-public class ROOT {
+public class ROOT
+{
+
+  protected EntrySetType entrySet;
 
-    protected EntrySetType entrySet;
-    protected EntryType entry;
+  protected EntryType entry;
 
-    /**
-     * Gets the value of the entrySet property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link EntrySetType }
-     *     
-     */
-    public EntrySetType getEntrySet() {
-        return entrySet;
-    }
+  /**
+   * Gets the value of the entrySet property.
+   * 
+   * @return possible object is {@link EntrySetType }
+   * 
+   */
+  public EntrySetType getEntrySet()
+  {
+    return entrySet;
+  }
 
-    /**
-     * Sets the value of the entrySet property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link EntrySetType }
-     *     
-     */
-    public void setEntrySet(EntrySetType value) {
-        this.entrySet = value;
-    }
+  /**
+   * Sets the value of the entrySet property.
+   * 
+   * @param value
+   *          allowed object is {@link EntrySetType }
+   * 
+   */
+  public void setEntrySet(EntrySetType value)
+  {
+    this.entrySet = value;
+  }
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link EntryType }
-     *     
-     */
-    public EntryType getEntry() {
-        return entry;
-    }
+  /**
+   * Gets the value of the entry property.
+   * 
+   * @return possible object is {@link EntryType }
+   * 
+   */
+  public EntryType getEntry()
+  {
+    return entry;
+  }
 
-    /**
-     * Sets the value of the entry property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link EntryType }
-     *     
-     */
-    public void setEntry(EntryType value) {
-        this.entry = value;
-    }
+  /**
+   * Sets the value of the entry property.
+   * 
+   * @param value
+   *          allowed object is {@link EntryType }
+   * 
+   */
+  public void setEntry(EntryType value)
+  {
+    this.entry = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/embl/XrefType.java b/src/jalview/xml/binding/embl/XrefType.java
index 244d0fe..d70f92c 100644
--- a/src/jalview/xml/binding/embl/XrefType.java
+++ b/src/jalview/xml/binding/embl/XrefType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:45 PM GMT 
 //
 
-
 package jalview.xml.binding.embl;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +12,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Database cross-reference.
  * 
- * 

Java class for XrefType complex type. + *

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

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

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

  * <complexType name="XrefType">
@@ -37,85 +38,85 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "XrefType")
-public class XrefType {
+public class XrefType
+{
+
+  @XmlAttribute(name = "db", required = true)
+  protected String db;
+
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
 
-    @XmlAttribute(name = "db", required = true)
-    protected String db;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "secondaryId")
-    protected String secondaryId;
+  @XmlAttribute(name = "secondaryId")
+  protected String secondaryId;
 
-    /**
-     * Gets the value of the db property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDb() {
-        return db;
-    }
+  /**
+   * Gets the value of the db property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDb()
+  {
+    return db;
+  }
 
-    /**
-     * Sets the value of the db property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDb(String value) {
-        this.db = value;
-    }
+  /**
+   * Sets the value of the db property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDb(String value)
+  {
+    this.db = value;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
-    /**
-     * Gets the value of the secondaryId property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSecondaryId() {
-        return secondaryId;
-    }
+  /**
+   * Gets the value of the secondaryId property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSecondaryId()
+  {
+    return secondaryId;
+  }
 
-    /**
-     * Sets the value of the secondaryId property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSecondaryId(String value) {
-        this.secondaryId = value;
-    }
+  /**
+   * Sets the value of the secondaryId property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSecondaryId(String value)
+  {
+    this.secondaryId = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index 2a40e11..5dcc0bd 100644
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -18,11 +17,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -61,266 +62,275 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "alcodon",
-    "alcodMap"
-})
+@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
 @XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame {
+public class AlcodonFrame
+{
+
+  protected List alcodon;
+
+  protected List alcodMap;
 
-    protected List alcodon;
-    protected List alcodMap;
+  /**
+   * Gets the value of the alcodon property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+   *       </sequence>
+   *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "mapping" }) + public static class AlcodMap + { + + @XmlElement(name = "Mapping", required = true) + protected Mapping mapping; + + @XmlAttribute(name = "dnasq", required = true) + protected String dnasq; /** - * Gets the value of the alcodon property. * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getAlcodon().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getAlcodMap().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link AlcodonFrame.AlcodMap } + * Sets the value of the mapping property. * + * @param value + * allowed object is {@link Mapping } * */ - public List getAlcodMap() { - if (alcodMap == null) { - alcodMap = new ArrayList(); - } - return this.alcodMap; + public void setMapping(Mapping value) + { + this.mapping = value; } - /** - *

Java class for anonymous complex type. + * Gets the value of the dnasq property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link String } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
-     *       </sequence>
-     *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public String getDnasq() + { + return dnasq; + } + + /** + * Sets the value of the dnasq property. * + * @param value + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "mapping" - }) - public static class AlcodMap { + public void setDnasq(String value) + { + this.dnasq = value; + } - @XmlElement(name = "Mapping", required = true) - protected Mapping mapping; - @XmlAttribute(name = "dnasq", required = true) - protected String dnasq; + } - /** - * - * a Mapping entry and an associated protein sequence - * - * - * @return - * possible object is - * {@link Mapping } - * - */ - public Mapping getMapping() { - return mapping; - } + /** + * + * specifies a series of aligned codons from an associated DNA sequence + * alignment that when translated correspond to columns of a peptide + * alignment. Element may have either all pos1,2,3 attributes specified, or + * none at all (indicating a gapped column with no translated peptide). + * + * + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Alcodon + { - /** - * Sets the value of the mapping property. - * - * @param value - * allowed object is - * {@link Mapping } - * - */ - public void setMapping(Mapping value) { - this.mapping = value; - } + @XmlAttribute(name = "pos1") + protected BigInteger pos1; - /** - * Gets the value of the dnasq property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDnasq() { - return dnasq; - } + @XmlAttribute(name = "pos2") + protected BigInteger pos2; - /** - * Sets the value of the dnasq property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDnasq(String value) { - this.dnasq = value; - } + @XmlAttribute(name = "pos3") + protected BigInteger pos3; + /** + * Gets the value of the pos1 property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPos1() + { + return pos1; } - /** + * Sets the value of the pos1 property. * - * specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment. - * Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide). - * + * @param value + * allowed object is {@link BigInteger } * - *

Java class for anonymous complex type. + */ + public void setPos1(BigInteger value) + { + this.pos1 = value; + } + + /** + * Gets the value of the pos2 property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link BigInteger } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public BigInteger getPos2() + { + return pos2; + } + + /** + * Sets the value of the pos2 property. * + * @param value + * allowed object is {@link BigInteger } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Alcodon { - - @XmlAttribute(name = "pos1") - protected BigInteger pos1; - @XmlAttribute(name = "pos2") - protected BigInteger pos2; - @XmlAttribute(name = "pos3") - protected BigInteger pos3; - - /** - * Gets the value of the pos1 property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPos1() { - return pos1; - } - - /** - * Sets the value of the pos1 property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPos1(BigInteger value) { - this.pos1 = value; - } - - /** - * Gets the value of the pos2 property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPos2() { - return pos2; - } - - /** - * Sets the value of the pos2 property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPos2(BigInteger value) { - this.pos2 = value; - } - - /** - * Gets the value of the pos3 property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPos3() { - return pos3; - } + public void setPos2(BigInteger value) + { + this.pos2 = value; + } - /** - * Sets the value of the pos3 property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPos3(BigInteger value) { - this.pos3 = value; - } + /** + * Gets the value of the pos3 property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPos3() + { + return pos3; + } + /** + * Sets the value of the pos3 property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setPos3(BigInteger value) + { + this.pos3 = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java index 8d99141..985736e 100644 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -70,733 +71,755 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "annotationElement",
-    "label",
-    "description",
-    "thresholdLine",
-    "contactmatrix",
-    "property"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "annotationElement", "label", "description", "thresholdLine",
+      "contactmatrix", "property" })
 @XmlRootElement(name = "Annotation")
-public class Annotation {
-
-    protected List annotationElement;
-    @XmlElement(required = true)
-    protected String label;
-    protected String description;
-    protected Annotation.ThresholdLine thresholdLine;
-    protected List contactmatrix;
-    protected List property;
-    @XmlAttribute(name = "graph", required = true)
-    protected boolean graph;
-    @XmlAttribute(name = "graphType")
-    protected Integer graphType;
-    @XmlAttribute(name = "sequenceRef")
-    protected String sequenceRef;
-    @XmlAttribute(name = "groupRef")
-    protected String groupRef;
-    @XmlAttribute(name = "graphColour")
-    protected Integer graphColour;
-    @XmlAttribute(name = "graphGroup")
-    protected Integer graphGroup;
-    @XmlAttribute(name = "graphHeight")
-    protected Integer graphHeight;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "scoreOnly")
-    protected Boolean scoreOnly;
-    @XmlAttribute(name = "score")
-    protected Double score;
-    @XmlAttribute(name = "visible")
-    protected Boolean visible;
-    @XmlAttribute(name = "centreColLabels")
-    protected Boolean centreColLabels;
-    @XmlAttribute(name = "scaleColLabels")
-    protected Boolean scaleColLabels;
-    @XmlAttribute(name = "showAllColLabels")
-    protected Boolean showAllColLabels;
-    @XmlAttribute(name = "autoCalculated")
-    protected Boolean autoCalculated;
-    @XmlAttribute(name = "belowAlignment")
-    protected Boolean belowAlignment;
-    @XmlAttribute(name = "calcId")
-    protected String calcId;
-
-    /**
-     * Gets the value of the annotationElement property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getAnnotationElement().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getContactmatrix().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getProperty().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Property } - * - * - */ - public List getProperty() { - if (property == null) { - property = new ArrayList(); - } - return this.property; - } - - /** - * Gets the value of the graph property. - * - */ - public boolean isGraph() { - return graph; - } - - /** - * Sets the value of the graph property. - * - */ - public void setGraph(boolean value) { - this.graph = value; - } - - /** - * Gets the value of the graphType property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getGraphType() { - return graphType; - } +public class Annotation +{ - /** - * Sets the value of the graphType property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setGraphType(Integer value) { - this.graphType = value; - } - - /** - * Gets the value of the sequenceRef property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getSequenceRef() { - return sequenceRef; - } - - /** - * Sets the value of the sequenceRef property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setSequenceRef(String value) { - this.sequenceRef = value; - } - - /** - * Gets the value of the groupRef property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getGroupRef() { - return groupRef; - } + protected List annotationElement; - /** - * Sets the value of the groupRef property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setGroupRef(String value) { - this.groupRef = value; - } + @XmlElement(required = true) + protected String label; + + protected String description; - /** - * Gets the value of the graphColour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getGraphColour() { - return graphColour; - } - - /** - * Sets the value of the graphColour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setGraphColour(Integer value) { - this.graphColour = value; - } - - /** - * Gets the value of the graphGroup property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getGraphGroup() { - return graphGroup; - } - - /** - * Sets the value of the graphGroup property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setGraphGroup(Integer value) { - this.graphGroup = value; - } - - /** - * Gets the value of the graphHeight property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getGraphHeight() { - return graphHeight; - } - - /** - * Sets the value of the graphHeight property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setGraphHeight(Integer value) { - this.graphHeight = value; - } - - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } - - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } - - /** - * Gets the value of the scoreOnly property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isScoreOnly() { - if (scoreOnly == null) { - return false; - } else { - return scoreOnly; - } - } - - /** - * Sets the value of the scoreOnly property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setScoreOnly(Boolean value) { - this.scoreOnly = value; - } - - /** - * Gets the value of the score property. - * - * @return - * possible object is - * {@link Double } - * - */ - public Double getScore() { - return score; - } + protected Annotation.ThresholdLine thresholdLine; + + protected List contactmatrix; + + protected List property; + + @XmlAttribute(name = "graph", required = true) + protected boolean graph; + + @XmlAttribute(name = "graphType") + protected Integer graphType; + + @XmlAttribute(name = "sequenceRef") + protected String sequenceRef; + + @XmlAttribute(name = "groupRef") + protected String groupRef; + + @XmlAttribute(name = "graphColour") + protected Integer graphColour; + + @XmlAttribute(name = "graphGroup") + protected Integer graphGroup; + + @XmlAttribute(name = "graphHeight") + protected Integer graphHeight; + + @XmlAttribute(name = "id") + protected String id; + + @XmlAttribute(name = "scoreOnly") + protected Boolean scoreOnly; + + @XmlAttribute(name = "score") + protected Double score; + + @XmlAttribute(name = "visible") + protected Boolean visible; + + @XmlAttribute(name = "centreColLabels") + protected Boolean centreColLabels; + + @XmlAttribute(name = "scaleColLabels") + protected Boolean scaleColLabels; + + @XmlAttribute(name = "showAllColLabels") + protected Boolean showAllColLabels; + + @XmlAttribute(name = "autoCalculated") + protected Boolean autoCalculated; + + @XmlAttribute(name = "belowAlignment") + protected Boolean belowAlignment; + + @XmlAttribute(name = "calcId") + protected String calcId; + + /** + * Gets the value of the annotationElement property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class ThresholdLine + { + + @XmlAttribute(name = "label") + protected String label; - /** - * Sets the value of the score property. - * - * @param value - * allowed object is - * {@link Double } - * - */ - public void setScore(Double value) { - this.score = value; - } + @XmlAttribute(name = "value") + protected Float value; - /** - * Gets the value of the visible property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isVisible() { - return visible; - } + @XmlAttribute(name = "colour") + protected Integer colour; /** - * Sets the value of the visible property. + * Gets the value of the label property. * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setVisible(Boolean value) { - this.visible = value; - } - - /** - * Gets the value of the centreColLabels property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isCentreColLabels() { - return centreColLabels; + public String getLabel() + { + return label; } /** - * Sets the value of the centreColLabels property. + * Sets the value of the label property. * * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setCentreColLabels(Boolean value) { - this.centreColLabels = value; - } - - /** - * Gets the value of the scaleColLabels property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isScaleColLabels() { - return scaleColLabels; + public void setLabel(String value) + { + this.label = value; } /** - * Sets the value of the scaleColLabels property. + * Gets the value of the value property. * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setScaleColLabels(Boolean value) { - this.scaleColLabels = value; - } - - /** - * Gets the value of the showAllColLabels property. + * @return possible object is {@link Float } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isShowAllColLabels() { - return showAllColLabels; + public Float getValue() + { + return value; } /** - * Sets the value of the showAllColLabels property. + * Sets the value of the value property. * * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowAllColLabels(Boolean value) { - this.showAllColLabels = value; - } - - /** - * Gets the value of the autoCalculated property. + * allowed object is {@link Float } * - * @return - * possible object is - * {@link Boolean } - * */ - public boolean isAutoCalculated() { - if (autoCalculated == null) { - return false; - } else { - return autoCalculated; - } + public void setValue(Float value) + { + this.value = value; } /** - * Sets the value of the autoCalculated property. + * Gets the value of the colour property. * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setAutoCalculated(Boolean value) { - this.autoCalculated = value; - } - - /** - * Gets the value of the belowAlignment property. + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link Boolean } - * */ - public boolean isBelowAlignment() { - if (belowAlignment == null) { - return true; - } else { - return belowAlignment; - } + public Integer getColour() + { + return colour; } /** - * Sets the value of the belowAlignment property. + * Sets the value of the colour property. * * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setBelowAlignment(Boolean value) { - this.belowAlignment = value; - } - - /** - * Gets the value of the calcId property. + * allowed object is {@link Integer } * - * @return - * possible object is - * {@link String } - * */ - public String getCalcId() { - return calcId; + public void setColour(Integer value) + { + this.colour = value; } - /** - * Sets the value of the calcId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setCalcId(String value) { - this.calcId = value; - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class ThresholdLine { - - @XmlAttribute(name = "label") - protected String label; - @XmlAttribute(name = "value") - protected Float value; - @XmlAttribute(name = "colour") - protected Integer colour; - - /** - * Gets the value of the label property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getLabel() { - return label; - } - - /** - * Sets the value of the label property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setLabel(String value) { - this.label = value; - } - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setValue(Float value) { - this.value = value; - } - - /** - * Gets the value of the colour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getColour() { - return colour; - } - - /** - * Sets the value of the colour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setColour(Integer value) { - this.colour = value; - } - - } + } } diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java index 27e0cc6..c7bc579 100644 --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for AnnotationColourScheme complex type. + *

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

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

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

  * <complexType name="AnnotationColourScheme">
@@ -40,215 +41,215 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme {
-
-    @XmlAttribute(name = "aboveThreshold")
-    protected Integer aboveThreshold;
-    @XmlAttribute(name = "annotation")
-    protected String annotation;
-    @XmlAttribute(name = "minColour")
-    protected Integer minColour;
-    @XmlAttribute(name = "maxColour")
-    protected Integer maxColour;
-    @XmlAttribute(name = "colourScheme")
-    protected String colourScheme;
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-    @XmlAttribute(name = "perSequence")
-    protected Boolean perSequence;
-    @XmlAttribute(name = "predefinedColours")
-    protected Boolean predefinedColours;
-
-    /**
-     * Gets the value of the aboveThreshold property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getAboveThreshold() {
-        return aboveThreshold;
-    }
-
-    /**
-     * Sets the value of the aboveThreshold property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setAboveThreshold(Integer value) {
-        this.aboveThreshold = value;
-    }
-
-    /**
-     * Gets the value of the annotation property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getAnnotation() {
-        return annotation;
-    }
-
-    /**
-     * Sets the value of the annotation property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setAnnotation(String value) {
-        this.annotation = value;
-    }
-
-    /**
-     * Gets the value of the minColour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getMinColour() {
-        return minColour;
-    }
-
-    /**
-     * Sets the value of the minColour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setMinColour(Integer value) {
-        this.minColour = value;
-    }
-
-    /**
-     * Gets the value of the maxColour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getMaxColour() {
-        return maxColour;
-    }
-
-    /**
-     * Sets the value of the maxColour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setMaxColour(Integer value) {
-        this.maxColour = value;
-    }
-
-    /**
-     * Gets the value of the colourScheme property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getColourScheme() {
-        return colourScheme;
-    }
-
-    /**
-     * Sets the value of the colourScheme property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setColourScheme(String value) {
-        this.colourScheme = value;
-    }
-
-    /**
-     * Gets the value of the threshold property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Float }
-     *     
-     */
-    public Float getThreshold() {
-        return threshold;
-    }
-
-    /**
-     * Sets the value of the threshold property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Float }
-     *     
-     */
-    public void setThreshold(Float value) {
-        this.threshold = value;
-    }
-
-    /**
-     * Gets the value of the perSequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isPerSequence() {
-        return perSequence;
-    }
-
-    /**
-     * Sets the value of the perSequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setPerSequence(Boolean value) {
-        this.perSequence = value;
-    }
-
-    /**
-     * Gets the value of the predefinedColours property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isPredefinedColours() {
-        return predefinedColours;
-    }
-
-    /**
-     * Sets the value of the predefinedColours property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setPredefinedColours(Boolean value) {
-        this.predefinedColours = value;
-    }
+public class AnnotationColourScheme
+{
+
+  @XmlAttribute(name = "aboveThreshold")
+  protected Integer aboveThreshold;
+
+  @XmlAttribute(name = "annotation")
+  protected String annotation;
+
+  @XmlAttribute(name = "minColour")
+  protected Integer minColour;
+
+  @XmlAttribute(name = "maxColour")
+  protected Integer maxColour;
+
+  @XmlAttribute(name = "colourScheme")
+  protected String colourScheme;
+
+  @XmlAttribute(name = "threshold")
+  protected Float threshold;
+
+  @XmlAttribute(name = "perSequence")
+  protected Boolean perSequence;
+
+  @XmlAttribute(name = "predefinedColours")
+  protected Boolean predefinedColours;
+
+  /**
+   * Gets the value of the aboveThreshold property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getAboveThreshold()
+  {
+    return aboveThreshold;
+  }
+
+  /**
+   * Sets the value of the aboveThreshold property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setAboveThreshold(Integer value)
+  {
+    this.aboveThreshold = value;
+  }
+
+  /**
+   * Gets the value of the annotation property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getAnnotation()
+  {
+    return annotation;
+  }
+
+  /**
+   * Sets the value of the annotation property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setAnnotation(String value)
+  {
+    this.annotation = value;
+  }
+
+  /**
+   * Gets the value of the minColour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getMinColour()
+  {
+    return minColour;
+  }
+
+  /**
+   * Sets the value of the minColour property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setMinColour(Integer value)
+  {
+    this.minColour = value;
+  }
+
+  /**
+   * Gets the value of the maxColour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getMaxColour()
+  {
+    return maxColour;
+  }
+
+  /**
+   * Sets the value of the maxColour property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setMaxColour(Integer value)
+  {
+    this.maxColour = value;
+  }
+
+  /**
+   * Gets the value of the colourScheme property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getColourScheme()
+  {
+    return colourScheme;
+  }
+
+  /**
+   * Sets the value of the colourScheme property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setColourScheme(String value)
+  {
+    this.colourScheme = value;
+  }
+
+  /**
+   * Gets the value of the threshold property.
+   * 
+   * @return possible object is {@link Float }
+   * 
+   */
+  public Float getThreshold()
+  {
+    return threshold;
+  }
+
+  /**
+   * Sets the value of the threshold property.
+   * 
+   * @param value
+   *          allowed object is {@link Float }
+   * 
+   */
+  public void setThreshold(Float value)
+  {
+    this.threshold = value;
+  }
+
+  /**
+   * Gets the value of the perSequence property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isPerSequence()
+  {
+    return perSequence;
+  }
+
+  /**
+   * Sets the value of the perSequence property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setPerSequence(Boolean value)
+  {
+    this.perSequence = value;
+  }
+
+  /**
+   * Gets the value of the predefinedColours property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isPredefinedColours()
+  {
+    return predefinedColours;
+  }
+
+  /**
+   * Sets the value of the predefinedColours property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setPredefinedColours(Boolean value)
+  {
+    this.predefinedColours = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index c5f75e0..e461296 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,11 +13,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -46,158 +47,159 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "displayCharacter",
-    "description",
-    "secondaryStructure",
-    "value"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "displayCharacter", "description", "secondaryStructure", "value" })
 @XmlRootElement(name = "annotationElement")
-public class AnnotationElement {
-
-    protected String displayCharacter;
-    protected String description;
-    protected String secondaryStructure;
-    protected Float value;
-    @XmlAttribute(name = "position", required = true)
-    protected int position;
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
-
-    /**
-     * Gets the value of the displayCharacter property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDisplayCharacter() {
-        return displayCharacter;
-    }
-
-    /**
-     * Sets the value of the displayCharacter property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDisplayCharacter(String value) {
-        this.displayCharacter = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * Gets the value of the secondaryStructure property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSecondaryStructure() {
-        return secondaryStructure;
-    }
-
-    /**
-     * Sets the value of the secondaryStructure property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSecondaryStructure(String value) {
-        this.secondaryStructure = value;
-    }
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Float }
-     *     
-     */
-    public Float getValue() {
-        return value;
-    }
-
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Float }
-     *     
-     */
-    public void setValue(Float value) {
-        this.value = value;
-    }
-
-    /**
-     * Gets the value of the position property.
-     * 
-     */
-    public int getPosition() {
-        return position;
-    }
-
-    /**
-     * Sets the value of the position property.
-     * 
-     */
-    public void setPosition(int value) {
-        this.position = value;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Integer }
-     *     
-     */
-    public Integer getColour() {
-        return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Integer }
-     *     
-     */
-    public void setColour(Integer value) {
-        this.colour = value;
-    }
+public class AnnotationElement
+{
+
+  protected String displayCharacter;
+
+  protected String description;
+
+  protected String secondaryStructure;
+
+  protected Float value;
+
+  @XmlAttribute(name = "position", required = true)
+  protected int position;
+
+  @XmlAttribute(name = "colour")
+  protected Integer colour;
+
+  /**
+   * Gets the value of the displayCharacter property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDisplayCharacter()
+  {
+    return displayCharacter;
+  }
+
+  /**
+   * Sets the value of the displayCharacter property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDisplayCharacter(String value)
+  {
+    this.displayCharacter = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
+
+  /**
+   * Gets the value of the secondaryStructure property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSecondaryStructure()
+  {
+    return secondaryStructure;
+  }
+
+  /**
+   * Sets the value of the secondaryStructure property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSecondaryStructure(String value)
+  {
+    this.secondaryStructure = value;
+  }
+
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link Float }
+   * 
+   */
+  public Float getValue()
+  {
+    return value;
+  }
+
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link Float }
+   * 
+   */
+  public void setValue(Float value)
+  {
+    this.value = value;
+  }
+
+  /**
+   * Gets the value of the position property.
+   * 
+   */
+  public int getPosition()
+  {
+    return position;
+  }
+
+  /**
+   * Sets the value of the position property.
+   * 
+   */
+  public void setPosition(int value)
+  {
+    this.position = value;
+  }
+
+  /**
+   * Gets the value of the colour property.
+   * 
+   * @return possible object is {@link Integer }
+   * 
+   */
+  public Integer getColour()
+  {
+    return colour;
+  }
+
+  /**
+   * Sets the value of the colour property.
+   * 
+   * @param value
+   *          allowed object is {@link Integer }
+   * 
+   */
+  public void setColour(Integer value)
+  {
+    this.colour = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index 9be9876..b1a738b 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for DoubleMatrix complex type. + *

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

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

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

  * <complexType name="DoubleMatrix">
@@ -41,146 +42,150 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
-    "row",
-    "d",
-    "e"
-})
-public class DoubleMatrix {
-
-    protected List row;
-    @XmlElement(name = "D")
-    protected DoubleVector d;
-    @XmlElement(name = "E")
-    protected DoubleVector e;
-    @XmlAttribute(name = "rows")
-    protected Integer rows;
-    @XmlAttribute(name = "columns")
-    protected Integer columns;
-
-    /**
-     * Gets the value of the row property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getRow().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link DoubleVector } + * + * + */ + public List getRow() + { + if (row == null) + { + row = new ArrayList(); } + return this.row; + } + + /** + * Gets the value of the d property. + * + * @return possible object is {@link DoubleVector } + * + */ + public DoubleVector getD() + { + return d; + } + + /** + * Sets the value of the d property. + * + * @param value + * allowed object is {@link DoubleVector } + * + */ + public void setD(DoubleVector value) + { + this.d = value; + } + + /** + * Gets the value of the e property. + * + * @return possible object is {@link DoubleVector } + * + */ + public DoubleVector getE() + { + return e; + } + + /** + * Sets the value of the e property. + * + * @param value + * allowed object is {@link DoubleVector } + * + */ + public void setE(DoubleVector value) + { + this.e = value; + } + + /** + * Gets the value of the rows property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getRows() + { + return rows; + } + + /** + * Sets the value of the rows property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setRows(Integer value) + { + this.rows = value; + } + + /** + * Gets the value of the columns property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getColumns() + { + return columns; + } + + /** + * Sets the value of the columns property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setColumns(Integer value) + { + this.columns = value; + } } diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java index 6546be9..12f39c0 100644 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for DoubleVector complex type. + *

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

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

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

  * <complexType name="DoubleVector">
@@ -36,41 +37,46 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
-    "v"
-})
-public class DoubleVector {
+@XmlType(
+  name = "DoubleVector",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "v" })
+public class DoubleVector
+{
 
-    @XmlElement(type = Double.class)
-    protected List v;
+  @XmlElement(type = Double.class)
+  protected List v;
 
-    /**
-     * Gets the value of the v property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getV().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Double } + * + * + */ + public List getV() + { + if (v == null) + { + v = new ArrayList(); } + return this.v; + } } diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java index a124e62..9ac7b58 100644 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for feature complex type. + *

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

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

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

  * <complexType name="feature">
@@ -53,311 +54,325 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
-    "otherData"
-})
-public class Feature {
-
-    protected List otherData;
-    @XmlAttribute(name = "begin", required = true)
-    protected int begin;
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "description")
-    protected String description;
-    @XmlAttribute(name = "status")
-    protected String status;
-    @XmlAttribute(name = "featureGroup")
-    protected String featureGroup;
-    @XmlAttribute(name = "score")
-    protected Float score;
-
-    /**
-     * Gets the value of the otherData property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getOtherData().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class OtherData + { + + @XmlAttribute(name = "key", required = true) + protected String key; + + @XmlAttribute(name = "key2") + protected String key2; + + @XmlAttribute(name = "value", required = true) + protected String value; /** - * Gets the value of the begin property. + * Gets the value of the key property. * - */ - public int getBegin() { - return begin; - } - - /** - * Sets the value of the begin property. - * - */ - public void setBegin(int value) { - this.begin = value; - } - - /** - * Gets the value of the end property. - * - */ - public int getEnd() { - return end; - } - - /** - * Sets the value of the end property. - * - */ - public void setEnd(int value) { - this.end = value; - } - - /** - * Gets the value of the type property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getType() { - return type; + public String getKey() + { + return key; } /** - * Sets the value of the type property. + * Sets the value of the key property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the description property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getDescription() { - return description; + public void setKey(String value) + { + this.key = value; } /** - * Sets the value of the description property. + * Gets the value of the key2 property. * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDescription(String value) { - this.description = value; - } - - /** - * Gets the value of the status property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getStatus() { - return status; + public String getKey2() + { + return key2; } /** - * Sets the value of the status property. + * Sets the value of the key2 property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setStatus(String value) { - this.status = value; - } - - /** - * Gets the value of the featureGroup property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getFeatureGroup() { - return featureGroup; + public void setKey2(String value) + { + this.key2 = value; } /** - * Sets the value of the featureGroup property. + * Gets the value of the value property. * - * @param value - * allowed object is - * {@link String } - * - */ - public void setFeatureGroup(String value) { - this.featureGroup = value; - } - - /** - * Gets the value of the score property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Float } - * */ - public Float getScore() { - return score; + public String getValue() + { + return value; } /** - * Sets the value of the score property. + * Sets the value of the value property. * * @param value - * allowed object is - * {@link Float } - * - */ - public void setScore(Float value) { - this.score = value; - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class OtherData { - - @XmlAttribute(name = "key", required = true) - protected String key; - @XmlAttribute(name = "key2") - protected String key2; - @XmlAttribute(name = "value", required = true) - protected String value; - - /** - * Gets the value of the key property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getKey() { - return key; - } - - /** - * Sets the value of the key property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setKey(String value) { - this.key = value; - } - - /** - * Gets the value of the key2 property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getKey2() { - return key2; - } - - /** - * Sets the value of the key2 property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setKey2(String value) { - this.key2 = value; - } - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - + public void setValue(String value) + { + this.value = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java index 61e66ce..1b1abff 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for FeatureMatcher complex type. + *

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

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

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

  * <complexType name="FeatureMatcher">
@@ -40,121 +41,124 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
-    "attributeName",
-    "condition",
-    "value"
-})
-public class FeatureMatcher {
+@XmlType(
+  name = "FeatureMatcher",
+  namespace = "www.jalview.org/colours",
+  propOrder =
+  { "attributeName", "condition", "value" })
+public class FeatureMatcher
+{
 
-    @XmlElement(namespace = "")
-    protected List attributeName;
-    @XmlElement(namespace = "", required = true)
-    protected String condition;
-    @XmlElement(namespace = "", required = true)
-    protected String value;
-    @XmlAttribute(name = "by")
-    protected FilterBy by;
+  @XmlElement(namespace = "")
+  protected List attributeName;
 
-    /**
-     * Gets the value of the attributeName property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getAttributeName().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getAttributeName() { - if (attributeName == null) { - attributeName = new ArrayList(); - } - return this.attributeName; - } + @XmlElement(namespace = "", required = true) + protected String condition; - /** - * Gets the value of the condition property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getCondition() { - return condition; - } + @XmlElement(namespace = "", required = true) + protected String value; - /** - * Sets the value of the condition property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setCondition(String value) { - this.condition = value; - } + @XmlAttribute(name = "by") + protected FilterBy by; - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; + /** + * Gets the value of the attributeName property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getAttributeName() + { + if (attributeName == null) + { + attributeName = new ArrayList(); } + return this.attributeName; + } - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } + /** + * Gets the value of the condition property. + * + * @return possible object is {@link String } + * + */ + public String getCondition() + { + return condition; + } - /** - * Gets the value of the by property. - * - * @return - * possible object is - * {@link FilterBy } - * - */ - public FilterBy getBy() { - return by; - } + /** + * Sets the value of the condition property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setCondition(String value) + { + this.condition = value; + } - /** - * Sets the value of the by property. - * - * @param value - * allowed object is - * {@link FilterBy } - * - */ - public void setBy(FilterBy value) { - this.by = value; - } + /** + * Gets the value of the value property. + * + * @return possible object is {@link String } + * + */ + public String getValue() + { + return value; + } + + /** + * Sets the value of the value property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setValue(String value) + { + this.value = value; + } + + /** + * Gets the value of the by property. + * + * @return possible object is {@link FilterBy } + * + */ + public FilterBy getBy() + { + return by; + } + + /** + * Sets the value of the by property. + * + * @param value + * allowed object is {@link FilterBy } + * + */ + public void setBy(FilterBy value) + { + this.by = value; + } } diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java index 24190b8..a071af8 100644 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** * A feature match condition, which may be simple or compound * - *

Java class for FeatureMatcherSet complex type. + *

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

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

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

  * <complexType name="FeatureMatcherSet">
@@ -51,142 +52,150 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
-    "matchCondition",
-    "compoundMatcher"
-})
-public class FeatureMatcherSet {
-
-    @XmlElement(namespace = "")
-    protected FeatureMatcher matchCondition;
-    @XmlElement(namespace = "")
-    protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+@XmlType(
+  name = "FeatureMatcherSet",
+  namespace = "www.jalview.org/colours",
+  propOrder =
+  { "matchCondition", "compoundMatcher" })
+public class FeatureMatcherSet
+{
+
+  @XmlElement(namespace = "")
+  protected FeatureMatcher matchCondition;
+
+  @XmlElement(namespace = "")
+  protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
+
+  /**
+   * Gets the value of the matchCondition property.
+   * 
+   * @return possible object is {@link FeatureMatcher }
+   * 
+   */
+  public FeatureMatcher getMatchCondition()
+  {
+    return matchCondition;
+  }
+
+  /**
+   * Sets the value of the matchCondition property.
+   * 
+   * @param value
+   *          allowed object is {@link FeatureMatcher }
+   * 
+   */
+  public void setMatchCondition(FeatureMatcher value)
+  {
+    this.matchCondition = value;
+  }
+
+  /**
+   * Gets the value of the compoundMatcher property.
+   * 
+   * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
+   * 
+   */
+  public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
+  {
+    return compoundMatcher;
+  }
+
+  /**
+   * Sets the value of the compoundMatcher property.
+   * 
+   * @param value
+   *          allowed object is {@link FeatureMatcherSet.CompoundMatcher }
+   * 
+   */
+  public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
+  {
+    this.compoundMatcher = value;
+  }
+
+  /**
+   * 

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+   *       </sequence>
+   *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "matcherSet" }) + public static class CompoundMatcher + { + + @XmlElement(namespace = "", required = true) + protected List matcherSet; + + @XmlAttribute(name = "and", required = true) + protected boolean and; /** - * Gets the value of the matchCondition property. + * Gets the value of the matcherSet property. * - * @return - * possible object is - * {@link FeatureMatcher } - * - */ - public FeatureMatcher getMatchCondition() { - return matchCondition; - } - - /** - * Sets the value of the matchCondition property. + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link FeatureMatcherSet } * - * @param value - * allowed object is - * {@link FeatureMatcher } - * - */ - public void setMatchCondition(FeatureMatcher value) { - this.matchCondition = value; - } - - /** - * Gets the value of the compoundMatcher property. * - * @return - * possible object is - * {@link FeatureMatcherSet.CompoundMatcher } - * */ - public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() { - return compoundMatcher; + public List getMatcherSet() + { + if (matcherSet == null) + { + matcherSet = new ArrayList(); + } + return this.matcherSet; } /** - * Sets the value of the compoundMatcher property. + * Gets the value of the and property. * - * @param value - * allowed object is - * {@link FeatureMatcherSet.CompoundMatcher } - * */ - public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) { - this.compoundMatcher = value; + public boolean isAnd() + { + return and; } - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
-     *       </sequence>
-     *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * + * Sets the value of the and property. * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "matcherSet" - }) - public static class CompoundMatcher { - - @XmlElement(namespace = "", required = true) - protected List matcherSet; - @XmlAttribute(name = "and", required = true) - protected boolean and; - - /** - * Gets the value of the matcherSet property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getMatcherSet().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link FeatureMatcherSet } - * - * - */ - public List getMatcherSet() { - if (matcherSet == null) { - matcherSet = new ArrayList(); - } - return this.matcherSet; - } - - /** - * Gets the value of the and property. - * - */ - public boolean isAnd() { - return and; - } - - /** - * Sets the value of the and property. - * - */ - public void setAnd(boolean value) { - this.and = value; - } - + public void setAnd(boolean value) + { + this.and = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java index 3a9428c..d71051e 100644 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@ -5,19 +5,21 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlEnum; import javax.xml.bind.annotation.XmlEnumValue; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for FilterBy. + *

+ * Java class for FilterBy. * - *

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

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

+ * *

  * <simpleType name="FilterBy">
  *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -31,31 +33,36 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum FilterBy {
-
-    @XmlEnumValue("byLabel")
-    BY_LABEL("byLabel"),
-    @XmlEnumValue("byScore")
-    BY_SCORE("byScore"),
-    @XmlEnumValue("byAttribute")
-    BY_ATTRIBUTE("byAttribute");
-    private final String value;
-
-    FilterBy(String v) {
-        value = v;
-    }
+public enum FilterBy
+{
 
-    public String value() {
-        return value;
-    }
+  @XmlEnumValue("byLabel")
+  BY_LABEL("byLabel"), @XmlEnumValue("byScore")
+  BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
+  BY_ATTRIBUTE("byAttribute");
+
+  private final String value;
+
+  FilterBy(String v)
+  {
+    value = v;
+  }
+
+  public String value()
+  {
+    return value;
+  }
 
-    public static FilterBy fromValue(String v) {
-        for (FilterBy c: FilterBy.values()) {
-            if (c.value.equals(v)) {
-                return c;
-            }
-        }
-        throw new IllegalArgumentException(v);
+  public static FilterBy fromValue(String v)
+  {
+    for (FilterBy c : FilterBy.values())
+    {
+      if (c.value.equals(v))
+      {
+        return c;
+      }
     }
+    throw new IllegalArgumentException(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 22b2533..b77d98d 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -22,11 +21,13 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 import javax.xml.datatype.XMLGregorianCalendar;
 
-
 /**
- * 

Java class for JalviewModel complex type. + *

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

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

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

  * <complexType name="JalviewModel">
@@ -381,2762 +382,3475 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
-    "creationDate",
-    "version",
-    "vamsasModel",
-    "jSeq",
-    "jGroup",
-    "viewport",
-    "userColours",
-    "tree",
-    "pcaViewer",
-    "featureSettings"
-})
-public class JalviewModel {
-
-    @XmlElement(required = true)
-    @XmlSchemaType(name = "dateTime")
-    protected XMLGregorianCalendar creationDate;
-    @XmlElement(required = true)
-    protected String version;
-    @XmlElement(required = true)
-    protected VAMSAS vamsasModel;
-    @XmlElement(name = "JSeq")
-    protected List jSeq;
-    @XmlElement(name = "JGroup")
-    protected List jGroup;
-    @XmlElement(name = "Viewport")
-    protected List viewport;
-    @XmlElement(name = "UserColours")
-    protected List userColours;
-    protected List tree;
-    @XmlElement(name = "PcaViewer")
-    protected List pcaViewer;
-    @XmlElement(name = "FeatureSettings")
-    protected JalviewModel.FeatureSettings featureSettings;
-
-    /**
-     * Gets the value of the creationDate property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public XMLGregorianCalendar getCreationDate() {
-        return creationDate;
-    }
-
-    /**
-     * Sets the value of the creationDate property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setCreationDate(XMLGregorianCalendar value) {
-        this.creationDate = value;
+@XmlType(
+  name = "JalviewModel",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
+      "userColours", "tree", "pcaViewer", "featureSettings" })
+public class JalviewModel
+{
+
+  @XmlElement(required = true)
+  @XmlSchemaType(name = "dateTime")
+  protected XMLGregorianCalendar creationDate;
+
+  @XmlElement(required = true)
+  protected String version;
+
+  @XmlElement(required = true)
+  protected VAMSAS vamsasModel;
+
+  @XmlElement(name = "JSeq")
+  protected List jSeq;
+
+  @XmlElement(name = "JGroup")
+  protected List jGroup;
+
+  @XmlElement(name = "Viewport")
+  protected List viewport;
+
+  @XmlElement(name = "UserColours")
+  protected List userColours;
+
+  protected List tree;
+
+  @XmlElement(name = "PcaViewer")
+  protected List pcaViewer;
+
+  @XmlElement(name = "FeatureSettings")
+  protected JalviewModel.FeatureSettings featureSettings;
+
+  /**
+   * Gets the value of the creationDate property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getCreationDate()
+  {
+    return creationDate;
+  }
+
+  /**
+   * Sets the value of the creationDate property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setCreationDate(XMLGregorianCalendar value)
+  {
+    this.creationDate = value;
+  }
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the vamsasModel property.
+   * 
+   * @return possible object is {@link VAMSAS }
+   * 
+   */
+  public VAMSAS getVamsasModel()
+  {
+    return vamsasModel;
+  }
+
+  /**
+   * Sets the value of the vamsasModel property.
+   * 
+   * @param value
+   *          allowed object is {@link VAMSAS }
+   * 
+   */
+  public void setVamsasModel(VAMSAS value)
+  {
+    this.vamsasModel = value;
+  }
+
+  /**
+   * Gets the value of the jSeq property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JSeq } + * + * + */ + public List getJSeq() + { + if (jSeq == null) + { + jSeq = new ArrayList(); } - - /** - * Gets the value of the version property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getVersion() { - return version; + return this.jSeq; + } + + /** + * Gets the value of the jGroup property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.JGroup } + * + * + */ + public List getJGroup() + { + if (jGroup == null) + { + jGroup = new ArrayList(); } - - /** - * Sets the value of the version property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setVersion(String value) { - this.version = value; + return this.jGroup; + } + + /** + * Gets the value of the viewport property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport } + * + * + */ + public List getViewport() + { + if (viewport == null) + { + viewport = new ArrayList(); } - - /** - * Gets the value of the vamsasModel property. - * - * @return - * possible object is - * {@link VAMSAS } - * - */ - public VAMSAS getVamsasModel() { - return vamsasModel; + return this.viewport; + } + + /** + * Gets the value of the userColours property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.UserColours } + * + * + */ + public List getUserColours() + { + if (userColours == null) + { + userColours = new ArrayList(); } - - /** - * Sets the value of the vamsasModel property. - * - * @param value - * allowed object is - * {@link VAMSAS } - * - */ - public void setVamsasModel(VAMSAS value) { - this.vamsasModel = value; + return this.userColours; + } + + /** + * Gets the value of the tree property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+   *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+   *                 </sequence>
+   *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+   *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="group" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "setting", "group" }) + public static class FeatureSettings + { + + @XmlElement(namespace = "www.jalview.org") + protected List setting; + + @XmlElement(namespace = "www.jalview.org") + protected List group; /** - * Gets the value of the jSeq property. + * Gets the value of the setting property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getJSeq().add(newItem);
+     * getSetting().add(newItem);
      * 
* * *

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

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

* For example, to add a new item, do as follows: + * *

-     *    getJGroup().add(newItem);
+     * getGroup().add(newItem);
      * 
* * *

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

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

- * For example, to add a new item, do as follows: + * The following schema fragment specifies the expected content contained + * within this class. + * *

-     *    getViewport().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
* * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Group + { + + @XmlAttribute(name = "name", required = true) + protected String name; + + @XmlAttribute(name = "display", required = true) + protected boolean display; + + /** + * Gets the value of the name property. + * + * @return possible object is {@link String } + * + */ + public String getName() + { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setName(String value) + { + this.name = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() + { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) + { + this.display = value; + } + + } + + /** + *

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

- * Objects of the following type(s) are allowed in the list - * {@link JalviewModel.Viewport } + * The following schema fragment specifies the expected content contained + * within this class. + * + *

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
* * */ - public List getViewport() { - if (viewport == null) { - viewport = new ArrayList(); + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "attributeName", "matcherSet" }) + public static class Setting + { + + @XmlElement(namespace = "www.jalview.org") + protected List attributeName; + + @XmlElement(namespace = "www.jalview.org") + protected FeatureMatcherSet matcherSet; + + @XmlAttribute(name = "type", required = true) + protected String type; + + @XmlAttribute(name = "colour", required = true) + protected int colour; + + @XmlAttribute(name = "display", required = true) + protected boolean display; + + @XmlAttribute(name = "order") + protected Float order; + + @XmlAttribute(name = "mincolour") + protected Integer mincolour; + + @XmlAttribute(name = "noValueColour") + protected NoValueColour noValueColour; + + @XmlAttribute(name = "threshold") + protected Float threshold; + + @XmlAttribute(name = "threshstate") + protected Integer threshstate; + + @XmlAttribute(name = "max") + protected Float max; + + @XmlAttribute(name = "min") + protected Float min; + + @XmlAttribute(name = "colourByLabel") + protected Boolean colourByLabel; + + @XmlAttribute(name = "autoScale") + protected Boolean autoScale; + + /** + * Gets the value of the attributeName property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String + * } + * + * + */ + public List getAttributeName() + { + if (attributeName == null) + { + attributeName = new ArrayList(); + } + return this.attributeName; + } + + /** + * Gets the value of the matcherSet property. + * + * @return possible object is {@link FeatureMatcherSet } + * + */ + public FeatureMatcherSet getMatcherSet() + { + return matcherSet; + } + + /** + * Sets the value of the matcherSet property. + * + * @param value + * allowed object is {@link FeatureMatcherSet } + * + */ + public void setMatcherSet(FeatureMatcherSet value) + { + this.matcherSet = value; + } + + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } + + /** + * Gets the value of the colour property. + * + */ + public int getColour() + { + return colour; + } + + /** + * Sets the value of the colour property. + * + */ + public void setColour(int value) + { + this.colour = value; + } + + /** + * Gets the value of the display property. + * + */ + public boolean isDisplay() + { + return display; + } + + /** + * Sets the value of the display property. + * + */ + public void setDisplay(boolean value) + { + this.display = value; + } + + /** + * Gets the value of the order property. + * + * @return possible object is {@link Float } + * + */ + public Float getOrder() + { + return order; + } + + /** + * Sets the value of the order property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setOrder(Float value) + { + this.order = value; + } + + /** + * Gets the value of the mincolour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getMincolour() + { + return mincolour; + } + + /** + * Sets the value of the mincolour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setMincolour(Integer value) + { + this.mincolour = value; + } + + /** + * Gets the value of the noValueColour property. + * + * @return possible object is {@link NoValueColour } + * + */ + public NoValueColour getNoValueColour() + { + if (noValueColour == null) + { + return NoValueColour.MIN; } - return this.viewport; + else + { + return noValueColour; + } + } + + /** + * Sets the value of the noValueColour property. + * + * @param value + * allowed object is {@link NoValueColour } + * + */ + public void setNoValueColour(NoValueColour value) + { + this.noValueColour = value; + } + + /** + * Gets the value of the threshold property. + * + * @return possible object is {@link Float } + * + */ + public Float getThreshold() + { + return threshold; + } + + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setThreshold(Float value) + { + this.threshold = value; + } + + /** + * Gets the value of the threshstate property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getThreshstate() + { + return threshstate; + } + + /** + * Sets the value of the threshstate property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setThreshstate(Integer value) + { + this.threshstate = value; + } + + /** + * Gets the value of the max property. + * + * @return possible object is {@link Float } + * + */ + public Float getMax() + { + return max; + } + + /** + * Sets the value of the max property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setMax(Float value) + { + this.max = value; + } + + /** + * Gets the value of the min property. + * + * @return possible object is {@link Float } + * + */ + public Float getMin() + { + return min; + } + + /** + * Sets the value of the min property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setMin(Float value) + { + this.min = value; + } + + /** + * Gets the value of the colourByLabel property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isColourByLabel() + { + return colourByLabel; + } + + /** + * Sets the value of the colourByLabel property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColourByLabel(Boolean value) + { + this.colourByLabel = value; + } + + /** + * Gets the value of the autoScale property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isAutoScale() + { + return autoScale; + } + + /** + * Sets the value of the autoScale property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setAutoScale(Boolean value) + { + this.autoScale = value; + } + } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+   *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "seq", "annotationColours" }) + public static class JGroup + { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List seq; + + @XmlElement(namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + + @XmlAttribute(name = "start") + protected Integer start; + + @XmlAttribute(name = "end") + protected Integer end; + + @XmlAttribute(name = "name") + protected String name; + + @XmlAttribute(name = "colour") + protected String colour; + + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + + @XmlAttribute(name = "outlineColour") + protected Integer outlineColour; + + @XmlAttribute(name = "displayBoxes") + protected Boolean displayBoxes; + + @XmlAttribute(name = "displayText") + protected Boolean displayText; + + @XmlAttribute(name = "colourText") + protected Boolean colourText; + + @XmlAttribute(name = "textCol1") + protected Integer textCol1; + + @XmlAttribute(name = "textCol2") + protected Integer textCol2; + + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; + + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; + + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; + + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; + + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; + + @XmlAttribute(name = "id") + protected String id; + /** - * Gets the value of the userColours property. + * Gets the value of the seq property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getUserColours().add(newItem);
+     * getSeq().add(newItem);
      * 
* * *

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

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

- * For example, to add a new item, do as follows: - *

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

- * Objects of the following type(s) are allowed in the list - * {@link JalviewModel.Tree } + */ + public void setAnnotationColours(AnnotationColourScheme value) + { + this.annotationColours = value; + } + + /** + * Gets the value of the start property. * + * @return possible object is {@link Integer } * */ - public List getTree() { - if (tree == null) { - tree = new ArrayList(); - } - return this.tree; + public Integer getStart() + { + return start; } /** - * Gets the value of the pcaViewer property. + * Sets the value of the start property. * - *

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

- * For example, to add a new item, do as follows: - *

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

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

Java class for anonymous complex type. + * Sets the value of the colour property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link String } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *                 </sequence>
-     *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="group" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public void setColour(String value) + { + this.colour = value; + } + + /** + * Gets the value of the consThreshold property. * + * @return possible object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "setting", - "group" - }) - public static class FeatureSettings { + public Integer getConsThreshold() + { + return consThreshold; + } - @XmlElement(namespace = "www.jalview.org") - protected List setting; - @XmlElement(namespace = "www.jalview.org") - protected List group; + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setConsThreshold(Integer value) + { + this.consThreshold = value; + } - /** - * Gets the value of the setting property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getSetting().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getGroup().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link JalviewModel.FeatureSettings.Group } - * - * - */ - public List getGroup() { - if (group == null) { - group = new ArrayList(); - } - return this.group; - } + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setPidThreshold(Integer value) + { + this.pidThreshold = value; + } + /** + * Gets the value of the outlineColour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getOutlineColour() + { + return outlineColour; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Group { - - @XmlAttribute(name = "name", required = true) - protected String name; - @XmlAttribute(name = "display", required = true) - protected boolean display; - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the display property. - * - */ - public boolean isDisplay() { - return display; - } - - /** - * Sets the value of the display property. - * - */ - public void setDisplay(boolean value) { - this.display = value; - } + /** + * Sets the value of the outlineColour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setOutlineColour(Integer value) + { + this.outlineColour = value; + } - } + /** + * Gets the value of the displayBoxes property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isDisplayBoxes() + { + return displayBoxes; + } + /** + * Sets the value of the displayBoxes property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setDisplayBoxes(Boolean value) + { + this.displayBoxes = value; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-         *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-         *       </sequence>
-         *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-         *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "attributeName", - "matcherSet" - }) - public static class Setting { - - @XmlElement(namespace = "www.jalview.org") - protected List attributeName; - @XmlElement(namespace = "www.jalview.org") - protected FeatureMatcherSet matcherSet; - @XmlAttribute(name = "type", required = true) - protected String type; - @XmlAttribute(name = "colour", required = true) - protected int colour; - @XmlAttribute(name = "display", required = true) - protected boolean display; - @XmlAttribute(name = "order") - protected Float order; - @XmlAttribute(name = "mincolour") - protected Integer mincolour; - @XmlAttribute(name = "noValueColour") - protected NoValueColour noValueColour; - @XmlAttribute(name = "threshold") - protected Float threshold; - @XmlAttribute(name = "threshstate") - protected Integer threshstate; - @XmlAttribute(name = "max") - protected Float max; - @XmlAttribute(name = "min") - protected Float min; - @XmlAttribute(name = "colourByLabel") - protected Boolean colourByLabel; - @XmlAttribute(name = "autoScale") - protected Boolean autoScale; - - /** - * Gets the value of the attributeName property. - * - *

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

- * For example, to add a new item, do as follows: - *

-             *    getAttributeName().add(newItem);
-             * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getAttributeName() { - if (attributeName == null) { - attributeName = new ArrayList(); - } - return this.attributeName; - } - - /** - * Gets the value of the matcherSet property. - * - * @return - * possible object is - * {@link FeatureMatcherSet } - * - */ - public FeatureMatcherSet getMatcherSet() { - return matcherSet; - } - - /** - * Sets the value of the matcherSet property. - * - * @param value - * allowed object is - * {@link FeatureMatcherSet } - * - */ - public void setMatcherSet(FeatureMatcherSet value) { - this.matcherSet = value; - } - - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } - - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the colour property. - * - */ - public int getColour() { - return colour; - } - - /** - * Sets the value of the colour property. - * - */ - public void setColour(int value) { - this.colour = value; - } - - /** - * Gets the value of the display property. - * - */ - public boolean isDisplay() { - return display; - } - - /** - * Sets the value of the display property. - * - */ - public void setDisplay(boolean value) { - this.display = value; - } - - /** - * Gets the value of the order property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getOrder() { - return order; - } - - /** - * Sets the value of the order property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setOrder(Float value) { - this.order = value; - } - - /** - * Gets the value of the mincolour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getMincolour() { - return mincolour; - } - - /** - * Sets the value of the mincolour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setMincolour(Integer value) { - this.mincolour = value; - } - - /** - * Gets the value of the noValueColour property. - * - * @return - * possible object is - * {@link NoValueColour } - * - */ - public NoValueColour getNoValueColour() { - if (noValueColour == null) { - return NoValueColour.MIN; - } else { - return noValueColour; - } - } - - /** - * Sets the value of the noValueColour property. - * - * @param value - * allowed object is - * {@link NoValueColour } - * - */ - public void setNoValueColour(NoValueColour value) { - this.noValueColour = value; - } - - /** - * Gets the value of the threshold property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getThreshold() { - return threshold; - } - - /** - * Sets the value of the threshold property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setThreshold(Float value) { - this.threshold = value; - } - - /** - * Gets the value of the threshstate property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getThreshstate() { - return threshstate; - } - - /** - * Sets the value of the threshstate property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setThreshstate(Integer value) { - this.threshstate = value; - } - - /** - * Gets the value of the max property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getMax() { - return max; - } - - /** - * Sets the value of the max property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setMax(Float value) { - this.max = value; - } - - /** - * Gets the value of the min property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getMin() { - return min; - } - - /** - * Sets the value of the min property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setMin(Float value) { - this.min = value; - } - - /** - * Gets the value of the colourByLabel property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isColourByLabel() { - return colourByLabel; - } - - /** - * Sets the value of the colourByLabel property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setColourByLabel(Boolean value) { - this.colourByLabel = value; - } - - /** - * Gets the value of the autoScale property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isAutoScale() { - return autoScale; - } - - /** - * Sets the value of the autoScale property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setAutoScale(Boolean value) { - this.autoScale = value; - } + /** + * Gets the value of the displayText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isDisplayText() + { + return displayText; + } - } + /** + * Sets the value of the displayText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setDisplayText(Boolean value) + { + this.displayText = value; + } + /** + * Gets the value of the colourText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isColourText() + { + return colourText; } + /** + * Sets the value of the colourText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColourText(Boolean value) + { + this.colourText = value; + } /** - *

Java class for anonymous complex type. + * Gets the value of the textCol1 property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link Integer } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public Integer getTextCol1() + { + return textCol1; + } + + /** + * Sets the value of the textCol1 property. * + * @param value + * allowed object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "seq", - "annotationColours" - }) - public static class JGroup { - - @XmlElement(namespace = "www.jalview.org", required = true) - protected List seq; - @XmlElement(namespace = "www.jalview.org") - protected AnnotationColourScheme annotationColours; - @XmlAttribute(name = "start") - protected Integer start; - @XmlAttribute(name = "end") - protected Integer end; - @XmlAttribute(name = "name") - protected String name; - @XmlAttribute(name = "colour") - protected String colour; - @XmlAttribute(name = "consThreshold") - protected Integer consThreshold; - @XmlAttribute(name = "pidThreshold") - protected Integer pidThreshold; - @XmlAttribute(name = "outlineColour") - protected Integer outlineColour; - @XmlAttribute(name = "displayBoxes") - protected Boolean displayBoxes; - @XmlAttribute(name = "displayText") - protected Boolean displayText; - @XmlAttribute(name = "colourText") - protected Boolean colourText; - @XmlAttribute(name = "textCol1") - protected Integer textCol1; - @XmlAttribute(name = "textCol2") - protected Integer textCol2; - @XmlAttribute(name = "textColThreshold") - protected Integer textColThreshold; - @XmlAttribute(name = "showUnconserved") - protected Boolean showUnconserved; - @XmlAttribute(name = "ignoreGapsinConsensus") - protected Boolean ignoreGapsinConsensus; - @XmlAttribute(name = "showConsensusHistogram") - protected Boolean showConsensusHistogram; - @XmlAttribute(name = "showSequenceLogo") - protected Boolean showSequenceLogo; - @XmlAttribute(name = "normaliseSequenceLogo") - protected Boolean normaliseSequenceLogo; - @XmlAttribute(name = "id") - protected String id; + public void setTextCol1(Integer value) + { + this.textCol1 = value; + } - /** - * Gets the value of the seq property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getSeq().add(newItem);
-         * 
- * - * - *

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <extension base="{www.jalview.org}pdbentry">
+   *                 <sequence>
+   *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+   *                     <complexType>
+   *                       <simpleContent>
+   *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *                           <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         </extension>
+   *                       </simpleContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *               </extension>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <sequence>
+   *                   <element name="secondaryStructure" maxOccurs="unbounded">
+   *                     <complexType>
+   *                       <complexContent>
+   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                         </restriction>
+   *                       </complexContent>
+   *                     </complexType>
+   *                   </element>
+   *                 </sequence>
+   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "features", "pdbids", "hiddenSequences", "rnaViewer" }) + public static class JSeq + { + + @XmlElement(namespace = "www.jalview.org") + protected List features; + + @XmlElement(namespace = "www.jalview.org") + protected List pdbids; + + @XmlElement(namespace = "www.jalview.org", type = Integer.class) + protected List hiddenSequences; + + @XmlElement(namespace = "www.jalview.org") + protected List rnaViewer; + + @XmlAttribute(name = "colour") + protected Integer colour; + + @XmlAttribute(name = "start", required = true) + protected int start; + + @XmlAttribute(name = "end", required = true) + protected int end; + + @XmlAttribute(name = "id", required = true) + protected String id; + + @XmlAttribute(name = "hidden") + protected Boolean hidden; + + @XmlAttribute(name = "viewreference") + protected Boolean viewreference; + + /** + * Gets the value of the features property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <extension base="{www.jalview.org}pdbentry">
+     *       <sequence>
+     *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <simpleContent>
+     *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </extension>
+     *             </simpleContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *     </extension>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "structureState" }) + public static class Pdbids extends Pdbentry + { + + @XmlElement(namespace = "www.jalview.org") + protected List structureState; + + /** + * Gets the value of the structureState property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+       * <complexType>
+       *   <simpleContent>
+       *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+       *       <attGroup ref="{www.jalview.org}swingwindow"/>
+       *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+       *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+       *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </extension>
+       *   </simpleContent>
+       * </complexType>
+       * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "value" }) + public static class StructureState + { + + @XmlValue + protected String value; + + @XmlAttribute(name = "visible") + protected Boolean visible; + + @XmlAttribute(name = "viewId") + protected String viewId; + + @XmlAttribute(name = "alignwithAlignPanel") + protected Boolean alignwithAlignPanel; + + @XmlAttribute(name = "colourwithAlignPanel") + protected Boolean colourwithAlignPanel; + + @XmlAttribute(name = "colourByJmol") + protected Boolean colourByJmol; + + @XmlAttribute(name = "type") + protected String type; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; - /** - * Gets the value of the annotationColours property. - * - * @return - * possible object is - * {@link AnnotationColourScheme } - * - */ - public AnnotationColourScheme getAnnotationColours() { - return annotationColours; - } + @XmlAttribute(name = "ypos") + protected Integer ypos; /** - * Sets the value of the annotationColours property. + * Gets the value of the value property. * - * @param value - * allowed object is - * {@link AnnotationColourScheme } - * - */ - public void setAnnotationColours(AnnotationColourScheme value) { - this.annotationColours = value; - } - - /** - * Gets the value of the start property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getStart() { - return start; + public String getValue() + { + return value; } /** - * Sets the value of the start property. + * Sets the value of the value property. * * @param value - * allowed object is - * {@link Integer } - * - */ - public void setStart(Integer value) { - this.start = value; - } - - /** - * Gets the value of the end property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getEnd() { - return end; + public void setValue(String value) + { + this.value = value; } /** - * Sets the value of the end property. + * Gets the value of the visible property. * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setEnd(Integer value) { - this.end = value; - } - - /** - * Gets the value of the name property. + * @return possible object is {@link Boolean } * - * @return - * possible object is - * {@link String } - * */ - public String getName() { - return name; + public Boolean isVisible() + { + return visible; } /** - * Sets the value of the name property. + * Sets the value of the visible property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the colour property. + * allowed object is {@link Boolean } * - * @return - * possible object is - * {@link String } - * */ - public String getColour() { - return colour; + public void setVisible(Boolean value) + { + this.visible = value; } /** - * Sets the value of the colour property. + * Gets the value of the viewId property. * - * @param value - * allowed object is - * {@link String } - * - */ - public void setColour(String value) { - this.colour = value; - } - - /** - * Gets the value of the consThreshold property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getConsThreshold() { - return consThreshold; + public String getViewId() + { + return viewId; } /** - * Sets the value of the consThreshold property. + * Sets the value of the viewId property. * * @param value - * allowed object is - * {@link Integer } - * - */ - public void setConsThreshold(Integer value) { - this.consThreshold = value; - } - - /** - * Gets the value of the pidThreshold property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getPidThreshold() { - return pidThreshold; + public void setViewId(String value) + { + this.viewId = value; } /** - * Sets the value of the pidThreshold property. + * Gets the value of the alignwithAlignPanel property. * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setPidThreshold(Integer value) { - this.pidThreshold = value; - } - - /** - * Gets the value of the outlineColour property. + * @return possible object is {@link Boolean } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getOutlineColour() { - return outlineColour; + public boolean isAlignwithAlignPanel() + { + if (alignwithAlignPanel == null) + { + return true; + } + else + { + return alignwithAlignPanel; + } } /** - * Sets the value of the outlineColour property. + * Sets the value of the alignwithAlignPanel property. * * @param value - * allowed object is - * {@link Integer } - * - */ - public void setOutlineColour(Integer value) { - this.outlineColour = value; - } - - /** - * Gets the value of the displayBoxes property. + * allowed object is {@link Boolean } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isDisplayBoxes() { - return displayBoxes; + public void setAlignwithAlignPanel(Boolean value) + { + this.alignwithAlignPanel = value; } /** - * Sets the value of the displayBoxes property. + * Gets the value of the colourwithAlignPanel property. * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setDisplayBoxes(Boolean value) { - this.displayBoxes = value; - } - - /** - * Gets the value of the displayText property. + * @return possible object is {@link Boolean } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isDisplayText() { - return displayText; + public boolean isColourwithAlignPanel() + { + if (colourwithAlignPanel == null) + { + return false; + } + else + { + return colourwithAlignPanel; + } } /** - * Sets the value of the displayText property. + * Sets the value of the colourwithAlignPanel property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link Boolean } + * */ - public void setDisplayText(Boolean value) { - this.displayText = value; + public void setColourwithAlignPanel(Boolean value) + { + this.colourwithAlignPanel = value; } /** - * Gets the value of the colourText property. + * Gets the value of the colourByJmol property. + * + * @return possible object is {@link Boolean } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isColourText() { - return colourText; + public boolean isColourByJmol() + { + if (colourByJmol == null) + { + return true; + } + else + { + return colourByJmol; + } } /** - * Sets the value of the colourText property. + * Sets the value of the colourByJmol property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link Boolean } + * */ - public void setColourText(Boolean value) { - this.colourText = value; + public void setColourByJmol(Boolean value) + { + this.colourByJmol = value; } /** - * Gets the value of the textCol1 property. + * Gets the value of the type property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getTextCol1() { - return textCol1; + public String getType() + { + return type; } /** - * Sets the value of the textCol1 property. + * Sets the value of the type property. * * @param value - * allowed object is - * {@link Integer } - * + * allowed object is {@link String } + * */ - public void setTextCol1(Integer value) { - this.textCol1 = value; + public void setType(String value) + { + this.type = value; } /** - * Gets the value of the textCol2 property. + * Gets the value of the width property. + * + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getTextCol2() { - return textCol2; + public Integer getWidth() + { + return width; } /** - * Sets the value of the textCol2 property. + * Sets the value of the width property. * * @param value - * allowed object is - * {@link Integer } - * + * allowed object is {@link Integer } + * */ - public void setTextCol2(Integer value) { - this.textCol2 = value; + public void setWidth(Integer value) + { + this.width = value; } /** - * Gets the value of the textColThreshold property. + * Gets the value of the height property. + * + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link Integer } - * */ - public Integer getTextColThreshold() { - return textColThreshold; + public Integer getHeight() + { + return height; } /** - * Sets the value of the textColThreshold property. + * Sets the value of the height property. * * @param value - * allowed object is - * {@link Integer } - * + * allowed object is {@link Integer } + * */ - public void setTextColThreshold(Integer value) { - this.textColThreshold = value; + public void setHeight(Integer value) + { + this.height = value; } /** - * Gets the value of the showUnconserved property. + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link Boolean } - * */ - public Boolean isShowUnconserved() { - return showUnconserved; + public Integer getXpos() + { + return xpos; } /** - * Sets the value of the showUnconserved property. + * Sets the value of the xpos property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link Integer } + * */ - public void setShowUnconserved(Boolean value) { - this.showUnconserved = value; + public void setXpos(Integer value) + { + this.xpos = value; } /** - * Gets the value of the ignoreGapsinConsensus property. + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } * - * @return - * possible object is - * {@link Boolean } - * */ - public boolean isIgnoreGapsinConsensus() { - if (ignoreGapsinConsensus == null) { - return true; - } else { - return ignoreGapsinConsensus; - } + public Integer getYpos() + { + return ypos; } /** - * Sets the value of the ignoreGapsinConsensus property. + * Sets the value of the ypos property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link Integer } + * */ - public void setIgnoreGapsinConsensus(Boolean value) { - this.ignoreGapsinConsensus = value; + public void setYpos(Integer value) + { + this.ypos = value; } + } + + } + + /** + *

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="secondaryStructure" maxOccurs="unbounded">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "secondaryStructure" }) + public static class RnaViewer + { + + @XmlElement(namespace = "www.jalview.org", required = true) + protected List secondaryStructure; + + @XmlAttribute(name = "title") + protected String title; + + @XmlAttribute(name = "viewId") + protected String viewId; + + @XmlAttribute(name = "dividerLocation") + protected Integer dividerLocation; + + @XmlAttribute(name = "selectedRna") + protected Integer selectedRna; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the secondaryStructure property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+       * <complexType>
+       *   <complexContent>
+       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+       *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+       *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+       *     </restriction>
+       *   </complexContent>
+       * </complexType>
+       * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SecondaryStructure + { + + @XmlAttribute(name = "title") + protected String title; + + @XmlAttribute(name = "annotationId", required = true) + protected String annotationId; + + @XmlAttribute(name = "gapped") + protected Boolean gapped; + + @XmlAttribute(name = "viewerState") + protected String viewerState; + /** - * Gets the value of the showConsensusHistogram property. + * Gets the value of the title property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Boolean } - * */ - public boolean isShowConsensusHistogram() { - if (showConsensusHistogram == null) { - return true; - } else { - return showConsensusHistogram; - } + public String getTitle() + { + return title; } /** - * Sets the value of the showConsensusHistogram property. + * Sets the value of the title property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link String } + * */ - public void setShowConsensusHistogram(Boolean value) { - this.showConsensusHistogram = value; + public void setTitle(String value) + { + this.title = value; } /** - * Gets the value of the showSequenceLogo property. + * Gets the value of the annotationId property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link Boolean } - * */ - public boolean isShowSequenceLogo() { - if (showSequenceLogo == null) { - return false; - } else { - return showSequenceLogo; - } + public String getAnnotationId() + { + return annotationId; } /** - * Sets the value of the showSequenceLogo property. + * Sets the value of the annotationId property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link String } + * */ - public void setShowSequenceLogo(Boolean value) { - this.showSequenceLogo = value; + public void setAnnotationId(String value) + { + this.annotationId = value; } /** - * Gets the value of the normaliseSequenceLogo property. + * Gets the value of the gapped property. + * + * @return possible object is {@link Boolean } * - * @return - * possible object is - * {@link Boolean } - * */ - public boolean isNormaliseSequenceLogo() { - if (normaliseSequenceLogo == null) { - return false; - } else { - return normaliseSequenceLogo; - } + public Boolean isGapped() + { + return gapped; } /** - * Sets the value of the normaliseSequenceLogo property. + * Sets the value of the gapped property. * * @param value - * allowed object is - * {@link Boolean } - * + * allowed object is {@link Boolean } + * */ - public void setNormaliseSequenceLogo(Boolean value) { - this.normaliseSequenceLogo = value; + public void setGapped(Boolean value) + { + this.gapped = value; } /** - * Gets the value of the id property. + * Gets the value of the viewerState property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getId() { - return id; + public String getViewerState() + { + return viewerState; } /** - * Sets the value of the id property. + * Sets the value of the viewerState property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link String } + * */ - public void setId(String value) { - this.id = value; + public void setViewerState(String value) + { + this.viewerState = value; } + } + + } + + } + + /** + *

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

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.PcaViewer.Axis } + * + * + */ + public List getAxis() + { + if (axis == null) + { + axis = new ArrayList(); + } + return this.axis; + } + + /** + * Gets the value of the seqPointMin property. + * + * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin } + * + */ + public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() + { + return seqPointMin; + } + + /** + * Sets the value of the seqPointMin property. + * + * @param value + * allowed object is {@link JalviewModel.PcaViewer.SeqPointMin } + * + */ + public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) + { + this.seqPointMin = value; + } + + /** + * Gets the value of the seqPointMax property. + * + * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax } + * + */ + public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() + { + return seqPointMax; + } + + /** + * Sets the value of the seqPointMax property. + * + * @param value + * allowed object is {@link JalviewModel.PcaViewer.SeqPointMax } + * + */ + public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) + { + this.seqPointMax = value; + } + + /** + * Gets the value of the pcaData property. + * + * @return possible object is {@link PcaDataType } + * + */ + public PcaDataType getPcaData() + { + return pcaData; + } + + /** + * Sets the value of the pcaData property. + * + * @param value + * allowed object is {@link PcaDataType } + * + */ + public void setPcaData(PcaDataType value) + { + this.pcaData = value; + } + + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the scoreModelName property. + * + * @return possible object is {@link String } + * + */ + public String getScoreModelName() + { + return scoreModelName; + } + + /** + * Sets the value of the scoreModelName property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setScoreModelName(String value) + { + this.scoreModelName = value; + } + + /** + * Gets the value of the xDim property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXDim() + { + return xDim; + } + + /** + * Sets the value of the xDim property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXDim(Integer value) + { + this.xDim = value; } + /** + * Gets the value of the yDim property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYDim() + { + return yDim; + } /** - *

Java class for anonymous complex type. + * Sets the value of the yDim property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link Integer } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <extension base="{www.jalview.org}pdbentry">
-     *                 <sequence>
-     *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *                     <complexType>
-     *                       <simpleContent>
-     *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *                           <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         </extension>
-     *                       </simpleContent>
-     *                     </complexType>
-     *                   </element>
-     *                 </sequence>
-     *               </extension>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <sequence>
-     *                   <element name="secondaryStructure" maxOccurs="unbounded">
-     *                     <complexType>
-     *                       <complexContent>
-     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         </restriction>
-     *                       </complexContent>
-     *                     </complexType>
-     *                   </element>
-     *                 </sequence>
-     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public void setYDim(Integer value) + { + this.yDim = value; + } + + /** + * Gets the value of the zDim property. * + * @return possible object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "features", - "pdbids", - "hiddenSequences", - "rnaViewer" - }) - public static class JSeq { - - @XmlElement(namespace = "www.jalview.org") - protected List features; - @XmlElement(namespace = "www.jalview.org") - protected List pdbids; - @XmlElement(namespace = "www.jalview.org", type = Integer.class) - protected List hiddenSequences; - @XmlElement(namespace = "www.jalview.org") - protected List rnaViewer; - @XmlAttribute(name = "colour") - protected Integer colour; - @XmlAttribute(name = "start", required = true) - protected int start; - @XmlAttribute(name = "end", required = true) - protected int end; - @XmlAttribute(name = "id", required = true) - protected String id; - @XmlAttribute(name = "hidden") - protected Boolean hidden; - @XmlAttribute(name = "viewreference") - protected Boolean viewreference; + public Integer getZDim() + { + return zDim; + } - /** - * Gets the value of the features property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getFeatures().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getPdbids().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getHiddenSequences().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getRnaViewer().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link JalviewModel.JSeq.RnaViewer } - * - * - */ - public List getRnaViewer() { - if (rnaViewer == null) { - rnaViewer = new ArrayList(); - } - return this.rnaViewer; - } + /** + * Gets the value of the scaleFactor property. + * + * @return possible object is {@link Float } + * + */ + public Float getScaleFactor() + { + return scaleFactor; + } - /** - * Gets the value of the colour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getColour() { - return colour; - } + /** + * Sets the value of the scaleFactor property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setScaleFactor(Float value) + { + this.scaleFactor = value; + } - /** - * Sets the value of the colour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setColour(Integer value) { - this.colour = value; - } + /** + * Gets the value of the showLabels property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowLabels() + { + return showLabels; + } - /** - * Gets the value of the start property. - * - */ - public int getStart() { - return start; - } + /** + * Sets the value of the showLabels property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowLabels(Boolean value) + { + this.showLabels = value; + } - /** - * Sets the value of the start property. - * - */ - public void setStart(int value) { - this.start = value; - } + /** + * Gets the value of the linkToAllViews property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isLinkToAllViews() + { + return linkToAllViews; + } - /** - * Gets the value of the end property. - * - */ - public int getEnd() { - return end; - } + /** + * Sets the value of the linkToAllViews property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setLinkToAllViews(Boolean value) + { + this.linkToAllViews = value; + } - /** - * Sets the value of the end property. - * - */ - public void setEnd(int value) { - this.end = value; - } + /** + * Gets the value of the includeGaps property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isIncludeGaps() + { + return includeGaps; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * Sets the value of the includeGaps property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setIncludeGaps(Boolean value) + { + this.includeGaps = value; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } + /** + * Gets the value of the matchGaps property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isMatchGaps() + { + return matchGaps; + } - /** - * Gets the value of the hidden property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isHidden() { - return hidden; - } + /** + * Sets the value of the matchGaps property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setMatchGaps(Boolean value) + { + this.matchGaps = value; + } - /** - * Sets the value of the hidden property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setHidden(Boolean value) { - this.hidden = value; - } + /** + * Gets the value of the includeGappedColumns property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isIncludeGappedColumns() + { + return includeGappedColumns; + } - /** - * Gets the value of the viewreference property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isViewreference() { - return viewreference; - } + /** + * Sets the value of the includeGappedColumns property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setIncludeGappedColumns(Boolean value) + { + this.includeGappedColumns = value; + } - /** - * Sets the value of the viewreference property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setViewreference(Boolean value) { - this.viewreference = value; - } + /** + * Gets the value of the denominateByShortestLength property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isDenominateByShortestLength() + { + return denominateByShortestLength; + } + /** + * Sets the value of the denominateByShortestLength property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setDenominateByShortestLength(Boolean value) + { + this.denominateByShortestLength = value; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <extension base="{www.jalview.org}pdbentry">
-         *       <sequence>
-         *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-         *           <complexType>
-         *             <simpleContent>
-         *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-         *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-         *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               </extension>
-         *             </simpleContent>
-         *           </complexType>
-         *         </element>
-         *       </sequence>
-         *     </extension>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "structureState" - }) - public static class Pdbids - extends Pdbentry - { + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } - @XmlElement(namespace = "www.jalview.org") - protected List structureState; - - /** - * Gets the value of the structureState property. - * - *

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

- * For example, to add a new item, do as follows: - *

-             *    getStructureState().add(newItem);
-             * 
- * - * - *

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

Java class for anonymous complex type. - * - *

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

-             * <complexType>
-             *   <simpleContent>
-             *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-             *       <attGroup ref="{www.jalview.org}swingwindow"/>
-             *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-             *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     </extension>
-             *   </simpleContent>
-             * </complexType>
-             * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "value" - }) - public static class StructureState { - - @XmlValue - protected String value; - @XmlAttribute(name = "visible") - protected Boolean visible; - @XmlAttribute(name = "viewId") - protected String viewId; - @XmlAttribute(name = "alignwithAlignPanel") - protected Boolean alignwithAlignPanel; - @XmlAttribute(name = "colourwithAlignPanel") - protected Boolean colourwithAlignPanel; - @XmlAttribute(name = "colourByJmol") - protected Boolean colourByJmol; - @XmlAttribute(name = "type") - protected String type; - @XmlAttribute(name = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - /** - * Gets the value of the visible property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isVisible() { - return visible; - } - - /** - * Sets the value of the visible property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setVisible(Boolean value) { - this.visible = value; - } - - /** - * Gets the value of the viewId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getViewId() { - return viewId; - } - - /** - * Sets the value of the viewId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setViewId(String value) { - this.viewId = value; - } - - /** - * Gets the value of the alignwithAlignPanel property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isAlignwithAlignPanel() { - if (alignwithAlignPanel == null) { - return true; - } else { - return alignwithAlignPanel; - } - } - - /** - * Sets the value of the alignwithAlignPanel property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setAlignwithAlignPanel(Boolean value) { - this.alignwithAlignPanel = value; - } - - /** - * Gets the value of the colourwithAlignPanel property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isColourwithAlignPanel() { - if (colourwithAlignPanel == null) { - return false; - } else { - return colourwithAlignPanel; - } - } - - /** - * Sets the value of the colourwithAlignPanel property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setColourwithAlignPanel(Boolean value) { - this.colourwithAlignPanel = value; - } - - /** - * Gets the value of the colourByJmol property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isColourByJmol() { - if (colourByJmol == null) { - return true; - } else { - return colourByJmol; - } - } - - /** - * Sets the value of the colourByJmol property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setColourByJmol(Boolean value) { - this.colourByJmol = value; - } - - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } - - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the width property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getWidth() { - return width; - } - - /** - * Sets the value of the width property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setWidth(Integer value) { - this.width = value; - } - - /** - * Gets the value of the height property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHeight() { - return height; - } - - /** - * Sets the value of the height property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setHeight(Integer value) { - this.height = value; - } - - /** - * Gets the value of the xpos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXpos() { - return xpos; - } - - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setXpos(Integer value) { - this.xpos = value; - } - - /** - * Gets the value of the ypos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYpos() { - return ypos; - } - - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setYpos(Integer value) { - this.ypos = value; - } - - } + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } - } + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <sequence>
-         *         <element name="secondaryStructure" maxOccurs="unbounded">
-         *           <complexType>
-         *             <complexContent>
-         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               </restriction>
-         *             </complexContent>
-         *           </complexType>
-         *         </element>
-         *       </sequence>
-         *       <attGroup ref="{www.jalview.org}swingwindow"/>
-         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "secondaryStructure" - }) - public static class RnaViewer { - - @XmlElement(namespace = "www.jalview.org", required = true) - protected List secondaryStructure; - @XmlAttribute(name = "title") - protected String title; - @XmlAttribute(name = "viewId") - protected String viewId; - @XmlAttribute(name = "dividerLocation") - protected Integer dividerLocation; - @XmlAttribute(name = "selectedRna") - protected Integer selectedRna; - @XmlAttribute(name = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; - - /** - * Gets the value of the secondaryStructure property. - * - *

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

- * For example, to add a new item, do as follows: - *

-             *    getSecondaryStructure().add(newItem);
-             * 
- * - * - *

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

Java class for anonymous complex type. - * - *

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

-             * <complexType>
-             *   <complexContent>
-             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     </restriction>
-             *   </complexContent>
-             * </complexType>
-             * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SecondaryStructure { - - @XmlAttribute(name = "title") - protected String title; - @XmlAttribute(name = "annotationId", required = true) - protected String annotationId; - @XmlAttribute(name = "gapped") - protected Boolean gapped; - @XmlAttribute(name = "viewerState") - protected String viewerState; - - /** - * Gets the value of the title property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTitle() { - return title; - } - - /** - * Sets the value of the title property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setTitle(String value) { - this.title = value; - } - - /** - * Gets the value of the annotationId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getAnnotationId() { - return annotationId; - } - - /** - * Sets the value of the annotationId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setAnnotationId(String value) { - this.annotationId = value; - } - - /** - * Gets the value of the gapped property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isGapped() { - return gapped; - } - - /** - * Sets the value of the gapped property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setGapped(Boolean value) { - this.gapped = value; - } - - /** - * Gets the value of the viewerState property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getViewerState() { - return viewerState; - } - - /** - * Sets the value of the viewerState property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setViewerState(String value) { - this.viewerState = value; - } - - } + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } - } + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXpos(Integer value) + { + this.xpos = value; + } + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; } + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } /** - *

Java class for anonymous complex type. + *

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

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

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

      * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="sequencePoint" maxOccurs="unbounded">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="axis" maxOccurs="3" minOccurs="3">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="seqPointMin">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="seqPointMax">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attGroup ref="{www.jalview.org}position"/>
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attGroup ref="{www.jalview.org}position"/>
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -3145,3670 +3859,3130 @@ public class JalviewModel {
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "sequencePoint",
-        "axis",
-        "seqPointMin",
-        "seqPointMax",
-        "pcaData"
-    })
-    public static class PcaViewer {
-
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List sequencePoint;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected List axis;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-        @XmlElement(namespace = "www.jalview.org", required = true)
-        protected PcaDataType pcaData;
-        @XmlAttribute(name = "title")
-        protected String title;
-        @XmlAttribute(name = "scoreModelName")
-        protected String scoreModelName;
-        @XmlAttribute(name = "xDim")
-        protected Integer xDim;
-        @XmlAttribute(name = "yDim")
-        protected Integer yDim;
-        @XmlAttribute(name = "zDim")
-        protected Integer zDim;
-        @XmlAttribute(name = "bgColour")
-        protected Integer bgColour;
-        @XmlAttribute(name = "scaleFactor")
-        protected Float scaleFactor;
-        @XmlAttribute(name = "showLabels")
-        protected Boolean showLabels;
-        @XmlAttribute(name = "linkToAllViews")
-        protected Boolean linkToAllViews;
-        @XmlAttribute(name = "includeGaps")
-        protected Boolean includeGaps;
-        @XmlAttribute(name = "matchGaps")
-        protected Boolean matchGaps;
-        @XmlAttribute(name = "includeGappedColumns")
-        protected Boolean includeGappedColumns;
-        @XmlAttribute(name = "denominateByShortestLength")
-        protected Boolean denominateByShortestLength;
-        @XmlAttribute(name = "width")
-        protected Integer width;
-        @XmlAttribute(name = "height")
-        protected Integer height;
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
-
-        /**
-         * Gets the value of the sequencePoint property.
-         * 
-         * 

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

- * For example, to add a new item, do as follows: - *

-         *    getSequencePoint().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getAxis().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link JalviewModel.PcaViewer.Axis } - * - * - */ - public List getAxis() { - if (axis == null) { - axis = new ArrayList(); - } - return this.axis; - } - - /** - * Gets the value of the seqPointMin property. - * - * @return - * possible object is - * {@link JalviewModel.PcaViewer.SeqPointMin } - * - */ - public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() { - return seqPointMin; - } - - /** - * Sets the value of the seqPointMin property. - * - * @param value - * allowed object is - * {@link JalviewModel.PcaViewer.SeqPointMin } - * - */ - public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) { - this.seqPointMin = value; - } - - /** - * Gets the value of the seqPointMax property. - * - * @return - * possible object is - * {@link JalviewModel.PcaViewer.SeqPointMax } - * - */ - public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() { - return seqPointMax; - } - - /** - * Sets the value of the seqPointMax property. - * - * @param value - * allowed object is - * {@link JalviewModel.PcaViewer.SeqPointMax } - * - */ - public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) { - this.seqPointMax = value; - } - - /** - * Gets the value of the pcaData property. - * - * @return - * possible object is - * {@link PcaDataType } - * - */ - public PcaDataType getPcaData() { - return pcaData; - } - - /** - * Sets the value of the pcaData property. - * - * @param value - * allowed object is - * {@link PcaDataType } - * - */ - public void setPcaData(PcaDataType value) { - this.pcaData = value; - } - - /** - * Gets the value of the title property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTitle() { - return title; - } - - /** - * Sets the value of the title property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setTitle(String value) { - this.title = value; - } - - /** - * Gets the value of the scoreModelName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getScoreModelName() { - return scoreModelName; - } - - /** - * Sets the value of the scoreModelName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setScoreModelName(String value) { - this.scoreModelName = value; - } - - /** - * Gets the value of the xDim property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXDim() { - return xDim; - } - - /** - * Sets the value of the xDim property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setXDim(Integer value) { - this.xDim = value; - } - - /** - * Gets the value of the yDim property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYDim() { - return yDim; - } + @XmlType(name = "") + public static class Axis + { + + @XmlAttribute(name = "xPos") + protected Float xPos; + + @XmlAttribute(name = "yPos") + protected Float yPos; + + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getXPos() + { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setXPos(Float value) + { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getYPos() + { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setYPos(Float value) + { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getZPos() + { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setZPos(Float value) + { + this.zPos = value; + } - /** - * Sets the value of the yDim property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setYDim(Integer value) { - this.yDim = value; - } + } - /** - * Gets the value of the zDim property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getZDim() { - return zDim; - } + /** + *

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}position"/>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SeqPointMax + { + + @XmlAttribute(name = "xPos") + protected Float xPos; + + @XmlAttribute(name = "yPos") + protected Float yPos; + + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getXPos() + { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setXPos(Float value) + { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getYPos() + { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setYPos(Float value) + { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getZPos() + { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setZPos(Float value) + { + this.zPos = value; + } - /** - * Sets the value of the zDim property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setZDim(Integer value) { - this.zDim = value; - } + } - /** - * Gets the value of the bgColour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getBgColour() { - return bgColour; - } + /** + *

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}position"/>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SeqPointMin + { + + @XmlAttribute(name = "xPos") + protected Float xPos; + + @XmlAttribute(name = "yPos") + protected Float yPos; + + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the xPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getXPos() + { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setXPos(Float value) + { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getYPos() + { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setYPos(Float value) + { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getZPos() + { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setZPos(Float value) + { + this.zPos = value; + } - /** - * Sets the value of the bgColour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setBgColour(Integer value) { - this.bgColour = value; - } + } - /** - * Gets the value of the scaleFactor property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getScaleFactor() { - return scaleFactor; - } + /** + *

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}position"/>
+     *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SequencePoint + { + + @XmlAttribute(name = "sequenceRef") + protected String sequenceRef; + + @XmlAttribute(name = "xPos") + protected Float xPos; + + @XmlAttribute(name = "yPos") + protected Float yPos; + + @XmlAttribute(name = "zPos") + protected Float zPos; + + /** + * Gets the value of the sequenceRef property. + * + * @return possible object is {@link String } + * + */ + public String getSequenceRef() + { + return sequenceRef; + } + + /** + * Sets the value of the sequenceRef property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setSequenceRef(String value) + { + this.sequenceRef = value; + } + + /** + * Gets the value of the xPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getXPos() + { + return xPos; + } + + /** + * Sets the value of the xPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setXPos(Float value) + { + this.xPos = value; + } + + /** + * Gets the value of the yPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getYPos() + { + return yPos; + } + + /** + * Sets the value of the yPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setYPos(Float value) + { + this.yPos = value; + } + + /** + * Gets the value of the zPos property. + * + * @return possible object is {@link Float } + * + */ + public Float getZPos() + { + return zPos; + } + + /** + * Sets the value of the zPos property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setZPos(Float value) + { + this.zPos = value; + } - /** - * Sets the value of the scaleFactor property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setScaleFactor(Float value) { - this.scaleFactor = value; - } + } - /** - * Gets the value of the showLabels property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowLabels() { - return showLabels; - } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence minOccurs="0">
+   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "title", "newick" }) + public static class Tree + { + + @XmlElement(namespace = "www.jalview.org") + protected String title; + + @XmlElement(namespace = "www.jalview.org") + protected String newick; + + @XmlAttribute(name = "fontName") + protected String fontName; + + @XmlAttribute(name = "fontSize") + protected Integer fontSize; + + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; + + @XmlAttribute(name = "threshold") + protected Float threshold; + + @XmlAttribute(name = "showBootstrap") + protected Boolean showBootstrap; + + @XmlAttribute(name = "showDistances") + protected Boolean showDistances; + + @XmlAttribute(name = "markUnlinked") + protected Boolean markUnlinked; + + @XmlAttribute(name = "fitToWindow") + protected Boolean fitToWindow; + + @XmlAttribute(name = "currentTree") + protected Boolean currentTree; + + @XmlAttribute(name = "columnWise") + protected Boolean columnWise; + + @XmlAttribute(name = "columnReference") + protected String columnReference; + + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; + + @XmlAttribute(name = "linkToAllViews") + protected Boolean linkToAllViews; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; - /** - * Sets the value of the showLabels property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowLabels(Boolean value) { - this.showLabels = value; - } + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } - /** - * Gets the value of the linkToAllViews property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isLinkToAllViews() { - return linkToAllViews; - } + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } - /** - * Sets the value of the linkToAllViews property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setLinkToAllViews(Boolean value) { - this.linkToAllViews = value; - } + /** + * Gets the value of the newick property. + * + * @return possible object is {@link String } + * + */ + public String getNewick() + { + return newick; + } - /** - * Gets the value of the includeGaps property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isIncludeGaps() { - return includeGaps; - } + /** + * Sets the value of the newick property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setNewick(String value) + { + this.newick = value; + } - /** - * Sets the value of the includeGaps property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setIncludeGaps(Boolean value) { - this.includeGaps = value; - } + /** + * Gets the value of the fontName property. + * + * @return possible object is {@link String } + * + */ + public String getFontName() + { + return fontName; + } - /** - * Gets the value of the matchGaps property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isMatchGaps() { - return matchGaps; - } + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setFontName(String value) + { + this.fontName = value; + } - /** - * Sets the value of the matchGaps property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setMatchGaps(Boolean value) { - this.matchGaps = value; - } + /** + * Gets the value of the fontSize property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontSize() + { + return fontSize; + } - /** - * Gets the value of the includeGappedColumns property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isIncludeGappedColumns() { - return includeGappedColumns; - } + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontSize(Integer value) + { + this.fontSize = value; + } - /** - * Sets the value of the includeGappedColumns property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setIncludeGappedColumns(Boolean value) { - this.includeGappedColumns = value; - } + /** + * Gets the value of the fontStyle property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontStyle() + { + return fontStyle; + } - /** - * Gets the value of the denominateByShortestLength property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isDenominateByShortestLength() { - return denominateByShortestLength; - } + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontStyle(Integer value) + { + this.fontStyle = value; + } - /** - * Sets the value of the denominateByShortestLength property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setDenominateByShortestLength(Boolean value) { - this.denominateByShortestLength = value; - } + /** + * Gets the value of the threshold property. + * + * @return possible object is {@link Float } + * + */ + public Float getThreshold() + { + return threshold; + } - /** - * Gets the value of the width property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getWidth() { - return width; - } + /** + * Sets the value of the threshold property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setThreshold(Float value) + { + this.threshold = value; + } - /** - * Sets the value of the width property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setWidth(Integer value) { - this.width = value; - } + /** + * Gets the value of the showBootstrap property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowBootstrap() + { + return showBootstrap; + } - /** - * Gets the value of the height property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHeight() { - return height; - } + /** + * Sets the value of the showBootstrap property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowBootstrap(Boolean value) + { + this.showBootstrap = value; + } - /** - * Sets the value of the height property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setHeight(Integer value) { - this.height = value; - } + /** + * Gets the value of the showDistances property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowDistances() + { + return showDistances; + } - /** - * Gets the value of the xpos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXpos() { - return xpos; - } + /** + * Sets the value of the showDistances property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowDistances(Boolean value) + { + this.showDistances = value; + } - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setXpos(Integer value) { - this.xpos = value; - } + /** + * Gets the value of the markUnlinked property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isMarkUnlinked() + { + return markUnlinked; + } - /** - * Gets the value of the ypos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYpos() { - return ypos; - } + /** + * Sets the value of the markUnlinked property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setMarkUnlinked(Boolean value) + { + this.markUnlinked = value; + } - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setYpos(Integer value) { - this.ypos = value; - } + /** + * Gets the value of the fitToWindow property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isFitToWindow() + { + return fitToWindow; + } + /** + * Sets the value of the fitToWindow property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFitToWindow(Boolean value) + { + this.fitToWindow = value; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Axis { - - @XmlAttribute(name = "xPos") - protected Float xPos; - @XmlAttribute(name = "yPos") - protected Float yPos; - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * Gets the value of the xPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getXPos() { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setXPos(Float value) { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getYPos() { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setYPos(Float value) { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getZPos() { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setZPos(Float value) { - this.zPos = value; - } + /** + * Gets the value of the currentTree property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isCurrentTree() + { + return currentTree; + } - } + /** + * Sets the value of the currentTree property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setCurrentTree(Boolean value) + { + this.currentTree = value; + } + /** + * Gets the value of the columnWise property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isColumnWise() + { + if (columnWise == null) + { + return false; + } + else + { + return columnWise; + } + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SeqPointMax { - - @XmlAttribute(name = "xPos") - protected Float xPos; - @XmlAttribute(name = "yPos") - protected Float yPos; - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * Gets the value of the xPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getXPos() { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setXPos(Float value) { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getYPos() { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setYPos(Float value) { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getZPos() { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setZPos(Float value) { - this.zPos = value; - } + /** + * Sets the value of the columnWise property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setColumnWise(Boolean value) + { + this.columnWise = value; + } + + /** + * Gets the value of the columnReference property. + * + * @return possible object is {@link String } + * + */ + public String getColumnReference() + { + return columnReference; + } + + /** + * Sets the value of the columnReference property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setColumnReference(String value) + { + this.columnReference = value; + } - } + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SeqPointMin { - - @XmlAttribute(name = "xPos") - protected Float xPos; - @XmlAttribute(name = "yPos") - protected Float yPos; - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * Gets the value of the xPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getXPos() { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setXPos(Float value) { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getYPos() { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setYPos(Float value) { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getZPos() { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setZPos(Float value) { - this.zPos = value; - } + /** + * Gets the value of the linkToAllViews property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isLinkToAllViews() + { + if (linkToAllViews == null) + { + return false; + } + else + { + return linkToAllViews; + } + } - } + /** + * Sets the value of the linkToAllViews property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setLinkToAllViews(Boolean value) + { + this.linkToAllViews = value; + } + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}position"/>
-         *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SequencePoint { - - @XmlAttribute(name = "sequenceRef") - protected String sequenceRef; - @XmlAttribute(name = "xPos") - protected Float xPos; - @XmlAttribute(name = "yPos") - protected Float yPos; - @XmlAttribute(name = "zPos") - protected Float zPos; - - /** - * Gets the value of the sequenceRef property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getSequenceRef() { - return sequenceRef; - } - - /** - * Sets the value of the sequenceRef property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setSequenceRef(String value) { - this.sequenceRef = value; - } - - /** - * Gets the value of the xPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getXPos() { - return xPos; - } - - /** - * Sets the value of the xPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setXPos(Float value) { - this.xPos = value; - } - - /** - * Gets the value of the yPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getYPos() { - return yPos; - } - - /** - * Sets the value of the yPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setYPos(Float value) { - this.yPos = value; - } - - /** - * Gets the value of the zPos property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getZPos() { - return zPos; - } - - /** - * Sets the value of the zPos property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setZPos(Float value) { - this.zPos = value; - } + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } - } + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; } + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } /** - *

Java class for anonymous complex type. + * Sets the value of the xpos property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link Integer } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence minOccurs="0">
-     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public void setXpos(Integer value) + { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. * + * @return possible object is {@link Integer } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "title", - "newick" - }) - public static class Tree { + public Integer getYpos() + { + return ypos; + } - @XmlElement(namespace = "www.jalview.org") - protected String title; - @XmlElement(namespace = "www.jalview.org") - protected String newick; - @XmlAttribute(name = "fontName") - protected String fontName; - @XmlAttribute(name = "fontSize") - protected Integer fontSize; - @XmlAttribute(name = "fontStyle") - protected Integer fontStyle; - @XmlAttribute(name = "threshold") - protected Float threshold; - @XmlAttribute(name = "showBootstrap") - protected Boolean showBootstrap; - @XmlAttribute(name = "showDistances") - protected Boolean showDistances; - @XmlAttribute(name = "markUnlinked") - protected Boolean markUnlinked; - @XmlAttribute(name = "fitToWindow") - protected Boolean fitToWindow; - @XmlAttribute(name = "currentTree") - protected Boolean currentTree; - @XmlAttribute(name = "columnWise") - protected Boolean columnWise; - @XmlAttribute(name = "columnReference") - protected String columnReference; - @XmlAttribute(name = "id") - @XmlJavaTypeAdapter(CollapsedStringAdapter.class) - @XmlID - @XmlSchemaType(name = "ID") - protected String id; - @XmlAttribute(name = "linkToAllViews") - protected Boolean linkToAllViews; - @XmlAttribute(name = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } - /** - * Gets the value of the title property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTitle() { - return title; - } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+   *       </sequence>
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "userColourScheme" }) + public static class UserColours + { + + @XmlElement( + name = "UserColourScheme", + namespace = "www.jalview.org", + required = true) + protected JalviewUserColours userColourScheme; + + @XmlAttribute(name = "id") + protected String id; - /** - * Sets the value of the title property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setTitle(String value) { - this.title = value; - } + /** + * Gets the value of the userColourScheme property. + * + * @return possible object is {@link JalviewUserColours } + * + */ + public JalviewUserColours getUserColourScheme() + { + return userColourScheme; + } - /** - * Gets the value of the newick property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getNewick() { - return newick; - } + /** + * Sets the value of the userColourScheme property. + * + * @param value + * allowed object is {@link JalviewUserColours } + * + */ + public void setUserColourScheme(JalviewUserColours value) + { + this.userColourScheme = value; + } - /** - * Sets the value of the newick property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setNewick(String value) { - this.newick = value; - } + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } - /** - * Gets the value of the fontName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getFontName() { - return fontName; - } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } - /** - * Sets the value of the fontName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setFontName(String value) { - this.fontName = value; - } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+   *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+   *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *               </extension>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *         <element name="overview" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+   *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attGroup ref="{www.jalview.org}swingwindow"/>
+   *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+   *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+   *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "annotationColours", "hiddenColumns", "calcIdParam", "overview" }) + public static class Viewport + { + + @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org") + protected AnnotationColourScheme annotationColours; + + @XmlElement(namespace = "www.jalview.org") + protected List hiddenColumns; + + @XmlElement(namespace = "www.jalview.org") + protected List calcIdParam; + + @XmlElement(namespace = "www.jalview.org") + protected JalviewModel.Viewport.Overview overview; + + @XmlAttribute(name = "conservationSelected") + protected Boolean conservationSelected; + + @XmlAttribute(name = "pidSelected") + protected Boolean pidSelected; + + @XmlAttribute(name = "bgColour") + protected String bgColour; + + @XmlAttribute(name = "consThreshold") + protected Integer consThreshold; + + @XmlAttribute(name = "pidThreshold") + protected Integer pidThreshold; + + @XmlAttribute(name = "title") + protected String title; + + @XmlAttribute(name = "showFullId") + protected Boolean showFullId; + + @XmlAttribute(name = "rightAlignIds") + protected Boolean rightAlignIds; + + @XmlAttribute(name = "showText") + protected Boolean showText; + + @XmlAttribute(name = "showColourText") + protected Boolean showColourText; + + @XmlAttribute(name = "showUnconserved") + protected Boolean showUnconserved; + + @XmlAttribute(name = "showBoxes") + protected Boolean showBoxes; + + @XmlAttribute(name = "wrapAlignment") + protected Boolean wrapAlignment; - /** - * Gets the value of the fontSize property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getFontSize() { - return fontSize; - } + @XmlAttribute(name = "renderGaps") + protected Boolean renderGaps; - /** - * Sets the value of the fontSize property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setFontSize(Integer value) { - this.fontSize = value; - } + @XmlAttribute(name = "showSequenceFeatures") + protected Boolean showSequenceFeatures; - /** - * Gets the value of the fontStyle property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getFontStyle() { - return fontStyle; - } + @XmlAttribute(name = "showNPfeatureTooltip") + protected Boolean showNPfeatureTooltip; - /** - * Sets the value of the fontStyle property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setFontStyle(Integer value) { - this.fontStyle = value; - } + @XmlAttribute(name = "showDbRefTooltip") + protected Boolean showDbRefTooltip; - /** - * Gets the value of the threshold property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getThreshold() { - return threshold; - } + @XmlAttribute(name = "followHighlight") + protected Boolean followHighlight; - /** - * Sets the value of the threshold property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setThreshold(Float value) { - this.threshold = value; - } + @XmlAttribute(name = "followSelection") + protected Boolean followSelection; - /** - * Gets the value of the showBootstrap property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowBootstrap() { - return showBootstrap; - } + @XmlAttribute(name = "showAnnotation") + protected Boolean showAnnotation; - /** - * Sets the value of the showBootstrap property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowBootstrap(Boolean value) { - this.showBootstrap = value; - } + @XmlAttribute(name = "centreColumnLabels") + protected Boolean centreColumnLabels; - /** - * Gets the value of the showDistances property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowDistances() { - return showDistances; - } + @XmlAttribute(name = "showGroupConservation") + protected Boolean showGroupConservation; - /** - * Sets the value of the showDistances property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowDistances(Boolean value) { - this.showDistances = value; - } + @XmlAttribute(name = "showGroupConsensus") + protected Boolean showGroupConsensus; - /** - * Gets the value of the markUnlinked property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isMarkUnlinked() { - return markUnlinked; - } + @XmlAttribute(name = "showConsensusHistogram") + protected Boolean showConsensusHistogram; - /** - * Sets the value of the markUnlinked property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setMarkUnlinked(Boolean value) { - this.markUnlinked = value; - } + @XmlAttribute(name = "showSequenceLogo") + protected Boolean showSequenceLogo; - /** - * Gets the value of the fitToWindow property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isFitToWindow() { - return fitToWindow; - } + @XmlAttribute(name = "normaliseSequenceLogo") + protected Boolean normaliseSequenceLogo; - /** - * Sets the value of the fitToWindow property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setFitToWindow(Boolean value) { - this.fitToWindow = value; - } + @XmlAttribute(name = "ignoreGapsinConsensus") + protected Boolean ignoreGapsinConsensus; - /** - * Gets the value of the currentTree property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isCurrentTree() { - return currentTree; - } + @XmlAttribute(name = "startRes") + protected Integer startRes; - /** - * Sets the value of the currentTree property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setCurrentTree(Boolean value) { - this.currentTree = value; - } + @XmlAttribute(name = "startSeq") + protected Integer startSeq; - /** - * Gets the value of the columnWise property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isColumnWise() { - if (columnWise == null) { - return false; - } else { - return columnWise; - } - } + @XmlAttribute(name = "charWidth") + protected Integer charWidth; - /** - * Sets the value of the columnWise property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setColumnWise(Boolean value) { - this.columnWise = value; - } + @XmlAttribute(name = "charHeight") + protected Integer charHeight; - /** - * Gets the value of the columnReference property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getColumnReference() { - return columnReference; - } + @XmlAttribute(name = "fontName") + protected String fontName; - /** - * Sets the value of the columnReference property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setColumnReference(String value) { - this.columnReference = value; - } + @XmlAttribute(name = "fontSize") + protected Integer fontSize; - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + @XmlAttribute(name = "fontStyle") + protected Integer fontStyle; - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } + @XmlAttribute(name = "scaleProteinAsCdna") + protected Boolean scaleProteinAsCdna; - /** - * Gets the value of the linkToAllViews property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isLinkToAllViews() { - if (linkToAllViews == null) { - return false; - } else { - return linkToAllViews; - } - } + @XmlAttribute(name = "viewName") + protected String viewName; - /** - * Sets the value of the linkToAllViews property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setLinkToAllViews(Boolean value) { - this.linkToAllViews = value; - } + @XmlAttribute(name = "sequenceSetId") + protected String sequenceSetId; + + @XmlAttribute(name = "gatheredViews") + protected Boolean gatheredViews; - /** - * Gets the value of the width property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getWidth() { - return width; - } + @XmlAttribute(name = "textCol1") + protected Integer textCol1; - /** - * Sets the value of the width property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setWidth(Integer value) { - this.width = value; - } + @XmlAttribute(name = "textCol2") + protected Integer textCol2; - /** - * Gets the value of the height property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHeight() { - return height; - } + @XmlAttribute(name = "textColThreshold") + protected Integer textColThreshold; - /** - * Sets the value of the height property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setHeight(Integer value) { - this.height = value; - } + @XmlAttribute(name = "id") + @XmlJavaTypeAdapter(CollapsedStringAdapter.class) + @XmlID + @XmlSchemaType(name = "ID") + protected String id; - /** - * Gets the value of the xpos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXpos() { - return xpos; - } + @XmlAttribute(name = "complementId") + protected String complementId; - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setXpos(Integer value) { - this.xpos = value; - } + @XmlAttribute(name = "showComplementFeatures") + protected Boolean showComplementFeatures; - /** - * Gets the value of the ypos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYpos() { - return ypos; - } + @XmlAttribute(name = "showComplementFeaturesOnTop") + protected Boolean showComplementFeaturesOnTop; - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setYpos(Integer value) { - this.ypos = value; - } + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the annotationColours property. + * + * @return possible object is {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme getAnnotationColours() + { + return annotationColours; } + /** + * Sets the value of the annotationColours property. + * + * @param value + * allowed object is {@link AnnotationColourScheme } + * + */ + public void setAnnotationColours(AnnotationColourScheme value) + { + this.annotationColours = value; + } /** - *

Java class for anonymous complex type. + * Gets the value of the hiddenColumns property. + * + *

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

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

+ * For example, to add a new item, do as follows: * *

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport.HiddenColumns } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "userColourScheme" - }) - public static class UserColours { - - @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true) - protected JalviewUserColours userColourScheme; - @XmlAttribute(name = "id") - protected String id; - - /** - * Gets the value of the userColourScheme property. - * - * @return - * possible object is - * {@link JalviewUserColours } - * - */ - public JalviewUserColours getUserColourScheme() { - return userColourScheme; - } - - /** - * Sets the value of the userColourScheme property. - * - * @param value - * allowed object is - * {@link JalviewUserColours } - * - */ - public void setUserColourScheme(JalviewUserColours value) { - this.userColourScheme = value; - } - - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } - - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } - + public List getHiddenColumns() + { + if (hiddenColumns == null) + { + hiddenColumns = new ArrayList(); + } + return this.hiddenColumns; } - /** - *

Java class for anonymous complex type. + * Gets the value of the calcIdParam property. + * + *

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

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

+ * For example, to add a new item, do as follows: * *

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

+ * Objects of the following type(s) are allowed in the list + * {@link JalviewModel.Viewport.CalcIdParam } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "annotationColours", - "hiddenColumns", - "calcIdParam", - "overview" - }) - public static class Viewport { - - @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org") - protected AnnotationColourScheme annotationColours; - @XmlElement(namespace = "www.jalview.org") - protected List hiddenColumns; - @XmlElement(namespace = "www.jalview.org") - protected List calcIdParam; - @XmlElement(namespace = "www.jalview.org") - protected JalviewModel.Viewport.Overview overview; - @XmlAttribute(name = "conservationSelected") - protected Boolean conservationSelected; - @XmlAttribute(name = "pidSelected") - protected Boolean pidSelected; - @XmlAttribute(name = "bgColour") - protected String bgColour; - @XmlAttribute(name = "consThreshold") - protected Integer consThreshold; - @XmlAttribute(name = "pidThreshold") - protected Integer pidThreshold; - @XmlAttribute(name = "title") - protected String title; - @XmlAttribute(name = "showFullId") - protected Boolean showFullId; - @XmlAttribute(name = "rightAlignIds") - protected Boolean rightAlignIds; - @XmlAttribute(name = "showText") - protected Boolean showText; - @XmlAttribute(name = "showColourText") - protected Boolean showColourText; - @XmlAttribute(name = "showUnconserved") - protected Boolean showUnconserved; - @XmlAttribute(name = "showBoxes") - protected Boolean showBoxes; - @XmlAttribute(name = "wrapAlignment") - protected Boolean wrapAlignment; - @XmlAttribute(name = "renderGaps") - protected Boolean renderGaps; - @XmlAttribute(name = "showSequenceFeatures") - protected Boolean showSequenceFeatures; - @XmlAttribute(name = "showNPfeatureTooltip") - protected Boolean showNPfeatureTooltip; - @XmlAttribute(name = "showDbRefTooltip") - protected Boolean showDbRefTooltip; - @XmlAttribute(name = "followHighlight") - protected Boolean followHighlight; - @XmlAttribute(name = "followSelection") - protected Boolean followSelection; - @XmlAttribute(name = "showAnnotation") - protected Boolean showAnnotation; - @XmlAttribute(name = "centreColumnLabels") - protected Boolean centreColumnLabels; - @XmlAttribute(name = "showGroupConservation") - protected Boolean showGroupConservation; - @XmlAttribute(name = "showGroupConsensus") - protected Boolean showGroupConsensus; - @XmlAttribute(name = "showConsensusHistogram") - protected Boolean showConsensusHistogram; - @XmlAttribute(name = "showSequenceLogo") - protected Boolean showSequenceLogo; - @XmlAttribute(name = "normaliseSequenceLogo") - protected Boolean normaliseSequenceLogo; - @XmlAttribute(name = "ignoreGapsinConsensus") - protected Boolean ignoreGapsinConsensus; - @XmlAttribute(name = "startRes") - protected Integer startRes; - @XmlAttribute(name = "startSeq") - protected Integer startSeq; - @XmlAttribute(name = "charWidth") - protected Integer charWidth; - @XmlAttribute(name = "charHeight") - protected Integer charHeight; - @XmlAttribute(name = "fontName") - protected String fontName; - @XmlAttribute(name = "fontSize") - protected Integer fontSize; - @XmlAttribute(name = "fontStyle") - protected Integer fontStyle; - @XmlAttribute(name = "scaleProteinAsCdna") - protected Boolean scaleProteinAsCdna; - @XmlAttribute(name = "viewName") - protected String viewName; - @XmlAttribute(name = "sequenceSetId") - protected String sequenceSetId; - @XmlAttribute(name = "gatheredViews") - protected Boolean gatheredViews; - @XmlAttribute(name = "textCol1") - protected Integer textCol1; - @XmlAttribute(name = "textCol2") - protected Integer textCol2; - @XmlAttribute(name = "textColThreshold") - protected Integer textColThreshold; - @XmlAttribute(name = "id") - @XmlJavaTypeAdapter(CollapsedStringAdapter.class) - @XmlID - @XmlSchemaType(name = "ID") - protected String id; - @XmlAttribute(name = "complementId") - protected String complementId; - @XmlAttribute(name = "showComplementFeatures") - protected Boolean showComplementFeatures; - @XmlAttribute(name = "showComplementFeaturesOnTop") - protected Boolean showComplementFeaturesOnTop; - @XmlAttribute(name = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; - - /** - * Gets the value of the annotationColours property. - * - * @return - * possible object is - * {@link AnnotationColourScheme } - * - */ - public AnnotationColourScheme getAnnotationColours() { - return annotationColours; - } - - /** - * Sets the value of the annotationColours property. - * - * @param value - * allowed object is - * {@link AnnotationColourScheme } - * - */ - public void setAnnotationColours(AnnotationColourScheme value) { - this.annotationColours = value; - } - - /** - * Gets the value of the hiddenColumns property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getHiddenColumns().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getCalcIdParam().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link JalviewModel.Viewport.CalcIdParam } - * - * - */ - public List getCalcIdParam() { - if (calcIdParam == null) { - calcIdParam = new ArrayList(); - } - return this.calcIdParam; - } - - /** - * Gets the value of the overview property. - * - * @return - * possible object is - * {@link JalviewModel.Viewport.Overview } - * - */ - public JalviewModel.Viewport.Overview getOverview() { - return overview; - } - - /** - * Sets the value of the overview property. - * - * @param value - * allowed object is - * {@link JalviewModel.Viewport.Overview } - * - */ - public void setOverview(JalviewModel.Viewport.Overview value) { - this.overview = value; - } - - /** - * Gets the value of the conservationSelected property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isConservationSelected() { - return conservationSelected; - } - - /** - * Sets the value of the conservationSelected property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setConservationSelected(Boolean value) { - this.conservationSelected = value; - } - - /** - * Gets the value of the pidSelected property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isPidSelected() { - return pidSelected; - } - - /** - * Sets the value of the pidSelected property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setPidSelected(Boolean value) { - this.pidSelected = value; - } - - /** - * Gets the value of the bgColour property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getBgColour() { - return bgColour; - } + public List getCalcIdParam() + { + if (calcIdParam == null) + { + calcIdParam = new ArrayList(); + } + return this.calcIdParam; + } - /** - * Sets the value of the bgColour property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setBgColour(String value) { - this.bgColour = value; - } + /** + * Gets the value of the overview property. + * + * @return possible object is {@link JalviewModel.Viewport.Overview } + * + */ + public JalviewModel.Viewport.Overview getOverview() + { + return overview; + } - /** - * Gets the value of the consThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getConsThreshold() { - return consThreshold; - } + /** + * Sets the value of the overview property. + * + * @param value + * allowed object is {@link JalviewModel.Viewport.Overview } + * + */ + public void setOverview(JalviewModel.Viewport.Overview value) + { + this.overview = value; + } - /** - * Sets the value of the consThreshold property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setConsThreshold(Integer value) { - this.consThreshold = value; - } + /** + * Gets the value of the conservationSelected property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isConservationSelected() + { + return conservationSelected; + } - /** - * Gets the value of the pidThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getPidThreshold() { - return pidThreshold; - } + /** + * Sets the value of the conservationSelected property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setConservationSelected(Boolean value) + { + this.conservationSelected = value; + } - /** - * Sets the value of the pidThreshold property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setPidThreshold(Integer value) { - this.pidThreshold = value; - } + /** + * Gets the value of the pidSelected property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isPidSelected() + { + return pidSelected; + } - /** - * Gets the value of the title property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTitle() { - return title; - } + /** + * Sets the value of the pidSelected property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setPidSelected(Boolean value) + { + this.pidSelected = value; + } - /** - * Sets the value of the title property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setTitle(String value) { - this.title = value; - } + /** + * Gets the value of the bgColour property. + * + * @return possible object is {@link String } + * + */ + public String getBgColour() + { + return bgColour; + } - /** - * Gets the value of the showFullId property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowFullId() { - return showFullId; - } + /** + * Sets the value of the bgColour property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setBgColour(String value) + { + this.bgColour = value; + } - /** - * Sets the value of the showFullId property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowFullId(Boolean value) { - this.showFullId = value; - } + /** + * Gets the value of the consThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getConsThreshold() + { + return consThreshold; + } - /** - * Gets the value of the rightAlignIds property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isRightAlignIds() { - return rightAlignIds; - } + /** + * Sets the value of the consThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setConsThreshold(Integer value) + { + this.consThreshold = value; + } - /** - * Sets the value of the rightAlignIds property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setRightAlignIds(Boolean value) { - this.rightAlignIds = value; - } + /** + * Gets the value of the pidThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getPidThreshold() + { + return pidThreshold; + } - /** - * Gets the value of the showText property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowText() { - return showText; - } + /** + * Sets the value of the pidThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setPidThreshold(Integer value) + { + this.pidThreshold = value; + } - /** - * Sets the value of the showText property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowText(Boolean value) { - this.showText = value; - } + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } - /** - * Gets the value of the showColourText property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowColourText() { - return showColourText; - } + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } - /** - * Sets the value of the showColourText property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowColourText(Boolean value) { - this.showColourText = value; - } + /** + * Gets the value of the showFullId property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowFullId() + { + return showFullId; + } - /** - * Gets the value of the showUnconserved property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isShowUnconserved() { - if (showUnconserved == null) { - return false; - } else { - return showUnconserved; - } - } + /** + * Sets the value of the showFullId property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowFullId(Boolean value) + { + this.showFullId = value; + } - /** - * Sets the value of the showUnconserved property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowUnconserved(Boolean value) { - this.showUnconserved = value; - } + /** + * Gets the value of the rightAlignIds property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isRightAlignIds() + { + return rightAlignIds; + } - /** - * Gets the value of the showBoxes property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowBoxes() { - return showBoxes; - } + /** + * Sets the value of the rightAlignIds property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setRightAlignIds(Boolean value) + { + this.rightAlignIds = value; + } - /** - * Sets the value of the showBoxes property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowBoxes(Boolean value) { - this.showBoxes = value; - } + /** + * Gets the value of the showText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowText() + { + return showText; + } - /** - * Gets the value of the wrapAlignment property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isWrapAlignment() { - return wrapAlignment; - } + /** + * Sets the value of the showText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowText(Boolean value) + { + this.showText = value; + } - /** - * Sets the value of the wrapAlignment property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setWrapAlignment(Boolean value) { - this.wrapAlignment = value; - } + /** + * Gets the value of the showColourText property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowColourText() + { + return showColourText; + } - /** - * Gets the value of the renderGaps property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isRenderGaps() { - return renderGaps; - } + /** + * Sets the value of the showColourText property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowColourText(Boolean value) + { + this.showColourText = value; + } - /** - * Sets the value of the renderGaps property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setRenderGaps(Boolean value) { - this.renderGaps = value; - } + /** + * Gets the value of the showUnconserved property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowUnconserved() + { + if (showUnconserved == null) + { + return false; + } + else + { + return showUnconserved; + } + } - /** - * Gets the value of the showSequenceFeatures property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowSequenceFeatures() { - return showSequenceFeatures; - } + /** + * Sets the value of the showUnconserved property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowUnconserved(Boolean value) + { + this.showUnconserved = value; + } - /** - * Sets the value of the showSequenceFeatures property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowSequenceFeatures(Boolean value) { - this.showSequenceFeatures = value; - } + /** + * Gets the value of the showBoxes property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowBoxes() + { + return showBoxes; + } - /** - * Gets the value of the showNPfeatureTooltip property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowNPfeatureTooltip() { - return showNPfeatureTooltip; - } + /** + * Sets the value of the showBoxes property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowBoxes(Boolean value) + { + this.showBoxes = value; + } - /** - * Sets the value of the showNPfeatureTooltip property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowNPfeatureTooltip(Boolean value) { - this.showNPfeatureTooltip = value; - } + /** + * Gets the value of the wrapAlignment property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isWrapAlignment() + { + return wrapAlignment; + } - /** - * Gets the value of the showDbRefTooltip property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowDbRefTooltip() { - return showDbRefTooltip; - } + /** + * Sets the value of the wrapAlignment property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setWrapAlignment(Boolean value) + { + this.wrapAlignment = value; + } - /** - * Sets the value of the showDbRefTooltip property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowDbRefTooltip(Boolean value) { - this.showDbRefTooltip = value; - } + /** + * Gets the value of the renderGaps property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isRenderGaps() + { + return renderGaps; + } - /** - * Gets the value of the followHighlight property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isFollowHighlight() { - if (followHighlight == null) { - return true; - } else { - return followHighlight; - } - } + /** + * Sets the value of the renderGaps property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setRenderGaps(Boolean value) + { + this.renderGaps = value; + } - /** - * Sets the value of the followHighlight property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setFollowHighlight(Boolean value) { - this.followHighlight = value; - } + /** + * Gets the value of the showSequenceFeatures property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowSequenceFeatures() + { + return showSequenceFeatures; + } - /** - * Gets the value of the followSelection property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isFollowSelection() { - if (followSelection == null) { - return true; - } else { - return followSelection; - } - } + /** + * Sets the value of the showSequenceFeatures property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowSequenceFeatures(Boolean value) + { + this.showSequenceFeatures = value; + } - /** - * Sets the value of the followSelection property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setFollowSelection(Boolean value) { - this.followSelection = value; - } + /** + * Gets the value of the showNPfeatureTooltip property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowNPfeatureTooltip() + { + return showNPfeatureTooltip; + } - /** - * Gets the value of the showAnnotation property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowAnnotation() { - return showAnnotation; - } + /** + * Sets the value of the showNPfeatureTooltip property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowNPfeatureTooltip(Boolean value) + { + this.showNPfeatureTooltip = value; + } - /** - * Sets the value of the showAnnotation property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowAnnotation(Boolean value) { - this.showAnnotation = value; - } + /** + * Gets the value of the showDbRefTooltip property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowDbRefTooltip() + { + return showDbRefTooltip; + } - /** - * Gets the value of the centreColumnLabels property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isCentreColumnLabels() { - if (centreColumnLabels == null) { - return false; - } else { - return centreColumnLabels; - } - } + /** + * Sets the value of the showDbRefTooltip property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowDbRefTooltip(Boolean value) + { + this.showDbRefTooltip = value; + } - /** - * Sets the value of the centreColumnLabels property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setCentreColumnLabels(Boolean value) { - this.centreColumnLabels = value; - } + /** + * Gets the value of the followHighlight property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isFollowHighlight() + { + if (followHighlight == null) + { + return true; + } + else + { + return followHighlight; + } + } - /** - * Gets the value of the showGroupConservation property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isShowGroupConservation() { - if (showGroupConservation == null) { - return false; - } else { - return showGroupConservation; - } - } + /** + * Sets the value of the followHighlight property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFollowHighlight(Boolean value) + { + this.followHighlight = value; + } - /** - * Sets the value of the showGroupConservation property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowGroupConservation(Boolean value) { - this.showGroupConservation = value; - } + /** + * Gets the value of the followSelection property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isFollowSelection() + { + if (followSelection == null) + { + return true; + } + else + { + return followSelection; + } + } - /** - * Gets the value of the showGroupConsensus property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isShowGroupConsensus() { - if (showGroupConsensus == null) { - return false; - } else { - return showGroupConsensus; - } - } + /** + * Sets the value of the followSelection property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setFollowSelection(Boolean value) + { + this.followSelection = value; + } - /** - * Sets the value of the showGroupConsensus property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowGroupConsensus(Boolean value) { - this.showGroupConsensus = value; - } + /** + * Gets the value of the showAnnotation property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowAnnotation() + { + return showAnnotation; + } - /** - * Gets the value of the showConsensusHistogram property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isShowConsensusHistogram() { - if (showConsensusHistogram == null) { - return true; - } else { - return showConsensusHistogram; - } - } + /** + * Sets the value of the showAnnotation property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowAnnotation(Boolean value) + { + this.showAnnotation = value; + } - /** - * Sets the value of the showConsensusHistogram property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowConsensusHistogram(Boolean value) { - this.showConsensusHistogram = value; - } + /** + * Gets the value of the centreColumnLabels property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isCentreColumnLabels() + { + if (centreColumnLabels == null) + { + return false; + } + else + { + return centreColumnLabels; + } + } - /** - * Gets the value of the showSequenceLogo property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isShowSequenceLogo() { - if (showSequenceLogo == null) { - return false; - } else { - return showSequenceLogo; - } - } + /** + * Sets the value of the centreColumnLabels property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setCentreColumnLabels(Boolean value) + { + this.centreColumnLabels = value; + } - /** - * Sets the value of the showSequenceLogo property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowSequenceLogo(Boolean value) { - this.showSequenceLogo = value; - } + /** + * Gets the value of the showGroupConservation property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowGroupConservation() + { + if (showGroupConservation == null) + { + return false; + } + else + { + return showGroupConservation; + } + } - /** - * Gets the value of the normaliseSequenceLogo property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isNormaliseSequenceLogo() { - if (normaliseSequenceLogo == null) { - return false; - } else { - return normaliseSequenceLogo; - } - } + /** + * Sets the value of the showGroupConservation property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowGroupConservation(Boolean value) + { + this.showGroupConservation = value; + } - /** - * Sets the value of the normaliseSequenceLogo property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setNormaliseSequenceLogo(Boolean value) { - this.normaliseSequenceLogo = value; - } + /** + * Gets the value of the showGroupConsensus property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowGroupConsensus() + { + if (showGroupConsensus == null) + { + return false; + } + else + { + return showGroupConsensus; + } + } - /** - * Gets the value of the ignoreGapsinConsensus property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isIgnoreGapsinConsensus() { - if (ignoreGapsinConsensus == null) { - return true; - } else { - return ignoreGapsinConsensus; - } - } + /** + * Sets the value of the showGroupConsensus property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowGroupConsensus(Boolean value) + { + this.showGroupConsensus = value; + } - /** - * Sets the value of the ignoreGapsinConsensus property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setIgnoreGapsinConsensus(Boolean value) { - this.ignoreGapsinConsensus = value; - } + /** + * Gets the value of the showConsensusHistogram property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowConsensusHistogram() + { + if (showConsensusHistogram == null) + { + return true; + } + else + { + return showConsensusHistogram; + } + } - /** - * Gets the value of the startRes property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getStartRes() { - return startRes; - } + /** + * Sets the value of the showConsensusHistogram property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowConsensusHistogram(Boolean value) + { + this.showConsensusHistogram = value; + } - /** - * Sets the value of the startRes property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setStartRes(Integer value) { - this.startRes = value; - } + /** + * Gets the value of the showSequenceLogo property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowSequenceLogo() + { + if (showSequenceLogo == null) + { + return false; + } + else + { + return showSequenceLogo; + } + } - /** - * Gets the value of the startSeq property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getStartSeq() { - return startSeq; - } + /** + * Sets the value of the showSequenceLogo property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowSequenceLogo(Boolean value) + { + this.showSequenceLogo = value; + } - /** - * Sets the value of the startSeq property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setStartSeq(Integer value) { - this.startSeq = value; - } + /** + * Gets the value of the normaliseSequenceLogo property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isNormaliseSequenceLogo() + { + if (normaliseSequenceLogo == null) + { + return false; + } + else + { + return normaliseSequenceLogo; + } + } - /** - * Gets the value of the charWidth property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getCharWidth() { - return charWidth; - } + /** + * Sets the value of the normaliseSequenceLogo property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setNormaliseSequenceLogo(Boolean value) + { + this.normaliseSequenceLogo = value; + } + + /** + * Gets the value of the ignoreGapsinConsensus property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isIgnoreGapsinConsensus() + { + if (ignoreGapsinConsensus == null) + { + return true; + } + else + { + return ignoreGapsinConsensus; + } + } - /** - * Sets the value of the charWidth property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setCharWidth(Integer value) { - this.charWidth = value; - } + /** + * Sets the value of the ignoreGapsinConsensus property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setIgnoreGapsinConsensus(Boolean value) + { + this.ignoreGapsinConsensus = value; + } - /** - * Gets the value of the charHeight property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getCharHeight() { - return charHeight; - } + /** + * Gets the value of the startRes property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStartRes() + { + return startRes; + } - /** - * Sets the value of the charHeight property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setCharHeight(Integer value) { - this.charHeight = value; - } + /** + * Sets the value of the startRes property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStartRes(Integer value) + { + this.startRes = value; + } - /** - * Gets the value of the fontName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getFontName() { - return fontName; - } + /** + * Gets the value of the startSeq property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStartSeq() + { + return startSeq; + } - /** - * Sets the value of the fontName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setFontName(String value) { - this.fontName = value; - } + /** + * Sets the value of the startSeq property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStartSeq(Integer value) + { + this.startSeq = value; + } - /** - * Gets the value of the fontSize property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getFontSize() { - return fontSize; - } + /** + * Gets the value of the charWidth property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getCharWidth() + { + return charWidth; + } - /** - * Sets the value of the fontSize property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setFontSize(Integer value) { - this.fontSize = value; - } + /** + * Sets the value of the charWidth property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setCharWidth(Integer value) + { + this.charWidth = value; + } - /** - * Gets the value of the fontStyle property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getFontStyle() { - return fontStyle; - } + /** + * Gets the value of the charHeight property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getCharHeight() + { + return charHeight; + } - /** - * Sets the value of the fontStyle property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setFontStyle(Integer value) { - this.fontStyle = value; - } + /** + * Sets the value of the charHeight property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setCharHeight(Integer value) + { + this.charHeight = value; + } - /** - * Gets the value of the scaleProteinAsCdna property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isScaleProteinAsCdna() { - if (scaleProteinAsCdna == null) { - return true; - } else { - return scaleProteinAsCdna; - } - } + /** + * Gets the value of the fontName property. + * + * @return possible object is {@link String } + * + */ + public String getFontName() + { + return fontName; + } - /** - * Sets the value of the scaleProteinAsCdna property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setScaleProteinAsCdna(Boolean value) { - this.scaleProteinAsCdna = value; - } + /** + * Sets the value of the fontName property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setFontName(String value) + { + this.fontName = value; + } - /** - * Gets the value of the viewName property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getViewName() { - return viewName; - } + /** + * Gets the value of the fontSize property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontSize() + { + return fontSize; + } - /** - * Sets the value of the viewName property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setViewName(String value) { - this.viewName = value; - } + /** + * Sets the value of the fontSize property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontSize(Integer value) + { + this.fontSize = value; + } - /** - * Gets the value of the sequenceSetId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getSequenceSetId() { - return sequenceSetId; - } + /** + * Gets the value of the fontStyle property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getFontStyle() + { + return fontStyle; + } - /** - * Sets the value of the sequenceSetId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setSequenceSetId(String value) { - this.sequenceSetId = value; - } + /** + * Sets the value of the fontStyle property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setFontStyle(Integer value) + { + this.fontStyle = value; + } - /** - * Gets the value of the gatheredViews property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isGatheredViews() { - return gatheredViews; - } + /** + * Gets the value of the scaleProteinAsCdna property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isScaleProteinAsCdna() + { + if (scaleProteinAsCdna == null) + { + return true; + } + else + { + return scaleProteinAsCdna; + } + } - /** - * Sets the value of the gatheredViews property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setGatheredViews(Boolean value) { - this.gatheredViews = value; - } + /** + * Sets the value of the scaleProteinAsCdna property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setScaleProteinAsCdna(Boolean value) + { + this.scaleProteinAsCdna = value; + } - /** - * Gets the value of the textCol1 property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextCol1() { - return textCol1; - } + /** + * Gets the value of the viewName property. + * + * @return possible object is {@link String } + * + */ + public String getViewName() + { + return viewName; + } - /** - * Sets the value of the textCol1 property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setTextCol1(Integer value) { - this.textCol1 = value; - } + /** + * Sets the value of the viewName property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setViewName(String value) + { + this.viewName = value; + } - /** - * Gets the value of the textCol2 property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextCol2() { - return textCol2; - } + /** + * Gets the value of the sequenceSetId property. + * + * @return possible object is {@link String } + * + */ + public String getSequenceSetId() + { + return sequenceSetId; + } - /** - * Sets the value of the textCol2 property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setTextCol2(Integer value) { - this.textCol2 = value; - } + /** + * Sets the value of the sequenceSetId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setSequenceSetId(String value) + { + this.sequenceSetId = value; + } - /** - * Gets the value of the textColThreshold property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getTextColThreshold() { - return textColThreshold; - } + /** + * Gets the value of the gatheredViews property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isGatheredViews() + { + return gatheredViews; + } - /** - * Sets the value of the textColThreshold property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setTextColThreshold(Integer value) { - this.textColThreshold = value; - } + /** + * Sets the value of the gatheredViews property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setGatheredViews(Boolean value) + { + this.gatheredViews = value; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * Gets the value of the textCol1 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol1() + { + return textCol1; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } + /** + * Sets the value of the textCol1 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol1(Integer value) + { + this.textCol1 = value; + } - /** - * Gets the value of the complementId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getComplementId() { - return complementId; - } + /** + * Gets the value of the textCol2 property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextCol2() + { + return textCol2; + } - /** - * Sets the value of the complementId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setComplementId(String value) { - this.complementId = value; - } + /** + * Sets the value of the textCol2 property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextCol2(Integer value) + { + this.textCol2 = value; + } - /** - * Gets the value of the showComplementFeatures property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isShowComplementFeatures() { - if (showComplementFeatures == null) { - return false; - } else { - return showComplementFeatures; - } - } + /** + * Gets the value of the textColThreshold property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getTextColThreshold() + { + return textColThreshold; + } - /** - * Sets the value of the showComplementFeatures property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowComplementFeatures(Boolean value) { - this.showComplementFeatures = value; - } + /** + * Sets the value of the textColThreshold property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setTextColThreshold(Integer value) + { + this.textColThreshold = value; + } - /** - * Gets the value of the showComplementFeaturesOnTop property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isShowComplementFeaturesOnTop() { - if (showComplementFeaturesOnTop == null) { - return false; - } else { - return showComplementFeaturesOnTop; - } - } + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } - /** - * Sets the value of the showComplementFeaturesOnTop property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowComplementFeaturesOnTop(Boolean value) { - this.showComplementFeaturesOnTop = value; - } + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } - /** - * Gets the value of the width property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getWidth() { - return width; - } + /** + * Gets the value of the complementId property. + * + * @return possible object is {@link String } + * + */ + public String getComplementId() + { + return complementId; + } - /** - * Sets the value of the width property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setWidth(Integer value) { - this.width = value; - } + /** + * Sets the value of the complementId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setComplementId(String value) + { + this.complementId = value; + } - /** - * Gets the value of the height property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHeight() { - return height; - } + /** + * Gets the value of the showComplementFeatures property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowComplementFeatures() + { + if (showComplementFeatures == null) + { + return false; + } + else + { + return showComplementFeatures; + } + } - /** - * Sets the value of the height property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setHeight(Integer value) { - this.height = value; - } + /** + * Sets the value of the showComplementFeatures property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowComplementFeatures(Boolean value) + { + this.showComplementFeatures = value; + } - /** - * Gets the value of the xpos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXpos() { - return xpos; - } + /** + * Gets the value of the showComplementFeaturesOnTop property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isShowComplementFeaturesOnTop() + { + if (showComplementFeaturesOnTop == null) + { + return false; + } + else + { + return showComplementFeaturesOnTop; + } + } - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setXpos(Integer value) { - this.xpos = value; - } + /** + * Sets the value of the showComplementFeaturesOnTop property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowComplementFeaturesOnTop(Boolean value) + { + this.showComplementFeaturesOnTop = value; + } - /** - * Gets the value of the ypos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYpos() { - return ypos; - } + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setYpos(Integer value) { - this.ypos = value; - } + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-         *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     </extension>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class CalcIdParam - extends WebServiceParameterSet - { + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; + } - @XmlAttribute(name = "calcId", required = true) - protected String calcId; - @XmlAttribute(name = "needsUpdate") - protected Boolean needsUpdate; - @XmlAttribute(name = "autoUpdate", required = true) - protected boolean autoUpdate; - - /** - * Gets the value of the calcId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getCalcId() { - return calcId; - } - - /** - * Sets the value of the calcId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setCalcId(String value) { - this.calcId = value; - } - - /** - * Gets the value of the needsUpdate property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isNeedsUpdate() { - if (needsUpdate == null) { - return false; - } else { - return needsUpdate; - } - } - - /** - * Sets the value of the needsUpdate property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setNeedsUpdate(Boolean value) { - this.needsUpdate = value; - } - - /** - * Gets the value of the autoUpdate property. - * - */ - public boolean isAutoUpdate() { - return autoUpdate; - } - - /** - * Sets the value of the autoUpdate property. - * - */ - public void setAutoUpdate(boolean value) { - this.autoUpdate = value; - } + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } - } + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXpos(Integer value) + { + this.xpos = value; + } + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class HiddenColumns { - - @XmlAttribute(name = "start") - protected Integer start; - @XmlAttribute(name = "end") - protected Integer end; - - /** - * Gets the value of the start property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getStart() { - return start; - } - - /** - * Sets the value of the start property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setStart(Integer value) { - this.start = value; - } - - /** - * Gets the value of the end property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getEnd() { - return end; - } - - /** - * Sets the value of the end property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setEnd(Integer value) { - this.end = value; - } + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } + /** + *

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </extension>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class CalcIdParam extends WebServiceParameterSet + { + + @XmlAttribute(name = "calcId", required = true) + protected String calcId; + + @XmlAttribute(name = "needsUpdate") + protected Boolean needsUpdate; + + @XmlAttribute(name = "autoUpdate", required = true) + protected boolean autoUpdate; + + /** + * Gets the value of the calcId property. + * + * @return possible object is {@link String } + * + */ + public String getCalcId() + { + return calcId; + } + + /** + * Sets the value of the calcId property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setCalcId(String value) + { + this.calcId = value; + } + + /** + * Gets the value of the needsUpdate property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isNeedsUpdate() + { + if (needsUpdate == null) + { + return false; } + else + { + return needsUpdate; + } + } + + /** + * Sets the value of the needsUpdate property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setNeedsUpdate(Boolean value) + { + this.needsUpdate = value; + } + + /** + * Gets the value of the autoUpdate property. + * + */ + public boolean isAutoUpdate() + { + return autoUpdate; + } + + /** + * Sets the value of the autoUpdate property. + * + */ + public void setAutoUpdate(boolean value) + { + this.autoUpdate = value; + } + } - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attGroup ref="{www.jalview.org}swingwindow"/>
-         *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Overview { - - @XmlAttribute(name = "showHidden") - protected Boolean showHidden; - @XmlAttribute(name = "residueColour") - protected Integer residueColour; - @XmlAttribute(name = "gapColour") - protected Integer gapColour; - @XmlAttribute(name = "hiddenColour") - protected Integer hiddenColour; - @XmlAttribute(name = "title") - protected String title; - @XmlAttribute(name = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; - - /** - * Gets the value of the showHidden property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isShowHidden() { - return showHidden; - } - - /** - * Sets the value of the showHidden property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setShowHidden(Boolean value) { - this.showHidden = value; - } - - /** - * Gets the value of the residueColour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getResidueColour() { - return residueColour; - } - - /** - * Sets the value of the residueColour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setResidueColour(Integer value) { - this.residueColour = value; - } - - /** - * Gets the value of the gapColour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getGapColour() { - return gapColour; - } - - /** - * Sets the value of the gapColour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setGapColour(Integer value) { - this.gapColour = value; - } - - /** - * Gets the value of the hiddenColour property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHiddenColour() { - return hiddenColour; - } - - /** - * Sets the value of the hiddenColour property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setHiddenColour(Integer value) { - this.hiddenColour = value; - } - - /** - * Gets the value of the title property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTitle() { - return title; - } - - /** - * Sets the value of the title property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setTitle(String value) { - this.title = value; - } - - /** - * Gets the value of the width property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getWidth() { - return width; - } - - /** - * Sets the value of the width property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setWidth(Integer value) { - this.width = value; - } - - /** - * Gets the value of the height property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getHeight() { - return height; - } - - /** - * Sets the value of the height property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setHeight(Integer value) { - this.height = value; - } - - /** - * Gets the value of the xpos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getXpos() { - return xpos; - } - - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setXpos(Integer value) { - this.xpos = value; - } - - /** - * Gets the value of the ypos property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getYpos() { - return ypos; - } - - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setYpos(Integer value) { - this.ypos = value; - } + /** + *

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class HiddenColumns + { + + @XmlAttribute(name = "start") + protected Integer start; + + @XmlAttribute(name = "end") + protected Integer end; + + /** + * Gets the value of the start property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getStart() + { + return start; + } + + /** + * Sets the value of the start property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setStart(Integer value) + { + this.start = value; + } + + /** + * Gets the value of the end property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getEnd() + { + return end; + } + + /** + * Sets the value of the end property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setEnd(Integer value) + { + this.end = value; + } - } + } + + /** + *

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

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

+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Overview + { + + @XmlAttribute(name = "showHidden") + protected Boolean showHidden; + + @XmlAttribute(name = "residueColour") + protected Integer residueColour; + + @XmlAttribute(name = "gapColour") + protected Integer gapColour; + + @XmlAttribute(name = "hiddenColour") + protected Integer hiddenColour; + + @XmlAttribute(name = "title") + protected String title; + + @XmlAttribute(name = "width") + protected Integer width; + + @XmlAttribute(name = "height") + protected Integer height; + + @XmlAttribute(name = "xpos") + protected Integer xpos; + + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the showHidden property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isShowHidden() + { + return showHidden; + } + + /** + * Sets the value of the showHidden property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setShowHidden(Boolean value) + { + this.showHidden = value; + } + + /** + * Gets the value of the residueColour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getResidueColour() + { + return residueColour; + } + + /** + * Sets the value of the residueColour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setResidueColour(Integer value) + { + this.residueColour = value; + } + + /** + * Gets the value of the gapColour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getGapColour() + { + return gapColour; + } + + /** + * Sets the value of the gapColour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setGapColour(Integer value) + { + this.gapColour = value; + } + + /** + * Gets the value of the hiddenColour property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHiddenColour() + { + return hiddenColour; + } + + /** + * Sets the value of the hiddenColour property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHiddenColour(Integer value) + { + this.hiddenColour = value; + } + + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the width property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getWidth() + { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setWidth(Integer value) + { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getHeight() + { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setHeight(Integer value) + { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getXpos() + { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setXpos(Integer value) + { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getYpos() + { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setYpos(Integer value) + { + this.ypos = value; + } } + } + } diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java index b62cf15..8a9f681 100644 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for JalviewUserColours complex type. + *

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

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

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

  * <complexType name="JalviewUserColours">
@@ -71,542 +72,556 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
-    "version",
-    "colour",
-    "filter"
-})
-public class JalviewUserColours {
-
-    @XmlElement(name = "Version", namespace = "")
-    protected String version;
-    @XmlElement(namespace = "")
-    protected List colour;
+@XmlType(
+  name = "JalviewUserColours",
+  namespace = "www.jalview.org/colours",
+  propOrder =
+  { "version", "colour", "filter" })
+public class JalviewUserColours
+{
+
+  @XmlElement(name = "Version", namespace = "")
+  protected String version;
+
+  @XmlElement(namespace = "")
+  protected List colour;
+
+  @XmlElement(namespace = "")
+  protected List filter;
+
+  @XmlAttribute(name = "schemeName")
+  protected String schemeName;
+
+  /**
+   * Gets the value of the version property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setVersion(String value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the colour property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+   *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+   *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "attributeName" }) + public static class Colour + { + @XmlElement(namespace = "") - protected List filter; - @XmlAttribute(name = "schemeName") - protected String schemeName; + protected List attributeName; + + @XmlAttribute(name = "Name") + protected String name; + + @XmlAttribute(name = "RGB", required = true) + protected String rgb; + + @XmlAttribute(name = "minRGB") + protected String minRGB; + + @XmlAttribute(name = "noValueColour") + protected NoValueColour noValueColour; + + @XmlAttribute(name = "threshType") + protected ThresholdType threshType; + + @XmlAttribute(name = "threshold") + protected Float threshold; + + @XmlAttribute(name = "max") + protected Float max; + + @XmlAttribute(name = "min") + protected Float min; + + @XmlAttribute(name = "colourByLabel") + protected Boolean colourByLabel; + + @XmlAttribute(name = "autoScale") + protected Boolean autoScale; /** - * Gets the value of the version property. + * Gets the value of the attributeName property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * * - * @return - * possible object is - * {@link String } - * */ - public String getVersion() { - return version; + public List getAttributeName() + { + if (attributeName == null) + { + attributeName = new ArrayList(); + } + return this.attributeName; } /** - * Sets the value of the version property. + * Gets the value of the name property. + * + * @return possible object is {@link String } + * + */ + public String getName() + { + return name; + } + + /** + * Sets the value of the name property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link String } + * */ - public void setVersion(String value) { - this.version = value; + public void setName(String value) + { + this.name = value; } /** - * Gets the value of the colour property. + * Gets the value of the rgb property. * - *

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

- * For example, to add a new item, do as follows: - *

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

- * Objects of the following type(s) are allowed in the list - * {@link JalviewUserColours.Colour } + */ + public void setRGB(String value) + { + this.rgb = value; + } + + /** + * Gets the value of the minRGB property. * + * @return possible object is {@link String } * */ - public List getColour() { - if (colour == null) { - colour = new ArrayList(); - } - return this.colour; + public String getMinRGB() + { + return minRGB; } /** - * Gets the value of the filter property. + * Sets the value of the minRGB property. * - *

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

- * For example, to add a new item, do as follows: - *

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

- * Objects of the following type(s) are allowed in the list - * {@link JalviewUserColours.Filter } + */ + public NoValueColour getNoValueColour() + { + if (noValueColour == null) + { + return NoValueColour.MIN; + } + else + { + return noValueColour; + } + } + + /** + * Sets the value of the noValueColour property. * + * @param value + * allowed object is {@link NoValueColour } * */ - public List getFilter() { - if (filter == null) { - filter = new ArrayList(); - } - return this.filter; + public void setNoValueColour(NoValueColour value) + { + this.noValueColour = value; } /** - * Gets the value of the schemeName property. + * Gets the value of the threshType property. + * + * @return possible object is {@link ThresholdType } * - * @return - * possible object is - * {@link String } - * */ - public String getSchemeName() { - return schemeName; + public ThresholdType getThreshType() + { + return threshType; } /** - * Sets the value of the schemeName property. + * Sets the value of the threshType property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link ThresholdType } + * */ - public void setSchemeName(String value) { - this.schemeName = value; + public void setThreshType(ThresholdType value) + { + this.threshType = value; } + /** + * Gets the value of the threshold property. + * + * @return possible object is {@link Float } + * + */ + public Float getThreshold() + { + return threshold; + } /** - *

Java class for anonymous complex type. + * Sets the value of the threshold property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link Float } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
-     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public void setThreshold(Float value) + { + this.threshold = value; + } + + /** + * Gets the value of the max property. + * + * @return possible object is {@link Float } + * + */ + public Float getMax() + { + return max; + } + + /** + * Sets the value of the max property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setMax(Float value) + { + this.max = value; + } + + /** + * Gets the value of the min property. * + * @return possible object is {@link Float } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "attributeName" - }) - public static class Colour { - - @XmlElement(namespace = "") - protected List attributeName; - @XmlAttribute(name = "Name") - protected String name; - @XmlAttribute(name = "RGB", required = true) - protected String rgb; - @XmlAttribute(name = "minRGB") - protected String minRGB; - @XmlAttribute(name = "noValueColour") - protected NoValueColour noValueColour; - @XmlAttribute(name = "threshType") - protected ThresholdType threshType; - @XmlAttribute(name = "threshold") - protected Float threshold; - @XmlAttribute(name = "max") - protected Float max; - @XmlAttribute(name = "min") - protected Float min; - @XmlAttribute(name = "colourByLabel") - protected Boolean colourByLabel; - @XmlAttribute(name = "autoScale") - protected Boolean autoScale; - - /** - * Gets the value of the attributeName property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getAttributeName().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getAttributeName() { - if (attributeName == null) { - attributeName = new ArrayList(); - } - return this.attributeName; - } - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the rgb property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getRGB() { - return rgb; - } - - /** - * Sets the value of the rgb property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setRGB(String value) { - this.rgb = value; - } - - /** - * Gets the value of the minRGB property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getMinRGB() { - return minRGB; - } - - /** - * Sets the value of the minRGB property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setMinRGB(String value) { - this.minRGB = value; - } - - /** - * Gets the value of the noValueColour property. - * - * @return - * possible object is - * {@link NoValueColour } - * - */ - public NoValueColour getNoValueColour() { - if (noValueColour == null) { - return NoValueColour.MIN; - } else { - return noValueColour; - } - } - - /** - * Sets the value of the noValueColour property. - * - * @param value - * allowed object is - * {@link NoValueColour } - * - */ - public void setNoValueColour(NoValueColour value) { - this.noValueColour = value; - } - - /** - * Gets the value of the threshType property. - * - * @return - * possible object is - * {@link ThresholdType } - * - */ - public ThresholdType getThreshType() { - return threshType; - } - - /** - * Sets the value of the threshType property. - * - * @param value - * allowed object is - * {@link ThresholdType } - * - */ - public void setThreshType(ThresholdType value) { - this.threshType = value; - } - - /** - * Gets the value of the threshold property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getThreshold() { - return threshold; - } - - /** - * Sets the value of the threshold property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setThreshold(Float value) { - this.threshold = value; - } - - /** - * Gets the value of the max property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getMax() { - return max; - } - - /** - * Sets the value of the max property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setMax(Float value) { - this.max = value; - } - - /** - * Gets the value of the min property. - * - * @return - * possible object is - * {@link Float } - * - */ - public Float getMin() { - return min; - } - - /** - * Sets the value of the min property. - * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setMin(Float value) { - this.min = value; - } - - /** - * Gets the value of the colourByLabel property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isColourByLabel() { - return colourByLabel; - } - - /** - * Sets the value of the colourByLabel property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setColourByLabel(Boolean value) { - this.colourByLabel = value; - } - - /** - * Gets the value of the autoScale property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isAutoScale() { - return autoScale; - } - - /** - * Sets the value of the autoScale property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setAutoScale(Boolean value) { - this.autoScale = value; - } + public Float getMin() + { + return min; + } + /** + * Sets the value of the min property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setMin(Float value) + { + this.min = value; } + /** + * Gets the value of the colourByLabel property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isColourByLabel() + { + return colourByLabel; + } /** - *

Java class for anonymous complex type. + * Sets the value of the colourByLabel property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link Boolean } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
-     *       </sequence>
-     *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public void setColourByLabel(Boolean value) + { + this.colourByLabel = value; + } + + /** + * Gets the value of the autoScale property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isAutoScale() + { + return autoScale; + } + + /** + * Sets the value of the autoScale property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setAutoScale(Boolean value) + { + this.autoScale = value; + } + + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+   *       </sequence>
+   *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "matcherSet" }) + public static class Filter + { + + @XmlElement(namespace = "", required = true) + protected FeatureMatcherSet matcherSet; + + @XmlAttribute(name = "featureType", required = true) + protected String featureType; + + /** + * Gets the value of the matcherSet property. + * + * @return possible object is {@link FeatureMatcherSet } + * + */ + public FeatureMatcherSet getMatcherSet() + { + return matcherSet; + } + + /** + * Sets the value of the matcherSet property. + * + * @param value + * allowed object is {@link FeatureMatcherSet } + * + */ + public void setMatcherSet(FeatureMatcherSet value) + { + this.matcherSet = value; + } + + /** + * Gets the value of the featureType property. * + * @return possible object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "matcherSet" - }) - public static class Filter { - - @XmlElement(namespace = "", required = true) - protected FeatureMatcherSet matcherSet; - @XmlAttribute(name = "featureType", required = true) - protected String featureType; - - /** - * Gets the value of the matcherSet property. - * - * @return - * possible object is - * {@link FeatureMatcherSet } - * - */ - public FeatureMatcherSet getMatcherSet() { - return matcherSet; - } - - /** - * Sets the value of the matcherSet property. - * - * @param value - * allowed object is - * {@link FeatureMatcherSet } - * - */ - public void setMatcherSet(FeatureMatcherSet value) { - this.matcherSet = value; - } - - /** - * Gets the value of the featureType property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getFeatureType() { - return featureType; - } - - /** - * Sets the value of the featureType property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setFeatureType(String value) { - this.featureType = value; - } + public String getFeatureType() + { + return featureType; + } + /** + * Sets the value of the featureType property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setFeatureType(String value) + { + this.featureType = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java index 7a86123..6d7f5f2 100644 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -18,15 +17,17 @@ import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlSeeAlso; import javax.xml.bind.annotation.XmlType; - /** * - * This effectively represents a java.util.MapList object - * + * This effectively represents a java.util.MapList object * - *

Java class for mapListType complex type. * - *

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

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

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

  * <complexType name="mapListType">
@@ -64,252 +65,271 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = {
-    "mapListFrom",
-    "mapListTo"
-})
-@XmlSeeAlso({
-    Mapping.class
-})
-public class MapListType {
+@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
+@XmlSeeAlso({ Mapping.class })
+public class MapListType
+{
+
+  protected List mapListFrom;
+
+  protected List mapListTo;
+
+  @XmlAttribute(name = "mapFromUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapFromUnit;
+
+  @XmlAttribute(name = "mapToUnit", required = true)
+  @XmlSchemaType(name = "positiveInteger")
+  protected BigInteger mapToUnit;
+
+  /**
+   * Gets the value of the mapListFrom property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class MapListFrom + { + + @XmlAttribute(name = "start", required = true) + protected int start; + + @XmlAttribute(name = "end", required = true) + protected int end; /** - * Gets the value of the mapListFrom property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getMapListFrom().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getMapListTo().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link MapListType.MapListTo } - * + * Sets the value of the start property. * */ - public List getMapListTo() { - if (mapListTo == null) { - mapListTo = new ArrayList(); - } - return this.mapListTo; + public void setStart(int value) + { + this.start = value; } /** - * Gets the value of the mapFromUnit property. + * Gets the value of the end property. * - * @return - * possible object is - * {@link BigInteger } - * */ - public BigInteger getMapFromUnit() { - return mapFromUnit; + public int getEnd() + { + return end; } /** - * Sets the value of the mapFromUnit property. + * Sets the value of the end property. * - * @param value - * allowed object is - * {@link BigInteger } - * */ - public void setMapFromUnit(BigInteger value) { - this.mapFromUnit = value; + public void setEnd(int value) + { + this.end = value; } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class MapListTo + { + + @XmlAttribute(name = "start", required = true) + protected int start; + + @XmlAttribute(name = "end", required = true) + protected int end; + /** - * Gets the value of the mapToUnit property. + * Gets the value of the start property. * - * @return - * possible object is - * {@link BigInteger } - * */ - public BigInteger getMapToUnit() { - return mapToUnit; + public int getStart() + { + return start; } /** - * Sets the value of the mapToUnit property. + * Sets the value of the start property. * - * @param value - * allowed object is - * {@link BigInteger } - * */ - public void setMapToUnit(BigInteger value) { - this.mapToUnit = value; + public void setStart(int value) + { + this.start = value; } - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * + * Gets the value of the end property. * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class MapListFrom { - - @XmlAttribute(name = "start", required = true) - protected int start; - @XmlAttribute(name = "end", required = true) - protected int end; - - /** - * Gets the value of the start property. - * - */ - public int getStart() { - return start; - } - - /** - * Sets the value of the start property. - * - */ - public void setStart(int value) { - this.start = value; - } - - /** - * Gets the value of the end property. - * - */ - public int getEnd() { - return end; - } - - /** - * Sets the value of the end property. - * - */ - public void setEnd(int value) { - this.end = value; - } - + public int getEnd() + { + return end; } - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * + * Sets the value of the end property. * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class MapListTo { - - @XmlAttribute(name = "start", required = true) - protected int start; - @XmlAttribute(name = "end", required = true) - protected int end; - - /** - * Gets the value of the start property. - * - */ - public int getStart() { - return start; - } - - /** - * Sets the value of the start property. - * - */ - public void setStart(int value) { - this.start = value; - } - - /** - * Gets the value of the end property. - * - */ - public int getEnd() { - return end; - } - - /** - * Sets the value of the end property. - * - */ - public void setEnd(int value) { - this.end = value; - } - + public void setEnd(int value) + { + this.end = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java index 10d3d5b..0d5acfb 100644 --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -15,17 +14,19 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; - /** * - * Represent the jalview.datamodel.Mapping object - it also provides - * a way of storing sequences that are mapped 'to' without adding them - * to the sequence set (which will mean they are then added to the alignment too). - * + * Represent the jalview.datamodel.Mapping object - it also provides a way of + * storing sequences that are mapped 'to' without adding them to the sequence + * set (which will mean they are then added to the alignment too). + * * - *

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -51,91 +52,86 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "sequence",
-    "dseqFor"
-})
+@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
 @XmlRootElement(name = "Mapping")
-public class Mapping
-    extends MapListType
+public class Mapping extends MapListType
 {
 
-    @XmlElement(name = "Sequence")
-    protected Sequence sequence;
-    protected String dseqFor;
-    @XmlAttribute(name = "mappingType")
-    protected String mappingType;
+  @XmlElement(name = "Sequence")
+  protected Sequence sequence;
+
+  protected String dseqFor;
+
+  @XmlAttribute(name = "mappingType")
+  protected String mappingType;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Sequence }
-     *     
-     */
-    public Sequence getSequence() {
-        return sequence;
-    }
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link Sequence }
+   * 
+   */
+  public Sequence getSequence()
+  {
+    return sequence;
+  }
 
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Sequence }
-     *     
-     */
-    public void setSequence(Sequence value) {
-        this.sequence = value;
-    }
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link Sequence }
+   * 
+   */
+  public void setSequence(Sequence value)
+  {
+    this.sequence = value;
+  }
 
-    /**
-     * Gets the value of the dseqFor property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDseqFor() {
-        return dseqFor;
-    }
+  /**
+   * Gets the value of the dseqFor property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDseqFor()
+  {
+    return dseqFor;
+  }
 
-    /**
-     * Sets the value of the dseqFor property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDseqFor(String value) {
-        this.dseqFor = value;
-    }
+  /**
+   * Sets the value of the dseqFor property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDseqFor(String value)
+  {
+    this.dseqFor = value;
+  }
 
-    /**
-     * Gets the value of the mappingType property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getMappingType() {
-        return mappingType;
-    }
+  /**
+   * Gets the value of the mappingType property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getMappingType()
+  {
+    return mappingType;
+  }
 
-    /**
-     * Sets the value of the mappingType property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setMappingType(String value) {
-        this.mappingType = value;
-    }
+  /**
+   * Sets the value of the mappingType property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setMappingType(String value)
+  {
+    this.mappingType = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java
index d884100..23aa9ac 100644
--- a/src/jalview/xml/binding/jalview/MatrixType.java
+++ b/src/jalview/xml/binding/jalview/MatrixType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

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">
@@ -47,285 +48,292 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "MatrixType", propOrder = {
-    "elements",
-    "groups",
-    "newick",
-    "property"
-})
-public class MatrixType {
+@XmlType(
+  name = "MatrixType",
+  propOrder =
+  { "elements", "groups", "newick", "property" })
+public class MatrixType
+{
 
-    @XmlElement(required = true)
-    protected String elements;
-    protected List groups;
-    protected List newick;
-    protected List property;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "rows", required = true)
-    protected BigInteger rows;
-    @XmlAttribute(name = "cols", required = true)
-    protected BigInteger cols;
-    @XmlAttribute(name = "treeMethod")
-    protected String treeMethod;
-    @XmlAttribute(name = "cutHeight")
-    protected Double cutHeight;
-    @XmlAttribute(name = "id")
-    protected String id;
+  @XmlElement(required = true)
+  protected String elements;
 
-    /**
-     * Gets the value of the elements property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getElements() {
-        return elements;
-    }
+  protected List groups;
 
-    /**
-     * Sets the value of the elements property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setElements(String value) {
-        this.elements = value;
-    }
+  protected List newick;
 
-    /**
-     * Gets the value of the groups property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getGroups().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getNewick().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - 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 } - * - * - */ - 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") + protected String id; - /** - * Gets the value of the cols property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getCols() { - return cols; - } + /** + * Gets the value of the elements property. + * + * @return possible object is {@link String } + * + */ + public String getElements() + { + return elements; + } - /** - * Sets the value of the cols property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setCols(BigInteger value) { - this.cols = value; - } + /** + * Sets the value of the elements property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setElements(String value) + { + this.elements = value; + } - /** - * Gets the value of the treeMethod property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getTreeMethod() { - return treeMethod; + /** + * Gets the value of the groups property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getNewick() + { + if (newick == null) + { + newick = new ArrayList(); } + return this.newick; + } - /** - * 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 } + * + * + */ + 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 22b78a5..77074d1 100644 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@ -5,19 +5,21 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlEnum; import javax.xml.bind.annotation.XmlEnumValue; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for NoValueColour. + *

+ * Java class for NoValueColour. * - *

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

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

+ * *

  * <simpleType name="NoValueColour">
  *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -31,31 +33,36 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum NoValueColour {
-
-    @XmlEnumValue("None")
-    NONE("None"),
-    @XmlEnumValue("Min")
-    MIN("Min"),
-    @XmlEnumValue("Max")
-    MAX("Max");
-    private final String value;
-
-    NoValueColour(String v) {
-        value = v;
-    }
+public enum NoValueColour
+{
 
-    public String value() {
-        return value;
-    }
+  @XmlEnumValue("None")
+  NONE("None"), @XmlEnumValue("Min")
+  MIN("Min"), @XmlEnumValue("Max")
+  MAX("Max");
+
+  private final String value;
+
+  NoValueColour(String v)
+  {
+    value = v;
+  }
+
+  public String value()
+  {
+    return value;
+  }
 
-    public static NoValueColour fromValue(String v) {
-        for (NoValueColour c: NoValueColour.values()) {
-            if (c.value.equals(v)) {
-                return c;
-            }
-        }
-        throw new IllegalArgumentException(v);
+  public static NoValueColour fromValue(String v)
+  {
+    for (NoValueColour c : NoValueColour.values())
+    {
+      if (c.value.equals(v))
+      {
+        return c;
+      }
     }
+    throw new IllegalArgumentException(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index f034a2a..448b35f 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.JAXBElement;
@@ -13,492 +12,567 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 import javax.xml.namespace.QName;
 
-
 /**
- * This object contains factory methods for each 
- * Java content interface and Java element interface 
- * generated in the jalview.xml.binding.jalview package. 
- * 

An ObjectFactory allows you to programatically - * construct new instances of the Java representation - * for XML content. The Java representation of XML - * content can consist of schema derived interfaces - * and classes representing the binding of schema - * type definitions, element declarations and model - * groups. Factory methods for each of these are - * provided in this class. + * This object contains factory methods for each Java content interface and Java + * element interface generated in the jalview.xml.binding.jalview package. + *

+ * An ObjectFactory allows you to programatically construct new instances of the + * Java representation for XML content. The Java representation of XML content + * can consist of schema derived interfaces and classes representing the binding + * of schema type definitions, element declarations and model groups. Factory + * methods for each of these are provided in this class. * */ @XmlRegistry -public class ObjectFactory { - - private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet"); - private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel"); - private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours"); - - /** - * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview - * - */ - public ObjectFactory() { - } - - /** - * Create an instance of {@link AlcodonFrame } - * - */ - public AlcodonFrame createAlcodonFrame() { - return new AlcodonFrame(); - } - - /** - * Create an instance of {@link MapListType } - * - */ - public MapListType createMapListType() { - return new MapListType(); - } - - /** - * Create an instance of {@link Sequence } - * - */ - public Sequence createSequence() { - return new Sequence(); - } - - /** - * Create an instance of {@link Annotation } - * - */ - public Annotation createAnnotation() { - return new Annotation(); - } - - /** - * Create an instance of {@link SequenceSet } - * - */ - public SequenceSet createSequenceSet() { - return new SequenceSet(); - } - - /** - * Create an instance of {@link FeatureMatcherSet } - * - */ - public FeatureMatcherSet createFeatureMatcherSet() { - return new FeatureMatcherSet(); - } - - /** - * Create an instance of {@link JalviewUserColours } - * - */ - public JalviewUserColours createJalviewUserColours() { - return new JalviewUserColours(); - } - - /** - * Create an instance of {@link Pdbentry } - * - */ - public Pdbentry createPdbentry() { - return new Pdbentry(); - } - - /** - * Create an instance of {@link Feature } - * - */ - public Feature createFeature() { - return new Feature(); - } - - /** - * Create an instance of {@link JalviewModel } - * - */ - public JalviewModel createJalviewModel() { - return new JalviewModel(); - } - - /** - * Create an instance of {@link JalviewModel.FeatureSettings } - * - */ - public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() { - return new JalviewModel.FeatureSettings(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer } - * - */ - public JalviewModel.PcaViewer createJalviewModelPcaViewer() { - return new JalviewModel.PcaViewer(); - } - - /** - * Create an instance of {@link JalviewModel.Viewport } - * - */ - public JalviewModel.Viewport createJalviewModelViewport() { - return new JalviewModel.Viewport(); - } - - /** - * Create an instance of {@link JalviewModel.JSeq } - * - */ - public JalviewModel.JSeq createJalviewModelJSeq() { - return new JalviewModel.JSeq(); - } - - /** - * Create an instance of {@link JalviewModel.JSeq.RnaViewer } - * - */ - public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() { - return new JalviewModel.JSeq.RnaViewer(); - } - - /** - * Create an instance of {@link JalviewModel.JSeq.Pdbids } - * - */ - public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() { - return new JalviewModel.JSeq.Pdbids(); - } - - /** - * Create an instance of {@link DoubleMatrix } - * - */ - public DoubleMatrix createDoubleMatrix() { - return new DoubleMatrix(); - } - - /** - * Create an instance of {@link AnnotationColourScheme } - * - */ - public AnnotationColourScheme createAnnotationColourScheme() { - return new AnnotationColourScheme(); - } - - /** - * Create an instance of {@link PcaDataType } - * - */ - public PcaDataType createPcaDataType() { - return new PcaDataType(); - } - - /** - * Create an instance of {@link DoubleVector } - * - */ - public DoubleVector createDoubleVector() { - return new DoubleVector(); - } - - /** - * Create an instance of {@link AlcodonFrame.Alcodon } - * - */ - public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() { - return new AlcodonFrame.Alcodon(); - } - - /** - * Create an instance of {@link AlcodonFrame.AlcodMap } - * - */ - public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() { - return new AlcodonFrame.AlcodMap(); - } - - /** - * Create an instance of {@link AnnotationElement } - * - */ - public AnnotationElement createAnnotationElement() { - return new AnnotationElement(); - } - - /** - * Create an instance of {@link Mapping } - * - */ - public Mapping createMapping() { - return new Mapping(); - } - - /** - * Create an instance of {@link MapListType.MapListFrom } - * - */ - public MapListType.MapListFrom createMapListTypeMapListFrom() { - return new MapListType.MapListFrom(); - } - - /** - * Create an instance of {@link MapListType.MapListTo } - * - */ - public MapListType.MapListTo createMapListTypeMapListTo() { - return new MapListType.MapListTo(); - } - - /** - * Create an instance of {@link SequenceType } - * - */ - public SequenceType createSequenceType() { - return new SequenceType(); - } - - /** - * Create an instance of {@link Sequence.DBRef } - * - */ - public Sequence.DBRef createSequenceDBRef() { - return new Sequence.DBRef(); - } - - /** - * Create an instance of {@link Annotation.ThresholdLine } - * - */ - public Annotation.ThresholdLine createAnnotationThresholdLine() { - return new Annotation.ThresholdLine(); - } - - /** - * Create an instance of {@link MatrixType } - * - */ - public MatrixType createMatrixType() { - return new MatrixType(); - } - - /** - * Create an instance of {@link jalview.xml.binding.jalview.Property } - * - */ - public jalview.xml.binding.jalview.Property createProperty() { - return new jalview.xml.binding.jalview.Property(); - } - - /** - * Create an instance of {@link SequenceSet.SequenceSetProperties } - * - */ - public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() { - return new SequenceSet.SequenceSetProperties(); - } - - /** - * Create an instance of {@link VAMSAS } - * - */ - public VAMSAS createVAMSAS() { - return new VAMSAS(); - } - - /** - * Create an instance of {@link FeatureMatcher } - * - */ - public FeatureMatcher createFeatureMatcher() { - return new FeatureMatcher(); - } - - /** - * Create an instance of {@link WebServiceParameterSet } - * - */ - public WebServiceParameterSet createWebServiceParameterSet() { - return new WebServiceParameterSet(); - } - - /** - * Create an instance of {@link FeatureMatcherSet.CompoundMatcher } - * - */ - public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() { - return new FeatureMatcherSet.CompoundMatcher(); - } - - /** - * Create an instance of {@link JalviewUserColours.Colour } - * - */ - public JalviewUserColours.Colour createJalviewUserColoursColour() { - return new JalviewUserColours.Colour(); - } - - /** - * Create an instance of {@link JalviewUserColours.Filter } - * - */ - public JalviewUserColours.Filter createJalviewUserColoursFilter() { - return new JalviewUserColours.Filter(); - } - - /** - * Create an instance of {@link Pdbentry.Property } - * - */ - public Pdbentry.Property createPdbentryProperty() { - return new Pdbentry.Property(); - } - - /** - * Create an instance of {@link Feature.OtherData } - * - */ - public Feature.OtherData createFeatureOtherData() { - return new Feature.OtherData(); - } - - /** - * Create an instance of {@link JalviewModel.JGroup } - * - */ - public JalviewModel.JGroup createJalviewModelJGroup() { - return new JalviewModel.JGroup(); - } - - /** - * Create an instance of {@link JalviewModel.UserColours } - * - */ - public JalviewModel.UserColours createJalviewModelUserColours() { - return new JalviewModel.UserColours(); - } - - /** - * Create an instance of {@link JalviewModel.Tree } - * - */ - public JalviewModel.Tree createJalviewModelTree() { - return new JalviewModel.Tree(); - } - - /** - * Create an instance of {@link JalviewModel.FeatureSettings.Setting } - * - */ - public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() { - return new JalviewModel.FeatureSettings.Setting(); - } - - /** - * Create an instance of {@link JalviewModel.FeatureSettings.Group } - * - */ - public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() { - return new JalviewModel.FeatureSettings.Group(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint } - * - */ - public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() { - return new JalviewModel.PcaViewer.SequencePoint(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer.Axis } - * - */ - public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() { - return new JalviewModel.PcaViewer.Axis(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin } - * - */ - public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() { - return new JalviewModel.PcaViewer.SeqPointMin(); - } - - /** - * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax } - * - */ - public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() { - return new JalviewModel.PcaViewer.SeqPointMax(); - } - - /** - * Create an instance of {@link JalviewModel.Viewport.HiddenColumns } - * - */ - public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() { - return new JalviewModel.Viewport.HiddenColumns(); - } - - /** - * Create an instance of {@link JalviewModel.Viewport.CalcIdParam } - * - */ - public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() { - return new JalviewModel.Viewport.CalcIdParam(); - } - - /** - * Create an instance of {@link JalviewModel.Viewport.Overview } - * - */ - public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() { - return new JalviewModel.Viewport.Overview(); - } - - /** - * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } - * - */ - public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() { - return new JalviewModel.JSeq.RnaViewer.SecondaryStructure(); - } - - /** - * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState } - * - */ - public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() { - return new JalviewModel.JSeq.Pdbids.StructureState(); - } - - /** - * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}} - * - */ - @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet") - public JAXBElement createWebServiceParameterSet(WebServiceParameterSet value) { - return new JAXBElement(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value); - } - - /** - * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}} - * - */ - @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel") - public JAXBElement createJalviewModel(JalviewModel value) { - return new JAXBElement(_JalviewModel_QNAME, JalviewModel.class, null, value); - } - - /** - * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}} - * - */ - @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours") - public JAXBElement createJalviewUserColours(JalviewUserColours value) { - return new JAXBElement(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value); - } +public class ObjectFactory +{ + + private final static QName _WebServiceParameterSet_QNAME = new QName( + "www.jalview.org/xml/wsparamset", "WebServiceParameterSet"); + + private final static QName _JalviewModel_QNAME = new QName( + "www.jalview.org", "JalviewModel"); + + private final static QName _JalviewUserColours_QNAME = new QName( + "www.jalview.org/colours", "JalviewUserColours"); + + /** + * Create a new ObjectFactory that can be used to create new instances of + * schema derived classes for package: jalview.xml.binding.jalview + * + */ + public ObjectFactory() + { + } + + /** + * Create an instance of {@link AlcodonFrame } + * + */ + public AlcodonFrame createAlcodonFrame() + { + return new AlcodonFrame(); + } + + /** + * Create an instance of {@link MapListType } + * + */ + public MapListType createMapListType() + { + return new MapListType(); + } + + /** + * Create an instance of {@link Sequence } + * + */ + public Sequence createSequence() + { + return new Sequence(); + } + + /** + * Create an instance of {@link Annotation } + * + */ + public Annotation createAnnotation() + { + return new Annotation(); + } + + /** + * Create an instance of {@link SequenceSet } + * + */ + public SequenceSet createSequenceSet() + { + return new SequenceSet(); + } + + /** + * Create an instance of {@link FeatureMatcherSet } + * + */ + public FeatureMatcherSet createFeatureMatcherSet() + { + return new FeatureMatcherSet(); + } + + /** + * Create an instance of {@link JalviewUserColours } + * + */ + public JalviewUserColours createJalviewUserColours() + { + return new JalviewUserColours(); + } + + /** + * Create an instance of {@link Pdbentry } + * + */ + public Pdbentry createPdbentry() + { + return new Pdbentry(); + } + + /** + * Create an instance of {@link Feature } + * + */ + public Feature createFeature() + { + return new Feature(); + } + + /** + * Create an instance of {@link JalviewModel } + * + */ + public JalviewModel createJalviewModel() + { + return new JalviewModel(); + } + + /** + * Create an instance of {@link JalviewModel.FeatureSettings } + * + */ + public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() + { + return new JalviewModel.FeatureSettings(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer } + * + */ + public JalviewModel.PcaViewer createJalviewModelPcaViewer() + { + return new JalviewModel.PcaViewer(); + } + + /** + * Create an instance of {@link JalviewModel.Viewport } + * + */ + public JalviewModel.Viewport createJalviewModelViewport() + { + return new JalviewModel.Viewport(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq } + * + */ + public JalviewModel.JSeq createJalviewModelJSeq() + { + return new JalviewModel.JSeq(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq.RnaViewer } + * + */ + public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() + { + return new JalviewModel.JSeq.RnaViewer(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq.Pdbids } + * + */ + public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() + { + return new JalviewModel.JSeq.Pdbids(); + } + + /** + * Create an instance of {@link DoubleMatrix } + * + */ + public DoubleMatrix createDoubleMatrix() + { + return new DoubleMatrix(); + } + + /** + * Create an instance of {@link AnnotationColourScheme } + * + */ + public AnnotationColourScheme createAnnotationColourScheme() + { + return new AnnotationColourScheme(); + } + + /** + * Create an instance of {@link PcaDataType } + * + */ + public PcaDataType createPcaDataType() + { + return new PcaDataType(); + } + + /** + * Create an instance of {@link DoubleVector } + * + */ + public DoubleVector createDoubleVector() + { + return new DoubleVector(); + } + + /** + * Create an instance of {@link AlcodonFrame.Alcodon } + * + */ + public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() + { + return new AlcodonFrame.Alcodon(); + } + + /** + * Create an instance of {@link AlcodonFrame.AlcodMap } + * + */ + public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() + { + return new AlcodonFrame.AlcodMap(); + } + + /** + * Create an instance of {@link AnnotationElement } + * + */ + public AnnotationElement createAnnotationElement() + { + return new AnnotationElement(); + } + + /** + * Create an instance of {@link Mapping } + * + */ + public Mapping createMapping() + { + return new Mapping(); + } + + /** + * Create an instance of {@link MapListType.MapListFrom } + * + */ + public MapListType.MapListFrom createMapListTypeMapListFrom() + { + return new MapListType.MapListFrom(); + } + + /** + * Create an instance of {@link MapListType.MapListTo } + * + */ + public MapListType.MapListTo createMapListTypeMapListTo() + { + return new MapListType.MapListTo(); + } + + /** + * Create an instance of {@link SequenceType } + * + */ + public SequenceType createSequenceType() + { + return new SequenceType(); + } + + /** + * Create an instance of {@link Sequence.DBRef } + * + */ + public Sequence.DBRef createSequenceDBRef() + { + return new Sequence.DBRef(); + } + + /** + * Create an instance of {@link Annotation.ThresholdLine } + * + */ + public Annotation.ThresholdLine createAnnotationThresholdLine() + { + return new Annotation.ThresholdLine(); + } + + /** + * Create an instance of {@link MatrixType } + * + */ + public MatrixType createMatrixType() + { + return new MatrixType(); + } + + /** + * Create an instance of {@link jalview.xml.binding.jalview.Property } + * + */ + public jalview.xml.binding.jalview.Property createProperty() + { + return new jalview.xml.binding.jalview.Property(); + } + + /** + * Create an instance of {@link SequenceSet.SequenceSetProperties } + * + */ + public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() + { + return new SequenceSet.SequenceSetProperties(); + } + + /** + * Create an instance of {@link VAMSAS } + * + */ + public VAMSAS createVAMSAS() + { + return new VAMSAS(); + } + + /** + * Create an instance of {@link FeatureMatcher } + * + */ + public FeatureMatcher createFeatureMatcher() + { + return new FeatureMatcher(); + } + + /** + * Create an instance of {@link WebServiceParameterSet } + * + */ + public WebServiceParameterSet createWebServiceParameterSet() + { + return new WebServiceParameterSet(); + } + + /** + * Create an instance of {@link FeatureMatcherSet.CompoundMatcher } + * + */ + public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() + { + return new FeatureMatcherSet.CompoundMatcher(); + } + + /** + * Create an instance of {@link JalviewUserColours.Colour } + * + */ + public JalviewUserColours.Colour createJalviewUserColoursColour() + { + return new JalviewUserColours.Colour(); + } + + /** + * Create an instance of {@link JalviewUserColours.Filter } + * + */ + public JalviewUserColours.Filter createJalviewUserColoursFilter() + { + return new JalviewUserColours.Filter(); + } + + /** + * Create an instance of {@link Pdbentry.Property } + * + */ + public Pdbentry.Property createPdbentryProperty() + { + return new Pdbentry.Property(); + } + + /** + * Create an instance of {@link Feature.OtherData } + * + */ + public Feature.OtherData createFeatureOtherData() + { + return new Feature.OtherData(); + } + + /** + * Create an instance of {@link JalviewModel.JGroup } + * + */ + public JalviewModel.JGroup createJalviewModelJGroup() + { + return new JalviewModel.JGroup(); + } + + /** + * Create an instance of {@link JalviewModel.UserColours } + * + */ + public JalviewModel.UserColours createJalviewModelUserColours() + { + return new JalviewModel.UserColours(); + } + + /** + * Create an instance of {@link JalviewModel.Tree } + * + */ + public JalviewModel.Tree createJalviewModelTree() + { + return new JalviewModel.Tree(); + } + + /** + * Create an instance of {@link JalviewModel.FeatureSettings.Setting } + * + */ + public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() + { + return new JalviewModel.FeatureSettings.Setting(); + } + + /** + * Create an instance of {@link JalviewModel.FeatureSettings.Group } + * + */ + public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() + { + return new JalviewModel.FeatureSettings.Group(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint } + * + */ + public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() + { + return new JalviewModel.PcaViewer.SequencePoint(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer.Axis } + * + */ + public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() + { + return new JalviewModel.PcaViewer.Axis(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin } + * + */ + public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() + { + return new JalviewModel.PcaViewer.SeqPointMin(); + } + + /** + * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax } + * + */ + public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() + { + return new JalviewModel.PcaViewer.SeqPointMax(); + } + + /** + * Create an instance of {@link JalviewModel.Viewport.HiddenColumns } + * + */ + public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() + { + return new JalviewModel.Viewport.HiddenColumns(); + } + + /** + * Create an instance of {@link JalviewModel.Viewport.CalcIdParam } + * + */ + public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() + { + return new JalviewModel.Viewport.CalcIdParam(); + } + + /** + * Create an instance of {@link JalviewModel.Viewport.Overview } + * + */ + public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() + { + return new JalviewModel.Viewport.Overview(); + } + + /** + * Create an instance of + * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } + * + */ + public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() + { + return new JalviewModel.JSeq.RnaViewer.SecondaryStructure(); + } + + /** + * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState } + * + */ + public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() + { + return new JalviewModel.JSeq.Pdbids.StructureState(); + } + + /** + * Create an instance of {@link JAXBElement + * }{@code <}{@link WebServiceParameterSet }{@code >}} + * + */ + @XmlElementDecl( + namespace = "www.jalview.org/xml/wsparamset", + name = "WebServiceParameterSet") + public JAXBElement createWebServiceParameterSet( + WebServiceParameterSet value) + { + return new JAXBElement( + _WebServiceParameterSet_QNAME, WebServiceParameterSet.class, + null, value); + } + + /** + * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel + * }{@code >}} + * + */ + @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel") + public JAXBElement createJalviewModel(JalviewModel value) + { + return new JAXBElement(_JalviewModel_QNAME, + JalviewModel.class, null, value); + } + + /** + * Create an instance of {@link JAXBElement + * }{@code <}{@link JalviewUserColours }{@code >}} + * + */ + @XmlElementDecl( + namespace = "www.jalview.org/colours", + name = "JalviewUserColours") + public JAXBElement createJalviewUserColours( + JalviewUserColours value) + { + return new JAXBElement(_JalviewUserColours_QNAME, + JalviewUserColours.class, null, value); + } } diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java index 06aecab..8719689 100644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -13,15 +12,17 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** * - * The results of a PCA calculation - * + * The results of a PCA calculation + * * - *

Java class for PcaDataType complex type. + *

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

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

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

  * <complexType name="PcaDataType">
@@ -40,90 +41,90 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
-    "pairwiseMatrix",
-    "tridiagonalMatrix",
-    "eigenMatrix"
-})
-public class PcaDataType {
+@XmlType(
+  name = "PcaDataType",
+  namespace = "www.jalview.org",
+  propOrder =
+  { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
+public class PcaDataType
+{
+
+  @XmlElement(required = true)
+  protected DoubleMatrix pairwiseMatrix;
+
+  @XmlElement(required = true)
+  protected DoubleMatrix tridiagonalMatrix;
 
-    @XmlElement(required = true)
-    protected DoubleMatrix pairwiseMatrix;
-    @XmlElement(required = true)
-    protected DoubleMatrix tridiagonalMatrix;
-    @XmlElement(required = true)
-    protected DoubleMatrix eigenMatrix;
+  @XmlElement(required = true)
+  protected DoubleMatrix eigenMatrix;
 
-    /**
-     * Gets the value of the pairwiseMatrix property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public DoubleMatrix getPairwiseMatrix() {
-        return pairwiseMatrix;
-    }
+  /**
+   * Gets the value of the pairwiseMatrix property.
+   * 
+   * @return possible object is {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix getPairwiseMatrix()
+  {
+    return pairwiseMatrix;
+  }
 
-    /**
-     * Sets the value of the pairwiseMatrix property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public void setPairwiseMatrix(DoubleMatrix value) {
-        this.pairwiseMatrix = value;
-    }
+  /**
+   * Sets the value of the pairwiseMatrix property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleMatrix }
+   * 
+   */
+  public void setPairwiseMatrix(DoubleMatrix value)
+  {
+    this.pairwiseMatrix = value;
+  }
 
-    /**
-     * Gets the value of the tridiagonalMatrix property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public DoubleMatrix getTridiagonalMatrix() {
-        return tridiagonalMatrix;
-    }
+  /**
+   * Gets the value of the tridiagonalMatrix property.
+   * 
+   * @return possible object is {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix getTridiagonalMatrix()
+  {
+    return tridiagonalMatrix;
+  }
 
-    /**
-     * Sets the value of the tridiagonalMatrix property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public void setTridiagonalMatrix(DoubleMatrix value) {
-        this.tridiagonalMatrix = value;
-    }
+  /**
+   * Sets the value of the tridiagonalMatrix property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleMatrix }
+   * 
+   */
+  public void setTridiagonalMatrix(DoubleMatrix value)
+  {
+    this.tridiagonalMatrix = value;
+  }
 
-    /**
-     * Gets the value of the eigenMatrix property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public DoubleMatrix getEigenMatrix() {
-        return eigenMatrix;
-    }
+  /**
+   * Gets the value of the eigenMatrix property.
+   * 
+   * @return possible object is {@link DoubleMatrix }
+   * 
+   */
+  public DoubleMatrix getEigenMatrix()
+  {
+    return eigenMatrix;
+  }
 
-    /**
-     * Sets the value of the eigenMatrix property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DoubleMatrix }
-     *     
-     */
-    public void setEigenMatrix(DoubleMatrix value) {
-        this.eigenMatrix = value;
-    }
+  /**
+   * Sets the value of the eigenMatrix property.
+   * 
+   * @param value
+   *          allowed object is {@link DoubleMatrix }
+   * 
+   */
+  public void setEigenMatrix(DoubleMatrix value)
+  {
+    this.eigenMatrix = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index 401022a..c0bedff 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for pdbentry complex type. + *

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

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

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

  * <complexType name="pdbentry">
@@ -49,199 +50,205 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
-    "property"
-})
-@XmlSeeAlso({
-    jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
-})
-public class Pdbentry {
-
-    protected List property;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "type")
-    protected String type;
-    @XmlAttribute(name = "file")
-    protected String file;
-
-    /**
-     * Gets the value of the property property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getProperty().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Property + { + + @XmlAttribute(name = "name", required = true) + protected String name; + + @XmlAttribute(name = "value", required = true) + protected String value; /** - * Gets the value of the id property. + * Gets the value of the name property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getId() { - return id; + public String getName() + { + return name; } /** - * Sets the value of the id property. + * Sets the value of the name property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } - - /** - * Gets the value of the type property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getType() { - return type; + public void setName(String value) + { + this.name = value; } /** - * Sets the value of the type property. + * Gets the value of the value property. * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the file property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getFile() { - return file; + public String getValue() + { + return value; } /** - * Sets the value of the file property. + * Sets the value of the value property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setFile(String value) { - this.file = value; - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Property { - - @XmlAttribute(name = "name", required = true) - protected String name; - @XmlAttribute(name = "value", required = true) - protected String value; - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - + public void setValue(String value) + { + this.value = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/Property.java b/src/jalview/xml/binding/jalview/Property.java index 3c0879d..ed57889 100644 --- a/src/jalview/xml/binding/jalview/Property.java +++ b/src/jalview/xml/binding/jalview/Property.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for property complex type. + *

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

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

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

  * <complexType name="property">
@@ -34,59 +35,59 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "property")
-public class Property {
+public class Property
+{
+
+  @XmlAttribute(name = "name")
+  protected String name;
 
-    @XmlAttribute(name = "name")
-    protected String name;
-    @XmlAttribute(name = "value")
-    protected String value;
+  @XmlAttribute(name = "value")
+  protected String value;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index d02fd03..15893d8 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -55,294 +56,300 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "dbRef"
-})
+@XmlType(name = "", propOrder = { "dbRef" })
 @XmlRootElement(name = "Sequence")
-public class Sequence
-    extends SequenceType
+public class Sequence extends SequenceType
 {
 
-    @XmlElement(name = "DBRef")
-    protected List dbRef;
-    @XmlAttribute(name = "dsseqid")
-    protected String dsseqid;
-    @XmlAttribute(name = "biotype")
-    protected String biotype;
+  @XmlElement(name = "DBRef")
+  protected List dbRef;
+
+  @XmlAttribute(name = "dsseqid")
+  protected String dsseqid;
+
+  @XmlAttribute(name = "biotype")
+  protected String biotype;
+
+  /**
+   * Gets the value of the dbRef property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+   *       </sequence>
+   *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "mapping" }) + public static class DBRef + { + + @XmlElement(name = "Mapping") + protected Mapping mapping; + + @XmlAttribute(name = "source") + protected String source; + + @XmlAttribute(name = "version") + protected String version; + + @XmlAttribute(name = "accessionId") + protected String accessionId; + + @XmlAttribute(name = "locus") + protected Boolean locus; + + @XmlAttribute(name = "canonical") + protected Boolean canonical; /** - * Gets the value of the dbRef property. + * Gets the value of the mapping property. * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getDBRef().add(newItem);
-     * 
+ */ + public Mapping getMapping() + { + return mapping; + } + + /** + * Sets the value of the mapping property. + * + * @param value + * allowed object is {@link Mapping } + * + */ + public void setMapping(Mapping value) + { + this.mapping = value; + } + + /** + * Gets the value of the source property. * + * @return possible object is {@link String } * - *

- * Objects of the following type(s) are allowed in the list - * {@link Sequence.DBRef } + */ + public String getSource() + { + return source; + } + + /** + * Sets the value of the source property. * + * @param value + * allowed object is {@link String } * */ - public List getDBRef() { - if (dbRef == null) { - dbRef = new ArrayList(); - } - return this.dbRef; + public void setSource(String value) + { + this.source = value; } /** - * Gets the value of the dsseqid property. + * Gets the value of the version property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getDsseqid() { - return dsseqid; + public String getVersion() + { + return version; } /** - * Sets the value of the dsseqid property. + * Sets the value of the version property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link String } + * */ - public void setDsseqid(String value) { - this.dsseqid = value; + public void setVersion(String value) + { + this.version = value; } /** - * Gets the value of the biotype property. + * Gets the value of the accessionId property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getBiotype() { - return biotype; + public String getAccessionId() + { + return accessionId; } /** - * Sets the value of the biotype property. + * Sets the value of the accessionId property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link String } + * */ - public void setBiotype(String value) { - this.biotype = value; + public void setAccessionId(String value) + { + this.accessionId = value; } + /** + * Gets the value of the locus property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isLocus() + { + if (locus == null) + { + return false; + } + else + { + return locus; + } + } /** - *

Java class for anonymous complex type. + * Sets the value of the locus property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link Boolean } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public void setLocus(Boolean value) + { + this.locus = value; + } + + /** + * Gets the value of the canonical property. * + * @return possible object is {@link Boolean } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "mapping" - }) - public static class DBRef { - - @XmlElement(name = "Mapping") - protected Mapping mapping; - @XmlAttribute(name = "source") - protected String source; - @XmlAttribute(name = "version") - protected String version; - @XmlAttribute(name = "accessionId") - protected String accessionId; - @XmlAttribute(name = "locus") - protected Boolean locus; - @XmlAttribute(name = "canonical") - protected Boolean canonical; - - /** - * Gets the value of the mapping property. - * - * @return - * possible object is - * {@link Mapping } - * - */ - public Mapping getMapping() { - return mapping; - } - - /** - * Sets the value of the mapping property. - * - * @param value - * allowed object is - * {@link Mapping } - * - */ - public void setMapping(Mapping value) { - this.mapping = value; - } - - /** - * Gets the value of the source property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getSource() { - return source; - } - - /** - * Sets the value of the source property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setSource(String value) { - this.source = value; - } - - /** - * Gets the value of the version property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getVersion() { - return version; - } - - /** - * Sets the value of the version property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setVersion(String value) { - this.version = value; - } - - /** - * Gets the value of the accessionId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getAccessionId() { - return accessionId; - } - - /** - * Sets the value of the accessionId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setAccessionId(String value) { - this.accessionId = value; - } - - /** - * Gets the value of the locus property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isLocus() { - if (locus == null) { - return false; - } else { - return locus; - } - } - - /** - * Sets the value of the locus property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setLocus(Boolean value) { - this.locus = value; - } - - /** - * Gets the value of the canonical property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public boolean isCanonical() { - if (canonical == null) { - return false; - } else { - return canonical; - } - } - - /** - * Sets the value of the canonical property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setCanonical(Boolean value) { - this.canonical = value; - } + public boolean isCanonical() + { + if (canonical == null) + { + return false; + } + else + { + return canonical; + } + } + /** + * Sets the value of the canonical property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setCanonical(Boolean value) + { + this.canonical = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index a915d94..6676f7b 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -52,267 +53,282 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "sequence",
-    "annotation",
-    "sequenceSetProperties",
-    "alcodonFrame"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet {
+public class SequenceSet
+{
 
-    @XmlElement(name = "Sequence")
-    protected List sequence;
-    @XmlElement(name = "Annotation")
-    protected List annotation;
-    protected List sequenceSetProperties;
-    @XmlElement(name = "AlcodonFrame")
-    protected List alcodonFrame;
-    @XmlAttribute(name = "gapChar", required = true)
-    protected String gapChar;
-    @XmlAttribute(name = "datasetId")
-    protected String datasetId;
+  @XmlElement(name = "Sequence")
+  protected List sequence;
 
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getSequence().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

- * For example, to add a new item, do as follows: - *

-     *    getAnnotation().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

- * For example, to add a new item, do as follows: - *

-     *    getSequenceSetProperties().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

- * For example, to add a new item, do as follows: - *

-     *    getAlcodonFrame().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class SequenceSetProperties + { + + @XmlAttribute(name = "key") + protected String key; + + @XmlAttribute(name = "value") + protected String value; /** - * Gets the value of the gapChar property. + * Gets the value of the key property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getGapChar() { - return gapChar; + public String getKey() + { + return key; } /** - * Sets the value of the gapChar property. + * Sets the value of the key property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setGapChar(String value) { - this.gapChar = value; - } - - /** - * Gets the value of the datasetId property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getDatasetId() { - return datasetId; + public void setKey(String value) + { + this.key = value; } /** - * Sets the value of the datasetId property. + * Gets the value of the value property. + * + * @return possible object is {@link String } * - * @param value - * allowed object is - * {@link String } - * */ - public void setDatasetId(String value) { - this.datasetId = value; + public String getValue() + { + return value; } - /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ * Sets the value of the value property. * + * @param value + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SequenceSetProperties { - - @XmlAttribute(name = "key") - protected String key; - @XmlAttribute(name = "value") - protected String value; - - /** - * Gets the value of the key property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getKey() { - return key; - } - - /** - * Sets the value of the key property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setKey(String value) { - this.key = value; - } - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - + public void setValue(String value) + { + this.value = value; } + } + } diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java index fa65d58..3de52d2 100644 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import javax.xml.bind.annotation.XmlAccessType; @@ -14,11 +13,13 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlSeeAlso; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for SequenceType complex type. + *

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

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

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

  * <complexType name="SequenceType">
@@ -38,116 +39,111 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = {
-    "sequence",
-    "name"
-})
-@XmlSeeAlso({
-    Sequence.class
-})
-public class SequenceType {
-
-    protected String sequence;
-    protected String name;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "description")
-    protected String description;
-
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSequence() {
-        return sequence;
-    }
-
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSequence(String value) {
-        this.sequence = value;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
+@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
+@XmlSeeAlso({ Sequence.class })
+public class SequenceType
+{
+
+  protected String sequence;
+
+  protected String name;
+
+  @XmlAttribute(name = "id")
+  protected String id;
+
+  @XmlAttribute(name = "description")
+  protected String description;
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSequence(String value)
+  {
+    this.sequence = value;
+  }
+
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
+
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
+
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
+
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
+
+  /**
+   * Gets the value of the description property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDescription()
+  {
+    return description;
+  }
+
+  /**
+   * Sets the value of the description property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDescription(String value)
+  {
+    this.description = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index 192caf8..6c9cbce 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -5,18 +5,20 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for ThresholdType. + *

+ * Java class for ThresholdType. * - *

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

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

+ * *

  * <simpleType name="ThresholdType">
  *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -30,18 +32,19 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum ThresholdType {
+public enum ThresholdType
+{
 
-    NONE,
-    ABOVE,
-    BELOW;
+  NONE, ABOVE, BELOW;
 
-    public String value() {
-        return name();
-    }
+  public String value()
+  {
+    return name();
+  }
 
-    public static ThresholdType fromValue(String v) {
-        return valueOf(v);
-    }
+  public static ThresholdType fromValue(String v)
+  {
+    return valueOf(v);
+  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index dd41877..10635e5 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:44 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,11 +14,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for VAMSAS complex type. + *

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

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

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

  * <complexType name="VAMSAS">
@@ -37,73 +38,77 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = {
-    "tree",
-    "sequenceSet"
-})
-public class VAMSAS {
+@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
+public class VAMSAS
+{
+
+  @XmlElement(name = "Tree")
+  protected List tree;
 
-    @XmlElement(name = "Tree")
-    protected List tree;
-    @XmlElement(name = "SequenceSet")
-    protected List sequenceSet;
+  @XmlElement(name = "SequenceSet")
+  protected List sequenceSet;
 
-    /**
-     * Gets the value of the tree property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getTree().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

- * For example, to add a new item, do as follows: - *

-     *    getSequenceSet().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link SequenceSet + * } + * + * + */ + public List getSequenceSet() + { + if (sequenceSet == null) + { + sequenceSet = new ArrayList(); } + return this.sequenceSet; + } } diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java index d3c2098..88f5a22 100644 --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -18,11 +17,13 @@ import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlSeeAlso; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for WebServiceParameterSet complex type. + *

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

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

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

  * <complexType name="WebServiceParameterSet">
@@ -43,152 +44,153 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
-    "version",
-    "description",
-    "serviceURL",
-    "parameters"
-})
+@XmlType(
+  name = "WebServiceParameterSet",
+  namespace = "www.jalview.org/xml/wsparamset",
+  propOrder =
+  { "version", "description", "serviceURL", "parameters" })
 @XmlSeeAlso({
-    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
-})
-public class WebServiceParameterSet {
-
-    @XmlElement(name = "Version", namespace = "")
-    protected String version;
-    @XmlElement(namespace = "")
-    protected String description;
-    @XmlElement(namespace = "", required = true)
-    @XmlSchemaType(name = "anyURI")
-    protected List serviceURL;
-    @XmlElement(namespace = "", required = true)
-    protected String parameters;
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
-
-    /**
-     * Gets the value of the version property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getVersion() {
-        return version;
-    }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setVersion(String value) {
-        this.version = value;
-    }
-
-    /**
-     * Gets the value of the description property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDescription() {
-        return description;
-    }
-
-    /**
-     * Sets the value of the description property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDescription(String value) {
-        this.description = value;
-    }
-
-    /**
-     * Gets the value of the serviceURL property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getServiceURL().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getServiceURL() + { + if (serviceURL == null) + { + serviceURL = new ArrayList(); } + return this.serviceURL; + } + + /** + * Gets the value of the parameters property. + * + * @return possible object is {@link String } + * + */ + public String getParameters() + { + return parameters; + } + + /** + * Sets the value of the parameters property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setParameters(String value) + { + this.parameters = value; + } + + /** + * Gets the value of the name property. + * + * @return possible object is {@link String } + * + */ + public String getName() + { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setName(String value) + { + this.name = value; + } } diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java index 2cfefda..e5bd209 100644 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@ -5,5 +5,7 @@ // Generated on: 2023.03.17 at 05:31:44 PM GMT // -@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) +@javax.xml.bind.annotation.XmlSchema( + namespace = "www.vamsas.ac.uk/jalview/version2", + elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) package jalview.xml.binding.jalview; diff --git a/src/jalview/xml/binding/uniprot/CitationType.java b/src/jalview/xml/binding/uniprot/CitationType.java index de12eb2..2622784 100644 --- a/src/jalview/xml/binding/uniprot/CitationType.java +++ b/src/jalview/xml/binding/uniprot/CitationType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -15,14 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - * Describes different types of citations. - * Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines. + * Describes different types of citations. Equivalent to the flat file RX-, RG-, + * RA-, RT- and RL-lines. * - *

Java class for citationType complex type. + *

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

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

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

  * <complexType name="citationType">
@@ -72,456 +73,457 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "citationType", propOrder = {
-    "title",
-    "editorList",
-    "authorList",
-    "locator",
-    "dbReference"
-})
-public class CitationType {
-
-    protected String title;
-    protected NameListType editorList;
-    protected NameListType authorList;
-    protected String locator;
-    protected List dbReference;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "date")
-    protected String date;
-    @XmlAttribute(name = "name")
-    protected String name;
-    @XmlAttribute(name = "volume")
-    protected String volume;
-    @XmlAttribute(name = "first")
-    protected String first;
-    @XmlAttribute(name = "last")
-    protected String last;
-    @XmlAttribute(name = "publisher")
-    protected String publisher;
-    @XmlAttribute(name = "city")
-    protected String city;
-    @XmlAttribute(name = "db")
-    protected String db;
-    @XmlAttribute(name = "number")
-    protected String number;
-    @XmlAttribute(name = "institute")
-    protected String institute;
-    @XmlAttribute(name = "country")
-    protected String country;
-
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getTitle() {
-        return title;
-    }
-
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setTitle(String value) {
-        this.title = value;
-    }
-
-    /**
-     * Gets the value of the editorList property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link NameListType }
-     *     
-     */
-    public NameListType getEditorList() {
-        return editorList;
-    }
-
-    /**
-     * Sets the value of the editorList property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link NameListType }
-     *     
-     */
-    public void setEditorList(NameListType value) {
-        this.editorList = value;
-    }
-
-    /**
-     * Gets the value of the authorList property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link NameListType }
-     *     
-     */
-    public NameListType getAuthorList() {
-        return authorList;
-    }
-
-    /**
-     * Sets the value of the authorList property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link NameListType }
-     *     
-     */
-    public void setAuthorList(NameListType value) {
-        this.authorList = value;
-    }
-
-    /**
-     * Gets the value of the locator property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getLocator() {
-        return locator;
-    }
-
-    /**
-     * Sets the value of the locator property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setLocator(String value) {
-        this.locator = value;
-    }
-
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getDbReference().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link DbReferenceType } - * - * - */ - public List getDbReference() { - if (dbReference == null) { - dbReference = new ArrayList(); - } - return this.dbReference; - } - - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } - - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the date property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDate() { - return date; - } - - /** - * Sets the value of the date property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDate(String value) { - this.date = value; - } - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the volume property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getVolume() { - return volume; - } - - /** - * Sets the value of the volume property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setVolume(String value) { - this.volume = value; - } - - /** - * Gets the value of the first property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getFirst() { - return first; - } - - /** - * Sets the value of the first property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setFirst(String value) { - this.first = value; - } - - /** - * Gets the value of the last property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getLast() { - return last; - } - - /** - * Sets the value of the last property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setLast(String value) { - this.last = value; - } - - /** - * Gets the value of the publisher property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getPublisher() { - return publisher; - } - - /** - * Sets the value of the publisher property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setPublisher(String value) { - this.publisher = value; - } - - /** - * Gets the value of the city property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getCity() { - return city; - } - - /** - * Sets the value of the city property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setCity(String value) { - this.city = value; - } - - /** - * Gets the value of the db property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDb() { - return db; - } - - /** - * Sets the value of the db property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDb(String value) { - this.db = value; - } - - /** - * Gets the value of the number property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getNumber() { - return number; - } - - /** - * Sets the value of the number property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setNumber(String value) { - this.number = value; - } - - /** - * Gets the value of the institute property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getInstitute() { - return institute; - } - - /** - * Sets the value of the institute property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setInstitute(String value) { - this.institute = value; - } - - /** - * Gets the value of the country property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getCountry() { - return country; - } - - /** - * Sets the value of the country property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setCountry(String value) { - this.country = value; - } +@XmlType( + name = "citationType", + propOrder = + { "title", "editorList", "authorList", "locator", "dbReference" }) +public class CitationType +{ + + protected String title; + + protected NameListType editorList; + + protected NameListType authorList; + + protected String locator; + + protected List dbReference; + + @XmlAttribute(name = "type", required = true) + protected String type; + + @XmlAttribute(name = "date") + protected String date; + + @XmlAttribute(name = "name") + protected String name; + + @XmlAttribute(name = "volume") + protected String volume; + + @XmlAttribute(name = "first") + protected String first; + + @XmlAttribute(name = "last") + protected String last; + + @XmlAttribute(name = "publisher") + protected String publisher; + + @XmlAttribute(name = "city") + protected String city; + + @XmlAttribute(name = "db") + protected String db; + + @XmlAttribute(name = "number") + protected String number; + + @XmlAttribute(name = "institute") + protected String institute; + + @XmlAttribute(name = "country") + protected String country; + + /** + * Gets the value of the title property. + * + * @return possible object is {@link String } + * + */ + public String getTitle() + { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setTitle(String value) + { + this.title = value; + } + + /** + * Gets the value of the editorList property. + * + * @return possible object is {@link NameListType } + * + */ + public NameListType getEditorList() + { + return editorList; + } + + /** + * Sets the value of the editorList property. + * + * @param value + * allowed object is {@link NameListType } + * + */ + public void setEditorList(NameListType value) + { + this.editorList = value; + } + + /** + * Gets the value of the authorList property. + * + * @return possible object is {@link NameListType } + * + */ + public NameListType getAuthorList() + { + return authorList; + } + + /** + * Sets the value of the authorList property. + * + * @param value + * allowed object is {@link NameListType } + * + */ + public void setAuthorList(NameListType value) + { + this.authorList = value; + } + + /** + * Gets the value of the locator property. + * + * @return possible object is {@link String } + * + */ + public String getLocator() + { + return locator; + } + + /** + * Sets the value of the locator property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setLocator(String value) + { + this.locator = value; + } + + /** + * Gets the value of the dbReference property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link DbReferenceType } + * + * + */ + public List getDbReference() + { + if (dbReference == null) + { + dbReference = new ArrayList(); + } + return this.dbReference; + } + + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } + + /** + * Gets the value of the date property. + * + * @return possible object is {@link String } + * + */ + public String getDate() + { + return date; + } + + /** + * Sets the value of the date property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDate(String value) + { + this.date = value; + } + + /** + * Gets the value of the name property. + * + * @return possible object is {@link String } + * + */ + public String getName() + { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setName(String value) + { + this.name = value; + } + + /** + * Gets the value of the volume property. + * + * @return possible object is {@link String } + * + */ + public String getVolume() + { + return volume; + } + + /** + * Sets the value of the volume property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setVolume(String value) + { + this.volume = value; + } + + /** + * Gets the value of the first property. + * + * @return possible object is {@link String } + * + */ + public String getFirst() + { + return first; + } + + /** + * Sets the value of the first property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setFirst(String value) + { + this.first = value; + } + + /** + * Gets the value of the last property. + * + * @return possible object is {@link String } + * + */ + public String getLast() + { + return last; + } + + /** + * Sets the value of the last property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setLast(String value) + { + this.last = value; + } + + /** + * Gets the value of the publisher property. + * + * @return possible object is {@link String } + * + */ + public String getPublisher() + { + return publisher; + } + + /** + * Sets the value of the publisher property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setPublisher(String value) + { + this.publisher = value; + } + + /** + * Gets the value of the city property. + * + * @return possible object is {@link String } + * + */ + public String getCity() + { + return city; + } + + /** + * Sets the value of the city property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setCity(String value) + { + this.city = value; + } + + /** + * Gets the value of the db property. + * + * @return possible object is {@link String } + * + */ + public String getDb() + { + return db; + } + + /** + * Sets the value of the db property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDb(String value) + { + this.db = value; + } + + /** + * Gets the value of the number property. + * + * @return possible object is {@link String } + * + */ + public String getNumber() + { + return number; + } + + /** + * Sets the value of the number property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setNumber(String value) + { + this.number = value; + } + + /** + * Gets the value of the institute property. + * + * @return possible object is {@link String } + * + */ + public String getInstitute() + { + return institute; + } + + /** + * Sets the value of the institute property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setInstitute(String value) + { + this.institute = value; + } + + /** + * Gets the value of the country property. + * + * @return possible object is {@link String } + * + */ + public String getCountry() + { + return country; + } + + /** + * Sets the value of the country property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setCountry(String value) + { + this.country = value; + } } diff --git a/src/jalview/xml/binding/uniprot/CofactorType.java b/src/jalview/xml/binding/uniprot/CofactorType.java index e9244e9..28e7220 100644 --- a/src/jalview/xml/binding/uniprot/CofactorType.java +++ b/src/jalview/xml/binding/uniprot/CofactorType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** * Describes a cofactor. * - *

Java class for cofactorType complex type. + *

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

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

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

  * <complexType name="cofactorType">
@@ -41,94 +42,94 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "cofactorType", propOrder = {
-    "name",
-    "dbReference"
-})
-public class CofactorType {
+@XmlType(name = "cofactorType", propOrder = { "name", "dbReference" })
+public class CofactorType
+{
 
-    @XmlElement(required = true)
-    protected String name;
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+  @XmlElement(required = true)
+  protected String name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  @XmlElement(required = true)
+  protected DbReferenceType dbReference;
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
+
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
+
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } } diff --git a/src/jalview/xml/binding/uniprot/CommentType.java b/src/jalview/xml/binding/uniprot/CommentType.java index e0692c9..f26c12b 100644 --- a/src/jalview/xml/binding/uniprot/CommentType.java +++ b/src/jalview/xml/binding/uniprot/CommentType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -17,14 +16,16 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlType; - /** - * Describes different types of general annotations. - * Equivalent to the flat file CC-line. + * Describes different types of general annotations. Equivalent to the flat file + * CC-line. * - *

Java class for commentType complex type. + *

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

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

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

  * <complexType name="commentType">
@@ -173,1619 +174,1673 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "commentType", propOrder = {
-    "molecule",
-    "absorption",
-    "kinetics",
-    "phDependence",
-    "redoxPotential",
-    "temperatureDependence",
-    "reaction",
-    "physiologicalReaction",
-    "cofactor",
-    "subcellularLocation",
-    "conflict",
-    "link",
-    "event",
-    "isoform",
-    "interactant",
-    "organismsDiffer",
-    "experiments",
-    "disease",
-    "location",
-    "text"
-})
-public class CommentType {
-
-    protected MoleculeType molecule;
-    protected CommentType.Absorption absorption;
-    protected CommentType.Kinetics kinetics;
-    protected CommentType.PhDependence phDependence;
-    protected CommentType.RedoxPotential redoxPotential;
-    protected CommentType.TemperatureDependence temperatureDependence;
-    protected ReactionType reaction;
-    protected List physiologicalReaction;
-    protected List cofactor;
-    protected List subcellularLocation;
-    protected CommentType.Conflict conflict;
-    protected List link;
-    protected List event;
-    protected List isoform;
-    protected List interactant;
-    @XmlElement(defaultValue = "false")
-    protected Boolean organismsDiffer;
-    protected Integer experiments;
-    protected CommentType.Disease disease;
-    protected List location;
-    protected List text;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "locationType")
-    protected String locationType;
-    @XmlAttribute(name = "name")
-    protected String name;
-    @XmlAttribute(name = "mass")
-    protected Float mass;
-    @XmlAttribute(name = "error")
-    protected String error;
-    @XmlAttribute(name = "method")
-    protected String method;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+@XmlType(
+  name = "commentType",
+  propOrder =
+  { "molecule", "absorption", "kinetics", "phDependence", "redoxPotential",
+      "temperatureDependence", "reaction", "physiologicalReaction",
+      "cofactor", "subcellularLocation", "conflict", "link", "event",
+      "isoform", "interactant", "organismsDiffer", "experiments", "disease",
+      "location", "text" })
+public class CommentType
+{
 
-    /**
-     * Gets the value of the molecule property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public MoleculeType getMolecule() {
-        return molecule;
-    }
+  protected MoleculeType molecule;
 
-    /**
-     * Sets the value of the molecule property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public void setMolecule(MoleculeType value) {
-        this.molecule = value;
-    }
+  protected CommentType.Absorption absorption;
 
-    /**
-     * Gets the value of the absorption property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.Absorption }
-     *     
-     */
-    public CommentType.Absorption getAbsorption() {
-        return absorption;
-    }
+  protected CommentType.Kinetics kinetics;
 
-    /**
-     * Sets the value of the absorption property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.Absorption }
-     *     
-     */
-    public void setAbsorption(CommentType.Absorption value) {
-        this.absorption = value;
-    }
+  protected CommentType.PhDependence phDependence;
 
-    /**
-     * Gets the value of the kinetics property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.Kinetics }
-     *     
-     */
-    public CommentType.Kinetics getKinetics() {
-        return kinetics;
-    }
+  protected CommentType.RedoxPotential redoxPotential;
 
-    /**
-     * Sets the value of the kinetics property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.Kinetics }
-     *     
-     */
-    public void setKinetics(CommentType.Kinetics value) {
-        this.kinetics = value;
-    }
+  protected CommentType.TemperatureDependence temperatureDependence;
 
-    /**
-     * Gets the value of the phDependence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.PhDependence }
-     *     
-     */
-    public CommentType.PhDependence getPhDependence() {
-        return phDependence;
-    }
+  protected ReactionType reaction;
 
-    /**
-     * Sets the value of the phDependence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.PhDependence }
-     *     
-     */
-    public void setPhDependence(CommentType.PhDependence value) {
-        this.phDependence = value;
-    }
+  protected List physiologicalReaction;
 
-    /**
-     * Gets the value of the redoxPotential property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.RedoxPotential }
-     *     
-     */
-    public CommentType.RedoxPotential getRedoxPotential() {
-        return redoxPotential;
-    }
+  protected List cofactor;
 
-    /**
-     * Sets the value of the redoxPotential property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.RedoxPotential }
-     *     
-     */
-    public void setRedoxPotential(CommentType.RedoxPotential value) {
-        this.redoxPotential = value;
-    }
+  protected List subcellularLocation;
 
-    /**
-     * Gets the value of the temperatureDependence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CommentType.TemperatureDependence }
-     *     
-     */
-    public CommentType.TemperatureDependence getTemperatureDependence() {
-        return temperatureDependence;
-    }
+  protected CommentType.Conflict conflict;
 
-    /**
-     * Sets the value of the temperatureDependence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CommentType.TemperatureDependence }
-     *     
-     */
-    public void setTemperatureDependence(CommentType.TemperatureDependence value) {
-        this.temperatureDependence = value;
+  protected List link;
+
+  protected List event;
+
+  protected List isoform;
+
+  protected List interactant;
+
+  @XmlElement(defaultValue = "false")
+  protected Boolean organismsDiffer;
+
+  protected Integer experiments;
+
+  protected CommentType.Disease disease;
+
+  protected List location;
+
+  protected List text;
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
+
+  @XmlAttribute(name = "locationType")
+  protected String locationType;
+
+  @XmlAttribute(name = "name")
+  protected String name;
+
+  @XmlAttribute(name = "mass")
+  protected Float mass;
+
+  @XmlAttribute(name = "error")
+  protected String error;
+
+  @XmlAttribute(name = "method")
+  protected String method;
+
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
+
+  /**
+   * Gets the value of the molecule property.
+   * 
+   * @return possible object is {@link MoleculeType }
+   * 
+   */
+  public MoleculeType getMolecule()
+  {
+    return molecule;
+  }
+
+  /**
+   * Sets the value of the molecule property.
+   * 
+   * @param value
+   *          allowed object is {@link MoleculeType }
+   * 
+   */
+  public void setMolecule(MoleculeType value)
+  {
+    this.molecule = value;
+  }
+
+  /**
+   * Gets the value of the absorption property.
+   * 
+   * @return possible object is {@link CommentType.Absorption }
+   * 
+   */
+  public CommentType.Absorption getAbsorption()
+  {
+    return absorption;
+  }
+
+  /**
+   * Sets the value of the absorption property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.Absorption }
+   * 
+   */
+  public void setAbsorption(CommentType.Absorption value)
+  {
+    this.absorption = value;
+  }
+
+  /**
+   * Gets the value of the kinetics property.
+   * 
+   * @return possible object is {@link CommentType.Kinetics }
+   * 
+   */
+  public CommentType.Kinetics getKinetics()
+  {
+    return kinetics;
+  }
+
+  /**
+   * Sets the value of the kinetics property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.Kinetics }
+   * 
+   */
+  public void setKinetics(CommentType.Kinetics value)
+  {
+    this.kinetics = value;
+  }
+
+  /**
+   * Gets the value of the phDependence property.
+   * 
+   * @return possible object is {@link CommentType.PhDependence }
+   * 
+   */
+  public CommentType.PhDependence getPhDependence()
+  {
+    return phDependence;
+  }
+
+  /**
+   * Sets the value of the phDependence property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.PhDependence }
+   * 
+   */
+  public void setPhDependence(CommentType.PhDependence value)
+  {
+    this.phDependence = value;
+  }
+
+  /**
+   * Gets the value of the redoxPotential property.
+   * 
+   * @return possible object is {@link CommentType.RedoxPotential }
+   * 
+   */
+  public CommentType.RedoxPotential getRedoxPotential()
+  {
+    return redoxPotential;
+  }
+
+  /**
+   * Sets the value of the redoxPotential property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.RedoxPotential }
+   * 
+   */
+  public void setRedoxPotential(CommentType.RedoxPotential value)
+  {
+    this.redoxPotential = value;
+  }
+
+  /**
+   * Gets the value of the temperatureDependence property.
+   * 
+   * @return possible object is {@link CommentType.TemperatureDependence }
+   * 
+   */
+  public CommentType.TemperatureDependence getTemperatureDependence()
+  {
+    return temperatureDependence;
+  }
+
+  /**
+   * Sets the value of the temperatureDependence property.
+   * 
+   * @param value
+   *          allowed object is {@link CommentType.TemperatureDependence }
+   * 
+   */
+  public void setTemperatureDependence(
+          CommentType.TemperatureDependence value)
+  {
+    this.temperatureDependence = value;
+  }
+
+  /**
+   * Gets the value of the reaction property.
+   * 
+   * @return possible object is {@link ReactionType }
+   * 
+   */
+  public ReactionType getReaction()
+  {
+    return reaction;
+  }
+
+  /**
+   * Sets the value of the reaction property.
+   * 
+   * @param value
+   *          allowed object is {@link ReactionType }
+   * 
+   */
+  public void setReaction(ReactionType value)
+  {
+    this.reaction = value;
+  }
+
+  /**
+   * Gets the value of the physiologicalReaction property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link SubcellularLocationType } + * + * + */ + public List getSubcellularLocation() + { + if (subcellularLocation == null) + { + subcellularLocation = new ArrayList(); + } + return this.subcellularLocation; + } + + /** + * Gets the value of the conflict property. + * + * @return possible object is {@link CommentType.Conflict } + * + */ + public CommentType.Conflict getConflict() + { + return conflict; + } + + /** + * Sets the value of the conflict property. + * + * @param value + * allowed object is {@link CommentType.Conflict } + * + */ + public void setConflict(CommentType.Conflict value) + { + this.conflict = value; + } + + /** + * Gets the value of the link property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link InteractantType } + * + * + */ + public List getInteractant() + { + if (interactant == null) + { + interactant = new ArrayList(); + } + return this.interactant; + } + + /** + * Gets the value of the organismsDiffer property. + * + * @return possible object is {@link Boolean } + * + */ + public Boolean isOrganismsDiffer() + { + return organismsDiffer; + } + + /** + * Sets the value of the organismsDiffer property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setOrganismsDiffer(Boolean value) + { + this.organismsDiffer = value; + } + + /** + * Gets the value of the experiments property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getExperiments() + { + return experiments; + } + + /** + * Sets the value of the experiments property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setExperiments(Integer value) + { + this.experiments = value; + } + + /** + * Gets the value of the disease property. + * + * @return possible object is {@link CommentType.Disease } + * + */ + public CommentType.Disease getDisease() + { + return disease; + } + + /** + * Sets the value of the disease property. + * + * @param value + * allowed object is {@link CommentType.Disease } + * + */ + public void setDisease(CommentType.Disease value) + { + this.disease = value; + } + + /** + * Gets the value of the location property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * + */ + public List getText() + { + if (text == null) + { + text = new ArrayList(); + } + return this.text; + } + + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } + + /** + * Gets the value of the locationType property. + * + * @return possible object is {@link String } + * + */ + public String getLocationType() + { + return locationType; + } + + /** + * Sets the value of the locationType property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setLocationType(String value) + { + this.locationType = value; + } + + /** + * Gets the value of the name property. + * + * @return possible object is {@link String } + * + */ + public String getName() + { + return name; + } + + /** + * Sets the value of the name property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setName(String value) + { + this.name = value; + } + + /** + * Gets the value of the mass property. + * + * @return possible object is {@link Float } + * + */ + public Float getMass() + { + return mass; + } + + /** + * Sets the value of the mass property. + * + * @param value + * allowed object is {@link Float } + * + */ + public void setMass(Float value) + { + this.mass = value; + } + + /** + * Gets the value of the error property. + * + * @return possible object is {@link String } + * + */ + public String getError() + { + return error; + } + + /** + * Sets the value of the error property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setError(String value) + { + this.error = value; + } + + /** + * Gets the value of the method property. + * + * @return possible object is {@link String } + * + */ + public String getMethod() + { + return method; + } + + /** + * Sets the value of the method property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setMethod(String value) + { + this.method = value; + } + + /** + * Gets the value of the evidence property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "max", "text" }) + public static class Absorption + { + + protected EvidencedStringType max; + + protected List text; /** - * Gets the value of the reaction property. + * Gets the value of the max property. + * + * @return possible object is {@link EvidencedStringType } * - * @return - * possible object is - * {@link ReactionType } - * */ - public ReactionType getReaction() { - return reaction; + public EvidencedStringType getMax() + { + return max; } /** - * Sets the value of the reaction property. + * Sets the value of the max property. * * @param value - * allowed object is - * {@link ReactionType } - * + * allowed object is {@link EvidencedStringType } + * */ - public void setReaction(ReactionType value) { - this.reaction = value; + public void setMax(EvidencedStringType value) + { + this.max = value; } /** - * Gets the value of the physiologicalReaction property. + * Gets the value of the text property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getPhysiologicalReaction().add(newItem);
+     * getText().add(newItem);
      * 
* * *

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="sequence" minOccurs="0">
+   *           <complexType>
+   *             <complexContent>
+   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *                 <attribute name="resource" use="required">
+   *                   <simpleType>
+   *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *                       <enumeration value="EMBL-CDS"/>
+   *                       <enumeration value="EMBL"/>
+   *                     </restriction>
+   *                   </simpleType>
+   *                 </attribute>
+   *                 <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+   *               </restriction>
+   *             </complexContent>
+   *           </complexType>
+   *         </element>
+   *       </sequence>
+   *       <attribute name="type" use="required">
+   *         <simpleType>
+   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             <enumeration value="frameshift"/>
+   *             <enumeration value="erroneous initiation"/>
+   *             <enumeration value="erroneous termination"/>
+   *             <enumeration value="erroneous gene model prediction"/>
+   *             <enumeration value="erroneous translation"/>
+   *             <enumeration value="miscellaneous discrepancy"/>
+   *           </restriction>
+   *         </simpleType>
+   *       </attribute>
+   *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "sequence" }) + public static class Conflict + { + + protected CommentType.Conflict.Sequence sequence; + + @XmlAttribute(name = "type", required = true) + protected String type; + + @XmlAttribute(name = "ref") + protected String ref; + /** - * Gets the value of the cofactor property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getCofactor().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getSubcellularLocation().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link SubcellularLocationType } + * Sets the value of the sequence property. * + * @param value + * allowed object is {@link CommentType.Conflict.Sequence } * */ - public List getSubcellularLocation() { - if (subcellularLocation == null) { - subcellularLocation = new ArrayList(); - } - return this.subcellularLocation; + public void setSequence(CommentType.Conflict.Sequence value) + { + this.sequence = value; } /** - * Gets the value of the conflict property. + * Gets the value of the type property. * - * @return - * possible object is - * {@link CommentType.Conflict } - * - */ - public CommentType.Conflict getConflict() { - return conflict; - } - - /** - * Sets the value of the conflict property. + * @return possible object is {@link String } * - * @param value - * allowed object is - * {@link CommentType.Conflict } - * */ - public void setConflict(CommentType.Conflict value) { - this.conflict = value; + public String getType() + { + return type; } /** - * Gets the value of the link property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getLink().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getEvent().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getIsoform().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: + * The following schema fragment specifies the expected content contained + * within this class. + * *

-     *    getInteractant().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="resource" use="required">
+     *         <simpleType>
+     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+     *             <enumeration value="EMBL-CDS"/>
+     *             <enumeration value="EMBL"/>
+     *           </restriction>
+     *         </simpleType>
+     *       </attribute>
+     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 
* * - *

- * Objects of the following type(s) are allowed in the list - * {@link InteractantType } - * - * */ - public List getInteractant() { - if (interactant == null) { - interactant = new ArrayList(); - } - return this.interactant; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Sequence + { + + @XmlAttribute(name = "resource", required = true) + protected String resource; + + @XmlAttribute(name = "id", required = true) + protected String id; + + @XmlAttribute(name = "version") + protected Integer version; + + /** + * Gets the value of the resource property. + * + * @return possible object is {@link String } + * + */ + public String getResource() + { + return resource; + } + + /** + * Sets the value of the resource property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setResource(String value) + { + this.resource = value; + } + + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } + + /** + * Gets the value of the version property. + * + * @return possible object is {@link Integer } + * + */ + public Integer getVersion() + { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is {@link Integer } + * + */ + public void setVersion(Integer value) + { + this.version = value; + } - /** - * Gets the value of the organismsDiffer property. - * - * @return - * possible object is - * {@link Boolean } - * - */ - public Boolean isOrganismsDiffer() { - return organismsDiffer; } - /** - * Sets the value of the organismsDiffer property. - * - * @param value - * allowed object is - * {@link Boolean } - * - */ - public void setOrganismsDiffer(Boolean value) { - this.organismsDiffer = value; - } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
+   *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
+   *       </sequence>
+   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "name", "acronym", "description", "dbReference" }) + public static class Disease + { + + @XmlElement(required = true) + protected String name; - /** - * Gets the value of the experiments property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getExperiments() { - return experiments; - } + @XmlElement(required = true) + protected String acronym; - /** - * Sets the value of the experiments property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setExperiments(Integer value) { - this.experiments = value; - } + @XmlElement(required = true) + protected String description; - /** - * Gets the value of the disease property. - * - * @return - * possible object is - * {@link CommentType.Disease } - * - */ - public CommentType.Disease getDisease() { - return disease; - } + @XmlElement(required = true) + protected DbReferenceType dbReference; - /** - * Sets the value of the disease property. - * - * @param value - * allowed object is - * {@link CommentType.Disease } - * - */ - public void setDisease(CommentType.Disease value) { - this.disease = value; - } + @XmlAttribute(name = "id", required = true) + protected String id; /** - * Gets the value of the location property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getLocation().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link LocationType } + * Gets the value of the name property. * + * @return possible object is {@link String } * */ - public List getLocation() { - if (location == null) { - location = new ArrayList(); - } - return this.location; + public String getName() + { + return name; } /** - * Gets the value of the text property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getText().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } + * Sets the value of the name property. * + * @param value + * allowed object is {@link String } * */ - public List getText() { - if (text == null) { - text = new ArrayList(); - } - return this.text; + public void setName(String value) + { + this.name = value; } /** - * Gets the value of the type property. + * Gets the value of the acronym property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getType() { - return type; + public String getAcronym() + { + return acronym; } /** - * Sets the value of the type property. + * Sets the value of the acronym property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the locationType property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getLocationType() { - return locationType; + public void setAcronym(String value) + { + this.acronym = value; } /** - * Sets the value of the locationType property. + * Gets the value of the description property. * - * @param value - * allowed object is - * {@link String } - * - */ - public void setLocationType(String value) { - this.locationType = value; - } - - /** - * Gets the value of the name property. + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getName() { - return name; + public String getDescription() + { + return description; } /** - * Sets the value of the name property. + * Sets the value of the description property. * * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the mass property. + * allowed object is {@link String } * - * @return - * possible object is - * {@link Float } - * */ - public Float getMass() { - return mass; + public void setDescription(String value) + { + this.description = value; } /** - * Sets the value of the mass property. + * Gets the value of the dbReference property. * - * @param value - * allowed object is - * {@link Float } - * - */ - public void setMass(Float value) { - this.mass = value; - } - - /** - * Gets the value of the error property. + * @return possible object is {@link DbReferenceType } * - * @return - * possible object is - * {@link String } - * */ - public String getError() { - return error; + public DbReferenceType getDbReference() + { + return dbReference; } /** - * Sets the value of the error property. + * Sets the value of the dbReference property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link DbReferenceType } + * */ - public void setError(String value) { - this.error = value; + public void setDbReference(DbReferenceType value) + { + this.dbReference = value; } /** - * Gets the value of the method property. + * Gets the value of the id property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getMethod() { - return method; + public String getId() + { + return id; } /** - * Sets the value of the method property. + * Sets the value of the id property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link String } + * */ - public void setMethod(String value) { - this.method = value; + public void setId(String value) + { + this.id = value; } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "km", "vmax", "text" }) + public static class Kinetics + { + + @XmlElement(name = "KM") + protected List km; + + @XmlElement(name = "Vmax") + protected List vmax; + + protected List text; + /** - * Gets the value of the evidence property. + * Gets the value of the km property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getEvidence().add(newItem);
+     * getKM().add(newItem);
      * 
* * *

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

Java class for anonymous complex type. + * Gets the value of the vmax property. * - *

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

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

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getVmax().add(newItem);
      * 
* * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "max", - "text" - }) - public static class Absorption { - - protected EvidencedStringType max; - protected List text; - - /** - * Gets the value of the max property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getMax() { - return max; - } - - /** - * Sets the value of the max property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setMax(EvidencedStringType value) { - this.max = value; - } - - /** - * Gets the value of the text property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getText().add(newItem);
-         * 
- * - * - *

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

Java class for anonymous complex type. - * - *

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

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

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } * * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "sequence" - }) - public static class Conflict { - - protected CommentType.Conflict.Sequence sequence; - @XmlAttribute(name = "type", required = true) - protected String type; - @XmlAttribute(name = "ref") - protected String ref; - - /** - * Gets the value of the sequence property. - * - * @return - * possible object is - * {@link CommentType.Conflict.Sequence } - * - */ - public CommentType.Conflict.Sequence getSequence() { - return sequence; - } - - /** - * Sets the value of the sequence property. - * - * @param value - * allowed object is - * {@link CommentType.Conflict.Sequence } - * - */ - public void setSequence(CommentType.Conflict.Sequence value) { - this.sequence = value; - } - - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } - - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the ref property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getRef() { - return ref; - } - - /** - * Sets the value of the ref property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setRef(String value) { - this.ref = value; - } - - - /** - *

Java class for anonymous complex type. - * - *

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

-         * <complexType>
-         *   <complexContent>
-         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       <attribute name="resource" use="required">
-         *         <simpleType>
-         *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-         *             <enumeration value="EMBL-CDS"/>
-         *             <enumeration value="EMBL"/>
-         *           </restriction>
-         *         </simpleType>
-         *       </attribute>
-         *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     </restriction>
-         *   </complexContent>
-         * </complexType>
-         * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Sequence { - - @XmlAttribute(name = "resource", required = true) - protected String resource; - @XmlAttribute(name = "id", required = true) - protected String id; - @XmlAttribute(name = "version") - protected Integer version; - - /** - * Gets the value of the resource property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getResource() { - return resource; - } - - /** - * Sets the value of the resource property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setResource(String value) { - this.resource = value; - } - - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } - - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } - - /** - * Gets the value of the version property. - * - * @return - * possible object is - * {@link Integer } - * - */ - public Integer getVersion() { - return version; - } - - /** - * Sets the value of the version property. - * - * @param value - * allowed object is - * {@link Integer } - * - */ - public void setVersion(Integer value) { - this.version = value; - } - - } - + public List getVmax() + { + if (vmax == null) + { + vmax = new ArrayList(); + } + return this.vmax; } - /** - *

Java class for anonymous complex type. + * Gets the value of the text property. + * + *

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

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

+ * For example, to add a new item, do as follows: * *

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

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "name", - "acronym", - "description", - "dbReference" - }) - public static class Disease { - - @XmlElement(required = true) - protected String name; - @XmlElement(required = true) - protected String acronym; - @XmlElement(required = true) - protected String description; - @XmlElement(required = true) - protected DbReferenceType dbReference; - @XmlAttribute(name = "id", required = true) - protected String id; - - /** - * Gets the value of the name property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getName() { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setName(String value) { - this.name = value; - } - - /** - * Gets the value of the acronym property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getAcronym() { - return acronym; - } - - /** - * Sets the value of the acronym property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setAcronym(String value) { - this.acronym = value; - } - - /** - * Gets the value of the description property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDescription() { - return description; - } - - /** - * Sets the value of the description property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDescription(String value) { - this.description = value; - } - - /** - * Gets the value of the dbReference property. - * - * @return - * possible object is - * {@link DbReferenceType } - * - */ - public DbReferenceType getDbReference() { - return dbReference; - } - - /** - * Sets the value of the dbReference property. - * - * @param value - * allowed object is - * {@link DbReferenceType } - * - */ - public void setDbReference(DbReferenceType value) { - this.dbReference = value; - } - - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } - - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; - } - + public List getText() + { + if (text == null) + { + text = new ArrayList(); + } + return this.text; } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Link + { + + @XmlAttribute(name = "uri", required = true) + @XmlSchemaType(name = "anyURI") + protected String uri; /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ * Gets the value of the uri property. * + * @return possible object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "km", - "vmax", - "text" - }) - public static class Kinetics { - - @XmlElement(name = "KM") - protected List km; - @XmlElement(name = "Vmax") - protected List vmax; - protected List text; - - /** - * Gets the value of the km property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getKM().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getVmax().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getText().add(newItem);
-         * 
- * - * - *

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

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ * Sets the value of the uri property. * + * @param value + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Link { - - @XmlAttribute(name = "uri", required = true) - @XmlSchemaType(name = "anyURI") - protected String uri; - - /** - * Gets the value of the uri property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getUri() { - return uri; - } - - /** - * Sets the value of the uri property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setUri(String value) { - this.uri = value; - } - + public void setUri(String value) + { + this.uri = value; } + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "text" }) + public static class PhDependence + { + + @XmlElement(required = true) + protected List text; /** - *

Java class for anonymous complex type. + * Gets the value of the text property. + * + *

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

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

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getText().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "text" - }) - public static class PhDependence { - - @XmlElement(required = true) - protected List text; - - /** - * Gets the value of the text property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getText().add(newItem);
-         * 
- * - * - *

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "text" }) + public static class RedoxPotential + { + + @XmlElement(required = true) + protected List text; /** - *

Java class for anonymous complex type. + * Gets the value of the text property. * - *

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

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

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getText().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "text" - }) - public static class RedoxPotential { - - @XmlElement(required = true) - protected List text; - - /** - * Gets the value of the text property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getText().add(newItem);
-         * 
- * - * - *

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "text" }) + public static class TemperatureDependence + { + + @XmlElement(required = true) + protected List text; /** - *

Java class for anonymous complex type. + * Gets the value of the text property. * - *

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

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

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getText().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "text" - }) - public static class TemperatureDependence { - - @XmlElement(required = true) - protected List text; - - /** - * Gets the value of the text property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getText().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getText() { - if (text == null) { - text = new ArrayList(); - } - return this.text; - } - + public List getText() + { + if (text == null) + { + text = new ArrayList(); + } + return this.text; } + } + } diff --git a/src/jalview/xml/binding/uniprot/ConsortiumType.java b/src/jalview/xml/binding/uniprot/ConsortiumType.java index 71db504..5230b13 100644 --- a/src/jalview/xml/binding/uniprot/ConsortiumType.java +++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -13,14 +12,16 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - * Describes the authors of a citation when these are represented by a consortium. - * Equivalent to the flat file RG-line. + * Describes the authors of a citation when these are represented by a + * consortium. Equivalent to the flat file RG-line. * - *

Java class for consortiumType complex type. + *

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

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

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

  * <complexType name="consortiumType">
@@ -36,33 +37,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "consortiumType")
-public class ConsortiumType {
+public class ConsortiumType
+{
 
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
+  @XmlAttribute(name = "name", required = true)
+  protected String name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/DbReferenceType.java b/src/jalview/xml/binding/uniprot/DbReferenceType.java
index 73ccfa8..076a37c 100644
--- a/src/jalview/xml/binding/uniprot/DbReferenceType.java
+++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,15 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes a database cross-reference.
- *             Equivalent to the flat file DR-line.
- *             
+ * Describes a database cross-reference. Equivalent to the flat file DR-line.
  * 
- * 

Java class for dbReferenceType complex type. * - *

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

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

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

  * <complexType name="dbReferenceType">
@@ -44,149 +44,153 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "dbReferenceType", propOrder = {
-    "molecule",
-    "property"
-})
-public class DbReferenceType {
-
-    protected MoleculeType molecule;
-    protected List property;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-
-    /**
-     * Gets the value of the molecule property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public MoleculeType getMolecule() {
-        return molecule;
-    }
+@XmlType(name = "dbReferenceType", propOrder = { "molecule", "property" })
+public class DbReferenceType
+{
 
-    /**
-     * Sets the value of the molecule property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link MoleculeType }
-     *     
-     */
-    public void setMolecule(MoleculeType value) {
-        this.molecule = value;
-    }
+  protected MoleculeType molecule;
 
-    /**
-     * Gets the value of the property property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getProperty().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link PropertyType } - * - * - */ - public List getProperty() { - if (property == null) { - property = new ArrayList(); - } - return this.property; - } + protected List property; - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } + @XmlAttribute(name = "type", required = true) + protected String type; - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } + @XmlAttribute(name = "id", required = true) + protected String id; - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + @XmlAttribute(name = "evidence") + protected List evidence; + + /** + * Gets the value of the molecule property. + * + * @return possible object is {@link MoleculeType } + * + */ + public MoleculeType getMolecule() + { + return molecule; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; + /** + * Sets the value of the molecule property. + * + * @param value + * allowed object is {@link MoleculeType } + * + */ + public void setMolecule(MoleculeType value) + { + this.molecule = value; + } + + /** + * Gets the value of the property property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } } diff --git a/src/jalview/xml/binding/uniprot/Entry.java b/src/jalview/xml/binding/uniprot/Entry.java index 21963a8..3cc0c73 100644 --- a/src/jalview/xml/binding/uniprot/Entry.java +++ b/src/jalview/xml/binding/uniprot/Entry.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -19,11 +18,13 @@ import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlType; import javax.xml.datatype.XMLGregorianCalendar; - /** - *

Java class for anonymous complex type. + *

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

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

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

  * <complexType>
@@ -65,561 +66,594 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "accession",
-    "name",
-    "protein",
-    "gene",
-    "organism",
-    "organismHost",
-    "geneLocation",
-    "reference",
-    "comment",
-    "dbReference",
-    "proteinExistence",
-    "keyword",
-    "feature",
-    "evidence",
-    "sequence"
-})
+@XmlType(
+  name = "",
+  propOrder =
+  { "accession", "name", "protein", "gene", "organism", "organismHost",
+      "geneLocation", "reference", "comment", "dbReference",
+      "proteinExistence", "keyword", "feature", "evidence", "sequence" })
 @XmlRootElement(name = "entry")
-public class Entry {
-
-    @XmlElement(required = true)
-    protected List accession;
-    @XmlElement(required = true)
-    protected List name;
-    @XmlElement(required = true)
-    protected ProteinType protein;
-    protected List gene;
-    @XmlElement(required = true)
-    protected OrganismType organism;
-    protected List organismHost;
-    protected List geneLocation;
-    @XmlElement(required = true)
-    protected List reference;
-    @XmlElement(nillable = true)
-    protected List comment;
-    protected List dbReference;
-    @XmlElement(required = true)
-    protected ProteinExistenceType proteinExistence;
-    protected List keyword;
-    protected List feature;
-    protected List evidence;
-    @XmlElement(required = true)
-    protected SequenceType sequence;
-    @XmlAttribute(name = "dataset", required = true)
-    protected String dataset;
-    @XmlAttribute(name = "created", required = true)
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar created;
-    @XmlAttribute(name = "modified", required = true)
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar modified;
-    @XmlAttribute(name = "version", required = true)
-    protected int version;
-
-    /**
-     * Gets the value of the accession property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getAccession().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getName().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getGene().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link GeneType } - * - * - */ - public List getGene() { - if (gene == null) { - gene = new ArrayList(); - } - return this.gene; - } + protected List gene; - /** - * Gets the value of the organism property. - * - * @return - * possible object is - * {@link OrganismType } - * - */ - public OrganismType getOrganism() { - return organism; - } + @XmlElement(required = true) + protected OrganismType organism; - /** - * Sets the value of the organism property. - * - * @param value - * allowed object is - * {@link OrganismType } - * - */ - public void setOrganism(OrganismType value) { - this.organism = value; - } + protected List organismHost; - /** - * Gets the value of the organismHost property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getOrganismHost().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getGeneLocation().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getReference().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getComment().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getDbReference().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link DbReferenceType } - * - * - */ - public List getDbReference() { - if (dbReference == null) { - dbReference = new ArrayList(); - } - return this.dbReference; - } + @XmlElement(required = true) + protected ProteinExistenceType proteinExistence; - /** - * Gets the value of the proteinExistence property. - * - * @return - * possible object is - * {@link ProteinExistenceType } - * - */ - public ProteinExistenceType getProteinExistence() { - return proteinExistence; - } + protected List keyword; - /** - * Sets the value of the proteinExistence property. - * - * @param value - * allowed object is - * {@link ProteinExistenceType } - * - */ - public void setProteinExistence(ProteinExistenceType value) { - this.proteinExistence = value; - } + protected List feature; - /** - * Gets the value of the keyword property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getKeyword().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getFeature().add(newItem);
-     * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidenceType } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + @XmlAttribute(name = "dataset", required = true) + protected String dataset; - /** - * Gets the value of the sequence property. - * - * @return - * possible object is - * {@link SequenceType } - * - */ - public SequenceType getSequence() { - return sequence; - } + @XmlAttribute(name = "created", required = true) + @XmlSchemaType(name = "date") + protected XMLGregorianCalendar created; - /** - * Sets the value of the sequence property. - * - * @param value - * allowed object is - * {@link SequenceType } - * - */ - public void setSequence(SequenceType value) { - this.sequence = value; - } + @XmlAttribute(name = "modified", required = true) + @XmlSchemaType(name = "date") + protected XMLGregorianCalendar modified; - /** - * Gets the value of the dataset property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDataset() { - return dataset; - } + @XmlAttribute(name = "version", required = true) + protected int version; - /** - * Sets the value of the dataset property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDataset(String value) { - this.dataset = value; + /** + * Gets the value of the accession property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getName() + { + if (name == null) + { + name = new ArrayList(); } - - /** - * Sets the value of the created property. - * - * @param value - * allowed object is - * {@link XMLGregorianCalendar } - * - */ - public void setCreated(XMLGregorianCalendar value) { - this.created = value; + return this.name; + } + + /** + * Gets the value of the protein property. + * + * @return possible object is {@link ProteinType } + * + */ + public ProteinType getProtein() + { + return protein; + } + + /** + * Sets the value of the protein property. + * + * @param value + * allowed object is {@link ProteinType } + * + */ + public void setProtein(ProteinType value) + { + this.protein = value; + } + + /** + * Gets the value of the gene property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link GeneType } + * + * + */ + public List getGene() + { + if (gene == null) + { + gene = new ArrayList(); } - - /** - * Gets the value of the modified property. - * - * @return - * possible object is - * {@link XMLGregorianCalendar } - * - */ - public XMLGregorianCalendar getModified() { - return modified; + return this.gene; + } + + /** + * Gets the value of the organism property. + * + * @return possible object is {@link OrganismType } + * + */ + public OrganismType getOrganism() + { + return organism; + } + + /** + * Sets the value of the organism property. + * + * @param value + * allowed object is {@link OrganismType } + * + */ + public void setOrganism(OrganismType value) + { + this.organism = value; + } + + /** + * Gets the value of the organismHost property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link DbReferenceType } + * + * + */ + public List getDbReference() + { + if (dbReference == null) + { + dbReference = new ArrayList(); + } + return this.dbReference; + } + + /** + * Gets the value of the proteinExistence property. + * + * @return possible object is {@link ProteinExistenceType } + * + */ + public ProteinExistenceType getProteinExistence() + { + return proteinExistence; + } + + /** + * Sets the value of the proteinExistence property. + * + * @param value + * allowed object is {@link ProteinExistenceType } + * + */ + public void setProteinExistence(ProteinExistenceType value) + { + this.proteinExistence = value; + } + + /** + * Gets the value of the keyword property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link EvidenceType } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } + + /** + * Gets the value of the sequence property. + * + * @return possible object is {@link SequenceType } + * + */ + public SequenceType getSequence() + { + return sequence; + } + + /** + * Sets the value of the sequence property. + * + * @param value + * allowed object is {@link SequenceType } + * + */ + public void setSequence(SequenceType value) + { + this.sequence = value; + } + + /** + * Gets the value of the dataset property. + * + * @return possible object is {@link String } + * + */ + public String getDataset() + { + return dataset; + } + + /** + * Sets the value of the dataset property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDataset(String value) + { + this.dataset = value; + } + + /** + * Gets the value of the created property. + * + * @return possible object is {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getCreated() + { + return created; + } + + /** + * Sets the value of the created property. + * + * @param value + * allowed object is {@link XMLGregorianCalendar } + * + */ + public void setCreated(XMLGregorianCalendar value) + { + this.created = value; + } + + /** + * Gets the value of the modified property. + * + * @return possible object is {@link XMLGregorianCalendar } + * + */ + public XMLGregorianCalendar getModified() + { + return modified; + } + + /** + * Sets the value of the modified property. + * + * @param value + * allowed object is {@link XMLGregorianCalendar } + * + */ + public void setModified(XMLGregorianCalendar value) + { + this.modified = value; + } + + /** + * Gets the value of the version property. + * + */ + public int getVersion() + { + return version; + } + + /** + * Sets the value of the version property. + * + */ + public void setVersion(int value) + { + this.version = value; + } } diff --git a/src/jalview/xml/binding/uniprot/EventType.java b/src/jalview/xml/binding/uniprot/EventType.java index 0b4d4bd..49ab079 100644 --- a/src/jalview/xml/binding/uniprot/EventType.java +++ b/src/jalview/xml/binding/uniprot/EventType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -13,13 +12,15 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** * Describes the type of events that cause alternative products. * - *

Java class for eventType complex type. + *

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

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

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

  * <complexType name="eventType">
@@ -44,33 +45,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "eventType")
-public class EventType {
+public class EventType
+{
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidenceType.java b/src/jalview/xml/binding/uniprot/EvidenceType.java
index 59c9857..1e6f734 100644
--- a/src/jalview/xml/binding/uniprot/EvidenceType.java
+++ b/src/jalview/xml/binding/uniprot/EvidenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.math.BigInteger;
@@ -14,14 +13,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the evidence for an annotation.
- *             No flat file equivalent.
+ * Describes the evidence for an annotation. No flat file equivalent.
  * 
- * 

Java class for evidenceType complex type. + *

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

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

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

  * <complexType name="evidenceType">
@@ -41,113 +41,110 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidenceType", propOrder = {
-    "source",
-    "importedFrom"
-})
-public class EvidenceType {
-
-    protected SourceType source;
-    protected ImportedFromType importedFrom;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "key", required = true)
-    protected BigInteger key;
-
-    /**
-     * Gets the value of the source property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link SourceType }
-     *     
-     */
-    public SourceType getSource() {
-        return source;
-    }
-
-    /**
-     * Sets the value of the source property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link SourceType }
-     *     
-     */
-    public void setSource(SourceType value) {
-        this.source = value;
-    }
-
-    /**
-     * Gets the value of the importedFrom property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link ImportedFromType }
-     *     
-     */
-    public ImportedFromType getImportedFrom() {
-        return importedFrom;
-    }
-
-    /**
-     * Sets the value of the importedFrom property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link ImportedFromType }
-     *     
-     */
-    public void setImportedFrom(ImportedFromType value) {
-        this.importedFrom = value;
-    }
-
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
-
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
-
-    /**
-     * Gets the value of the key property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getKey() {
-        return key;
-    }
-
-    /**
-     * Sets the value of the key property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setKey(BigInteger value) {
-        this.key = value;
-    }
+@XmlType(name = "evidenceType", propOrder = { "source", "importedFrom" })
+public class EvidenceType
+{
+
+  protected SourceType source;
+
+  protected ImportedFromType importedFrom;
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
+
+  @XmlAttribute(name = "key", required = true)
+  protected BigInteger key;
+
+  /**
+   * Gets the value of the source property.
+   * 
+   * @return possible object is {@link SourceType }
+   * 
+   */
+  public SourceType getSource()
+  {
+    return source;
+  }
+
+  /**
+   * Sets the value of the source property.
+   * 
+   * @param value
+   *          allowed object is {@link SourceType }
+   * 
+   */
+  public void setSource(SourceType value)
+  {
+    this.source = value;
+  }
+
+  /**
+   * Gets the value of the importedFrom property.
+   * 
+   * @return possible object is {@link ImportedFromType }
+   * 
+   */
+  public ImportedFromType getImportedFrom()
+  {
+    return importedFrom;
+  }
+
+  /**
+   * Sets the value of the importedFrom property.
+   * 
+   * @param value
+   *          allowed object is {@link ImportedFromType }
+   * 
+   */
+  public void setImportedFrom(ImportedFromType value)
+  {
+    this.importedFrom = value;
+  }
+
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
+
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
+
+  /**
+   * Gets the value of the key property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getKey()
+  {
+    return key;
+  }
+
+  /**
+   * Sets the value of the key property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setKey(BigInteger value)
+  {
+    this.key = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/EvidencedStringType.java b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
index 0fa25a6..0de4239 100644
--- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java
+++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
- * 

Java class for evidencedStringType complex type. + *

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

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

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

  * <complexType name="evidencedStringType">
@@ -44,93 +45,94 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "evidencedStringType", propOrder = {
-    "value"
-})
-public class EvidencedStringType {
+@XmlType(name = "evidencedStringType", propOrder = { "value" })
+public class EvidencedStringType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-    @XmlAttribute(name = "status")
-    protected String status;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  @XmlAttribute(name = "status")
+  protected String status;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + /** + * Gets the value of the value property. + * + * @return possible object is {@link String } + * + */ + public String getValue() + { + return value; + } - /** - * Gets the value of the status property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getStatus() { - return status; - } + /** + * Sets the value of the value property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setValue(String value) + { + this.value = value; + } - /** - * Sets the value of the status property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setStatus(String value) { - this.status = value; + /** + * Gets the value of the evidence property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } + + /** + * Gets the value of the status property. + * + * @return possible object is {@link String } + * + */ + public String getStatus() + { + return status; + } + + /** + * Sets the value of the status property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setStatus(String value) + { + this.status = value; + } } diff --git a/src/jalview/xml/binding/uniprot/FeatureType.java b/src/jalview/xml/binding/uniprot/FeatureType.java index f818e2e..e4bdc31 100644 --- a/src/jalview/xml/binding/uniprot/FeatureType.java +++ b/src/jalview/xml/binding/uniprot/FeatureType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,14 +15,16 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - * Describes different types of sequence annotations. - * Equivalent to the flat file FT-line. + * Describes different types of sequence annotations. Equivalent to the flat + * file FT-line. * - *

Java class for featureType complex type. + *

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

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

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

  * <complexType name="featureType">
@@ -100,254 +101,259 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "featureType", propOrder = {
-    "original",
-    "variation",
-    "location"
-})
-public class FeatureType {
+@XmlType(
+  name = "featureType",
+  propOrder =
+  { "original", "variation", "location" })
+public class FeatureType
+{
 
-    protected String original;
-    protected List variation;
-    @XmlElement(required = true)
-    protected LocationType location;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "status")
-    protected String status;
-    @XmlAttribute(name = "id")
-    protected String id;
-    @XmlAttribute(name = "description")
-    protected String description;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-    @XmlAttribute(name = "ref")
-    protected String ref;
+  protected String original;
 
-    /**
-     * Gets the value of the original property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getOriginal() {
-        return original;
-    }
+  protected List variation;
 
-    /**
-     * Sets the value of the original property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setOriginal(String value) {
-        this.original = value;
-    }
+  @XmlElement(required = true)
+  protected LocationType location;
 
-    /**
-     * Gets the value of the variation property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getVariation().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getVariation() { - if (variation == null) { - variation = new ArrayList(); - } - return this.variation; - } + @XmlAttribute(name = "type", required = true) + protected String type; - /** - * Gets the value of the location property. - * - * @return - * possible object is - * {@link LocationType } - * - */ - public LocationType getLocation() { - return location; - } + @XmlAttribute(name = "status") + protected String status; - /** - * Sets the value of the location property. - * - * @param value - * allowed object is - * {@link LocationType } - * - */ - public void setLocation(LocationType value) { - this.location = value; - } + @XmlAttribute(name = "id") + protected String id; - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } + @XmlAttribute(name = "description") + protected String description; - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } + @XmlAttribute(name = "evidence") + protected List evidence; - /** - * Gets the value of the status property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getStatus() { - return status; - } + @XmlAttribute(name = "ref") + protected String ref; - /** - * Sets the value of the status property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setStatus(String value) { - this.status = value; - } + /** + * Gets the value of the original property. + * + * @return possible object is {@link String } + * + */ + public String getOriginal() + { + return original; + } - /** - * Gets the value of the id property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getId() { - return id; - } + /** + * Sets the value of the original property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setOriginal(String value) + { + this.original = value; + } - /** - * Sets the value of the id property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setId(String value) { - this.id = value; + /** + * Gets the value of the variation property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getVariation() + { + if (variation == null) + { + variation = new ArrayList(); } + return this.variation; + } - /** - * Gets the value of the description property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDescription() { - return description; - } + /** + * Gets the value of the location property. + * + * @return possible object is {@link LocationType } + * + */ + public LocationType getLocation() + { + return location; + } - /** - * Sets the value of the description property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDescription(String value) { - this.description = value; - } + /** + * Sets the value of the location property. + * + * @param value + * allowed object is {@link LocationType } + * + */ + public void setLocation(LocationType value) + { + this.location = value; + } - /** - * Gets the value of the evidence property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } - /** - * Gets the value of the ref property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getRef() { - return ref; - } + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } + + /** + * Gets the value of the status property. + * + * @return possible object is {@link String } + * + */ + public String getStatus() + { + return status; + } + + /** + * Sets the value of the status property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setStatus(String value) + { + this.status = value; + } - /** - * Sets the value of the ref property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setRef(String value) { - this.ref = value; + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } + + /** + * Gets the value of the description property. + * + * @return possible object is {@link String } + * + */ + public String getDescription() + { + return description; + } + + /** + * Sets the value of the description property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDescription(String value) + { + this.description = value; + } + + /** + * Gets the value of the evidence property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } + + /** + * Gets the value of the ref property. + * + * @return possible object is {@link String } + * + */ + public String getRef() + { + return ref; + } + + /** + * Sets the value of the ref property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setRef(String value) + { + this.ref = value; + } } diff --git a/src/jalview/xml/binding/uniprot/GeneLocationType.java b/src/jalview/xml/binding/uniprot/GeneLocationType.java index f2d5638..7ab7959 100644 --- a/src/jalview/xml/binding/uniprot/GeneLocationType.java +++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -15,14 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - * Describes non-nuclear gene locations (organelles and plasmids). - * Equivalent to the flat file OG-line. + * Describes non-nuclear gene locations (organelles and plasmids). Equivalent to + * the flat file OG-line. * - *

Java class for geneLocationType complex type. + *

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

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

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

  * <complexType name="geneLocationType">
@@ -56,97 +57,102 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneLocationType", propOrder = {
-    "name"
-})
-public class GeneLocationType {
+@XmlType(name = "geneLocationType", propOrder = { "name" })
+public class GeneLocationType
+{
 
-    protected List name;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+  protected List name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getName().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link StatusType } - * - * - */ - public List getName() { - if (name == null) { - name = new ArrayList(); - } - return this.name; - } + @XmlAttribute(name = "type", required = true) + protected String type; - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } + @XmlAttribute(name = "evidence") + protected List evidence; - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; + /** + * Gets the value of the name property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link StatusType + * } + * + * + */ + public List getName() + { + if (name == null) + { + name = new ArrayList(); } + return this.name; + } + + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } - /** - * Gets the value of the evidence property. - * - *

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } } diff --git a/src/jalview/xml/binding/uniprot/GeneNameType.java b/src/jalview/xml/binding/uniprot/GeneNameType.java index 71af71f..bd21a83 100644 --- a/src/jalview/xml/binding/uniprot/GeneNameType.java +++ b/src/jalview/xml/binding/uniprot/GeneNameType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,14 +15,16 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; import javax.xml.bind.annotation.XmlValue; - /** - * Describes different types of gene designations. - * Equivalent to the flat file GN-line. + * Describes different types of gene designations. Equivalent to the flat file + * GN-line. * - *

Java class for geneNameType complex type. + *

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

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

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

  * <complexType name="geneNameType">
@@ -48,93 +49,94 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneNameType", propOrder = {
-    "value"
-})
-public class GeneNameType {
+@XmlType(name = "geneNameType", propOrder = { "value" })
+public class GeneNameType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + /** + * Gets the value of the value property. + * + * @return possible object is {@link String } + * + */ + public String getValue() + { + return value; + } - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } + /** + * Sets the value of the value property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setValue(String value) + { + this.value = value; + } - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; + /** + * Gets the value of the evidence property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } + + /** + * Gets the value of the type property. + * + * @return possible object is {@link String } + * + */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setType(String value) + { + this.type = value; + } } diff --git a/src/jalview/xml/binding/uniprot/GeneType.java b/src/jalview/xml/binding/uniprot/GeneType.java index 5fa628e..cbd47bf 100644 --- a/src/jalview/xml/binding/uniprot/GeneType.java +++ b/src/jalview/xml/binding/uniprot/GeneType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -15,14 +14,15 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - * Describes a gene. - * Equivalent to the flat file GN-line. + * Describes a gene. Equivalent to the flat file GN-line. * - *

Java class for geneType complex type. + *

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

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

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

  * <complexType name="geneType">
@@ -39,41 +39,43 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "geneType", propOrder = {
-    "name"
-})
-public class GeneType {
+@XmlType(name = "geneType", propOrder = { "name" })
+public class GeneType
+{
 
-    @XmlElement(required = true)
-    protected List name;
+  @XmlElement(required = true)
+  protected List name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getName().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link GeneNameType } + * + * + */ + public List getName() + { + if (name == null) + { + name = new ArrayList(); } + return this.name; + } } diff --git a/src/jalview/xml/binding/uniprot/ImportedFromType.java b/src/jalview/xml/binding/uniprot/ImportedFromType.java index 3d6c308..e003273 100644 --- a/src/jalview/xml/binding/uniprot/ImportedFromType.java +++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -13,13 +12,16 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database. + * Describes the source of the evidence, when it is not assigned by UniProt, but + * imported from an external database. * - *

Java class for importedFromType complex type. + *

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

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

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

  * <complexType name="importedFromType">
@@ -36,36 +38,34 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "importedFromType", propOrder = {
-    "dbReference"
-})
-public class ImportedFromType {
+@XmlType(name = "importedFromType", propOrder = { "dbReference" })
+public class ImportedFromType
+{
 
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
+  @XmlElement(required = true)
+  protected DbReferenceType dbReference;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/InteractantType.java b/src/jalview/xml/binding/uniprot/InteractantType.java
index c9cadc2..0ab941a 100644
--- a/src/jalview/xml/binding/uniprot/InteractantType.java
+++ b/src/jalview/xml/binding/uniprot/InteractantType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for interactantType complex type. + *

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

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

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

  * <complexType name="interactantType">
@@ -33,87 +34,84 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "interactantType", propOrder = {
-    "id",
-    "label"
-})
-public class InteractantType {
+@XmlType(name = "interactantType", propOrder = { "id", "label" })
+public class InteractantType
+{
+
+  protected String id;
+
+  protected String label;
 
-    protected String id;
-    protected String label;
-    @XmlAttribute(name = "intactId", required = true)
-    protected String intactId;
+  @XmlAttribute(name = "intactId", required = true)
+  protected String intactId;
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
-    /**
-     * Gets the value of the label property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getLabel() {
-        return label;
-    }
+  /**
+   * Gets the value of the label property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getLabel()
+  {
+    return label;
+  }
 
-    /**
-     * Sets the value of the label property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setLabel(String value) {
-        this.label = value;
-    }
+  /**
+   * Sets the value of the label property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setLabel(String value)
+  {
+    this.label = value;
+  }
 
-    /**
-     * Gets the value of the intactId property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getIntactId() {
-        return intactId;
-    }
+  /**
+   * Gets the value of the intactId property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getIntactId()
+  {
+    return intactId;
+  }
 
-    /**
-     * Sets the value of the intactId property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setIntactId(String value) {
-        this.intactId = value;
-    }
+  /**
+   * Sets the value of the intactId property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setIntactId(String value)
+  {
+    this.intactId = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/IsoformType.java b/src/jalview/xml/binding/uniprot/IsoformType.java
index ea55664..20fbbb5 100644
--- a/src/jalview/xml/binding/uniprot/IsoformType.java
+++ b/src/jalview/xml/binding/uniprot/IsoformType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -17,13 +16,15 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
  * Describes isoforms in 'alternative products' annotations.
  * 
- * 

Java class for isoformType complex type. + *

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

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

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

  * <complexType name="isoformType">
@@ -69,302 +70,316 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "isoformType", propOrder = {
-    "id",
-    "name",
-    "sequence",
-    "text"
-})
-public class IsoformType {
+@XmlType(
+  name = "isoformType",
+  propOrder =
+  { "id", "name", "sequence", "text" })
+public class IsoformType
+{
 
-    @XmlElement(required = true)
-    protected List id;
-    @XmlElement(required = true)
-    protected List name;
-    @XmlElement(required = true)
-    protected IsoformType.Sequence sequence;
-    protected List text;
+  @XmlElement(required = true)
+  protected List id;
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getId().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getId() { - if (id == null) { - id = new ArrayList(); - } - return this.id; + @XmlElement(required = true) + protected List name; + + @XmlElement(required = true) + protected IsoformType.Sequence sequence; + + protected List text; + + /** + * Gets the value of the id property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

- * For example, to add a new item, do as follows: - *

-     *    getName().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link IsoformType.Name } + * + * + */ + public List getName() + { + if (name == null) + { + name = new ArrayList(); + } + return this.name; + } + + /** + * Gets the value of the sequence property. + * + * @return possible object is {@link IsoformType.Sequence } + * + */ + public IsoformType.Sequence getSequence() + { + return sequence; + } + + /** + * Sets the value of the sequence property. + * + * @param value + * allowed object is {@link IsoformType.Sequence } + * + */ + public void setSequence(IsoformType.Sequence value) + { + this.sequence = value; + } + + /** + * Gets the value of the text property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "value" }) + public static class Name + { + + @XmlValue + protected String value; + + @XmlAttribute(name = "evidence") + protected List evidence; /** - * Gets the value of the sequence property. + * Gets the value of the value property. + * + * @return possible object is {@link String } * - * @return - * possible object is - * {@link IsoformType.Sequence } - * */ - public IsoformType.Sequence getSequence() { - return sequence; + public String getValue() + { + return value; } /** - * Sets the value of the sequence property. + * Sets the value of the value property. * * @param value - * allowed object is - * {@link IsoformType.Sequence } - * + * allowed object is {@link String } + * */ - public void setSequence(IsoformType.Sequence value) { - this.sequence = value; + public void setValue(String value) + { + this.value = value; } /** - * Gets the value of the text property. + * Gets the value of the evidence property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getText().add(newItem);
+     * getEvidence().add(newItem);
      * 
* * *

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <attribute name="type" use="required">
+   *         <simpleType>
+   *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
+   *             <enumeration value="not described"/>
+   *             <enumeration value="described"/>
+   *             <enumeration value="displayed"/>
+   *             <enumeration value="external"/>
+   *           </restriction>
+   *         </simpleType>
+   *       </attribute>
+   *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Sequence + { + + @XmlAttribute(name = "type", required = true) + protected String type; + + @XmlAttribute(name = "ref") + protected String ref; /** - *

Java class for anonymous complex type. + * Gets the value of the type property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link String } * - *

-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
-     * 
+ */ + public String getType() + { + return type; + } + + /** + * Sets the value of the type property. * + * @param value + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "value" - }) - public static class Name { - - @XmlValue - protected String value; - @XmlAttribute(name = "evidence") - protected List evidence; - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - /** - * Gets the value of the evidence property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getEvidence().add(newItem);
-         * 
- * - * - *

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

Java class for anonymous complex type. + * Gets the value of the ref property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link String } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="type" use="required">
-     *         <simpleType>
-     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-     *             <enumeration value="not described"/>
-     *             <enumeration value="described"/>
-     *             <enumeration value="displayed"/>
-     *             <enumeration value="external"/>
-     *           </restriction>
-     *         </simpleType>
-     *       </attribute>
-     *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public String getRef() + { + return ref; + } + + /** + * Sets the value of the ref property. * + * @param value + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Sequence { - - @XmlAttribute(name = "type", required = true) - protected String type; - @XmlAttribute(name = "ref") - protected String ref; - - /** - * Gets the value of the type property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getType() { - return type; - } - - /** - * Sets the value of the type property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setType(String value) { - this.type = value; - } - - /** - * Gets the value of the ref property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getRef() { - return ref; - } - - /** - * Sets the value of the ref property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setRef(String value) { - this.ref = value; - } - + public void setRef(String value) + { + this.ref = value; } + } + } diff --git a/src/jalview/xml/binding/uniprot/KeywordType.java b/src/jalview/xml/binding/uniprot/KeywordType.java index f6409ee..a4e2b7c 100644 --- a/src/jalview/xml/binding/uniprot/KeywordType.java +++ b/src/jalview/xml/binding/uniprot/KeywordType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; import javax.xml.bind.annotation.XmlValue; - /** - *

Java class for keywordType complex type. + *

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

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

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

  * <complexType name="keywordType">
@@ -36,93 +37,94 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "keywordType", propOrder = {
-    "value"
-})
-public class KeywordType {
+@XmlType(name = "keywordType", propOrder = { "value" })
+public class KeywordType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  @XmlAttribute(name = "id", required = true)
+  protected String id;
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } + + /** + * Gets the value of the id property. + * + * @return possible object is {@link String } + * + */ + public String getId() + { + return id; + } + + /** + * Sets the value of the id property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setId(String value) + { + this.id = value; + } } diff --git a/src/jalview/xml/binding/uniprot/LocationType.java b/src/jalview/xml/binding/uniprot/LocationType.java index 62e9999..ae3f321 100644 --- a/src/jalview/xml/binding/uniprot/LocationType.java +++ b/src/jalview/xml/binding/uniprot/LocationType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -13,13 +12,17 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry. + * Describes a sequence location as either a range with a begin and end or as a + * position. The 'sequence' attribute is only used when the location is not on + * the canonical sequence displayed in the current entry. * - *

Java class for locationType complex type. + *

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

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

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

  * <complexType name="locationType">
@@ -41,113 +44,109 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "locationType", propOrder = {
-    "begin",
-    "end",
-    "position"
-})
-public class LocationType {
-
-    protected PositionType begin;
-    protected PositionType end;
-    protected PositionType position;
-    @XmlAttribute(name = "sequence")
-    protected String sequence;
-
-    /**
-     * Gets the value of the begin property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link PositionType }
-     *     
-     */
-    public PositionType getBegin() {
-        return begin;
-    }
-
-    /**
-     * Sets the value of the begin property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link PositionType }
-     *     
-     */
-    public void setBegin(PositionType value) {
-        this.begin = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link PositionType }
-     *     
-     */
-    public PositionType getEnd() {
-        return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link PositionType }
-     *     
-     */
-    public void setEnd(PositionType value) {
-        this.end = value;
-    }
-
-    /**
-     * Gets the value of the position property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link PositionType }
-     *     
-     */
-    public PositionType getPosition() {
-        return position;
-    }
-
-    /**
-     * Sets the value of the position property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link PositionType }
-     *     
-     */
-    public void setPosition(PositionType value) {
-        this.position = value;
-    }
-
-    /**
-     * Gets the value of the sequence property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getSequence() {
-        return sequence;
-    }
-
-    /**
-     * Sets the value of the sequence property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setSequence(String value) {
-        this.sequence = value;
-    }
+@XmlType(name = "locationType", propOrder = { "begin", "end", "position" })
+public class LocationType
+{
+
+  protected PositionType begin;
+
+  protected PositionType end;
+
+  protected PositionType position;
+
+  @XmlAttribute(name = "sequence")
+  protected String sequence;
+
+  /**
+   * Gets the value of the begin property.
+   * 
+   * @return possible object is {@link PositionType }
+   * 
+   */
+  public PositionType getBegin()
+  {
+    return begin;
+  }
+
+  /**
+   * Sets the value of the begin property.
+   * 
+   * @param value
+   *          allowed object is {@link PositionType }
+   * 
+   */
+  public void setBegin(PositionType value)
+  {
+    this.begin = value;
+  }
+
+  /**
+   * Gets the value of the end property.
+   * 
+   * @return possible object is {@link PositionType }
+   * 
+   */
+  public PositionType getEnd()
+  {
+    return end;
+  }
+
+  /**
+   * Sets the value of the end property.
+   * 
+   * @param value
+   *          allowed object is {@link PositionType }
+   * 
+   */
+  public void setEnd(PositionType value)
+  {
+    this.end = value;
+  }
+
+  /**
+   * Gets the value of the position property.
+   * 
+   * @return possible object is {@link PositionType }
+   * 
+   */
+  public PositionType getPosition()
+  {
+    return position;
+  }
+
+  /**
+   * Sets the value of the position property.
+   * 
+   * @param value
+   *          allowed object is {@link PositionType }
+   * 
+   */
+  public void setPosition(PositionType value)
+  {
+    this.position = value;
+  }
+
+  /**
+   * Gets the value of the sequence property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getSequence()
+  {
+    return sequence;
+  }
+
+  /**
+   * Sets the value of the sequence property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setSequence(String value)
+  {
+    this.sequence = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/MoleculeType.java b/src/jalview/xml/binding/uniprot/MoleculeType.java
index 8b52523..67e43d1 100644
--- a/src/jalview/xml/binding/uniprot/MoleculeType.java
+++ b/src/jalview/xml/binding/uniprot/MoleculeType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,13 +13,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
  * Describes a molecule by name or unique identifier.
  * 
- * 

Java class for moleculeType complex type. + *

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

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

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

  * <complexType name="moleculeType">
@@ -35,62 +36,60 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "moleculeType", propOrder = {
-    "value"
-})
-public class MoleculeType {
+@XmlType(name = "moleculeType", propOrder = { "value" })
+public class MoleculeType
+{
+
+  @XmlValue
+  protected String value;
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "id")
-    protected String id;
+  @XmlAttribute(name = "id")
+  protected String id;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getId() {
-        return id;
-    }
+  /**
+   * Gets the value of the id property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getId()
+  {
+    return id;
+  }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setId(String value) {
-        this.id = value;
-    }
+  /**
+   * Sets the value of the id property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setId(String value)
+  {
+    this.id = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/NameListType.java b/src/jalview/xml/binding/uniprot/NameListType.java
index be68867..17918fb 100644
--- a/src/jalview/xml/binding/uniprot/NameListType.java
+++ b/src/jalview/xml/binding/uniprot/NameListType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * 

Java class for nameListType complex type. + *

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

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

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

  * <complexType name="nameListType">
@@ -38,45 +39,45 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "nameListType", propOrder = {
-    "consortiumOrPerson"
-})
-public class NameListType {
+@XmlType(name = "nameListType", propOrder = { "consortiumOrPerson" })
+public class NameListType
+{
 
-    @XmlElements({
-        @XmlElement(name = "consortium", type = ConsortiumType.class),
-        @XmlElement(name = "person", type = PersonType.class)
-    })
-    protected List consortiumOrPerson;
+  @XmlElements({
+      @XmlElement(name = "consortium", type = ConsortiumType.class),
+      @XmlElement(name = "person", type = PersonType.class) })
+  protected List consortiumOrPerson;
 
-    /**
-     * Gets the value of the consortiumOrPerson property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getConsortiumOrPerson().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link ConsortiumType } {@link PersonType } + * + * + */ + public List getConsortiumOrPerson() + { + if (consortiumOrPerson == null) + { + consortiumOrPerson = new ArrayList(); } + return this.consortiumOrPerson; + } } diff --git a/src/jalview/xml/binding/uniprot/ObjectFactory.java b/src/jalview/xml/binding/uniprot/ObjectFactory.java index e2bb255..bf570f3 100644 --- a/src/jalview/xml/binding/uniprot/ObjectFactory.java +++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.JAXBElement; @@ -13,496 +12,558 @@ import javax.xml.bind.annotation.XmlElementDecl; import javax.xml.bind.annotation.XmlRegistry; import javax.xml.namespace.QName; - /** - * This object contains factory methods for each - * Java content interface and Java element interface - * generated in the jalview.xml.binding.uniprot package. - *

An ObjectFactory allows you to programatically - * construct new instances of the Java representation - * for XML content. The Java representation of XML - * content can consist of schema derived interfaces - * and classes representing the binding of schema - * type definitions, element declarations and model - * groups. Factory methods for each of these are - * provided in this class. + * This object contains factory methods for each Java content interface and Java + * element interface generated in the jalview.xml.binding.uniprot package. + *

+ * An ObjectFactory allows you to programatically construct new instances of the + * Java representation for XML content. The Java representation of XML content + * can consist of schema derived interfaces and classes representing the binding + * of schema type definitions, element declarations and model groups. Factory + * methods for each of these are provided in this class. * */ @XmlRegistry -public class ObjectFactory { - - private final static QName _Copyright_QNAME = new QName("http://uniprot.org/uniprot", "copyright"); - - /** - * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.uniprot - * - */ - public ObjectFactory() { - } - - /** - * Create an instance of {@link SourceDataType } - * - */ - public SourceDataType createSourceDataType() { - return new SourceDataType(); - } - - /** - * Create an instance of {@link IsoformType } - * - */ - public IsoformType createIsoformType() { - return new IsoformType(); - } - - /** - * Create an instance of {@link CommentType } - * - */ - public CommentType createCommentType() { - return new CommentType(); - } - - /** - * Create an instance of {@link CommentType.Conflict } - * - */ - public CommentType.Conflict createCommentTypeConflict() { - return new CommentType.Conflict(); - } - - /** - * Create an instance of {@link OrganismType } - * - */ - public OrganismType createOrganismType() { - return new OrganismType(); - } - - /** - * Create an instance of {@link ProteinType } - * - */ - public ProteinType createProteinType() { - return new ProteinType(); - } - - /** - * Create an instance of {@link Entry } - * - */ - public Entry createEntry() { - return new Entry(); - } - - /** - * Create an instance of {@link GeneType } - * - */ - public GeneType createGeneType() { - return new GeneType(); - } - - /** - * Create an instance of {@link GeneLocationType } - * - */ - public GeneLocationType createGeneLocationType() { - return new GeneLocationType(); - } - - /** - * Create an instance of {@link ReferenceType } - * - */ - public ReferenceType createReferenceType() { - return new ReferenceType(); - } - - /** - * Create an instance of {@link DbReferenceType } - * - */ - public DbReferenceType createDbReferenceType() { - return new DbReferenceType(); - } - - /** - * Create an instance of {@link ProteinExistenceType } - * - */ - public ProteinExistenceType createProteinExistenceType() { - return new ProteinExistenceType(); - } - - /** - * Create an instance of {@link KeywordType } - * - */ - public KeywordType createKeywordType() { - return new KeywordType(); - } - - /** - * Create an instance of {@link FeatureType } - * - */ - public FeatureType createFeatureType() { - return new FeatureType(); - } - - /** - * Create an instance of {@link EvidenceType } - * - */ - public EvidenceType createEvidenceType() { - return new EvidenceType(); - } - - /** - * Create an instance of {@link SequenceType } - * - */ - public SequenceType createSequenceType() { - return new SequenceType(); - } - - /** - * Create an instance of {@link Uniprot } - * - */ - public Uniprot createUniprot() { - return new Uniprot(); - } - - /** - * Create an instance of {@link StatusType } - * - */ - public StatusType createStatusType() { - return new StatusType(); - } - - /** - * Create an instance of {@link PositionType } - * - */ - public PositionType createPositionType() { - return new PositionType(); - } - - /** - * Create an instance of {@link ConsortiumType } - * - */ - public ConsortiumType createConsortiumType() { - return new ConsortiumType(); - } - - /** - * Create an instance of {@link GeneNameType } - * - */ - public GeneNameType createGeneNameType() { - return new GeneNameType(); - } - - /** - * Create an instance of {@link LocationType } - * - */ - public LocationType createLocationType() { - return new LocationType(); - } - - /** - * Create an instance of {@link CitationType } - * - */ - public CitationType createCitationType() { - return new CitationType(); - } - - /** - * Create an instance of {@link PropertyType } - * - */ - public PropertyType createPropertyType() { - return new PropertyType(); - } - - /** - * Create an instance of {@link PhysiologicalReactionType } - * - */ - public PhysiologicalReactionType createPhysiologicalReactionType() { - return new PhysiologicalReactionType(); - } - - /** - * Create an instance of {@link CofactorType } - * - */ - public CofactorType createCofactorType() { - return new CofactorType(); - } - - /** - * Create an instance of {@link EvidencedStringType } - * - */ - public EvidencedStringType createEvidencedStringType() { - return new EvidencedStringType(); - } - - /** - * Create an instance of {@link PersonType } - * - */ - public PersonType createPersonType() { - return new PersonType(); - } - - /** - * Create an instance of {@link ImportedFromType } - * - */ - public ImportedFromType createImportedFromType() { - return new ImportedFromType(); - } - - /** - * Create an instance of {@link EventType } - * - */ - public EventType createEventType() { - return new EventType(); - } - - /** - * Create an instance of {@link InteractantType } - * - */ - public InteractantType createInteractantType() { - return new InteractantType(); - } - - /** - * Create an instance of {@link NameListType } - * - */ - public NameListType createNameListType() { - return new NameListType(); - } - - /** - * Create an instance of {@link ReactionType } - * - */ - public ReactionType createReactionType() { - return new ReactionType(); - } - - /** - * Create an instance of {@link SourceType } - * - */ - public SourceType createSourceType() { - return new SourceType(); - } - - /** - * Create an instance of {@link MoleculeType } - * - */ - public MoleculeType createMoleculeType() { - return new MoleculeType(); - } - - /** - * Create an instance of {@link OrganismNameType } - * - */ - public OrganismNameType createOrganismNameType() { - return new OrganismNameType(); - } - - /** - * Create an instance of {@link SubcellularLocationType } - * - */ - public SubcellularLocationType createSubcellularLocationType() { - return new SubcellularLocationType(); - } - - /** - * Create an instance of {@link SourceDataType.Strain } - * - */ - public SourceDataType.Strain createSourceDataTypeStrain() { - return new SourceDataType.Strain(); - } - - /** - * Create an instance of {@link SourceDataType.Plasmid } - * - */ - public SourceDataType.Plasmid createSourceDataTypePlasmid() { - return new SourceDataType.Plasmid(); - } - - /** - * Create an instance of {@link SourceDataType.Transposon } - * - */ - public SourceDataType.Transposon createSourceDataTypeTransposon() { - return new SourceDataType.Transposon(); - } - - /** - * Create an instance of {@link SourceDataType.Tissue } - * - */ - public SourceDataType.Tissue createSourceDataTypeTissue() { - return new SourceDataType.Tissue(); - } - - /** - * Create an instance of {@link IsoformType.Name } - * - */ - public IsoformType.Name createIsoformTypeName() { - return new IsoformType.Name(); - } - - /** - * Create an instance of {@link IsoformType.Sequence } - * - */ - public IsoformType.Sequence createIsoformTypeSequence() { - return new IsoformType.Sequence(); - } - - /** - * Create an instance of {@link CommentType.Absorption } - * - */ - public CommentType.Absorption createCommentTypeAbsorption() { - return new CommentType.Absorption(); - } - - /** - * Create an instance of {@link CommentType.Kinetics } - * - */ - public CommentType.Kinetics createCommentTypeKinetics() { - return new CommentType.Kinetics(); - } - - /** - * Create an instance of {@link CommentType.PhDependence } - * - */ - public CommentType.PhDependence createCommentTypePhDependence() { - return new CommentType.PhDependence(); - } - - /** - * Create an instance of {@link CommentType.RedoxPotential } - * - */ - public CommentType.RedoxPotential createCommentTypeRedoxPotential() { - return new CommentType.RedoxPotential(); - } - - /** - * Create an instance of {@link CommentType.TemperatureDependence } - * - */ - public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() { - return new CommentType.TemperatureDependence(); - } - - /** - * Create an instance of {@link CommentType.Link } - * - */ - public CommentType.Link createCommentTypeLink() { - return new CommentType.Link(); - } - - /** - * Create an instance of {@link CommentType.Disease } - * - */ - public CommentType.Disease createCommentTypeDisease() { - return new CommentType.Disease(); - } - - /** - * Create an instance of {@link CommentType.Conflict.Sequence } - * - */ - public CommentType.Conflict.Sequence createCommentTypeConflictSequence() { - return new CommentType.Conflict.Sequence(); - } - - /** - * Create an instance of {@link OrganismType.Lineage } - * - */ - public OrganismType.Lineage createOrganismTypeLineage() { - return new OrganismType.Lineage(); - } - - /** - * Create an instance of {@link ProteinType.RecommendedName } - * - */ - public ProteinType.RecommendedName createProteinTypeRecommendedName() { - return new ProteinType.RecommendedName(); - } - - /** - * Create an instance of {@link ProteinType.AlternativeName } - * - */ - public ProteinType.AlternativeName createProteinTypeAlternativeName() { - return new ProteinType.AlternativeName(); - } - - /** - * Create an instance of {@link ProteinType.SubmittedName } - * - */ - public ProteinType.SubmittedName createProteinTypeSubmittedName() { - return new ProteinType.SubmittedName(); - } - - /** - * Create an instance of {@link ProteinType.Domain } - * - */ - public ProteinType.Domain createProteinTypeDomain() { - return new ProteinType.Domain(); - } - - /** - * Create an instance of {@link ProteinType.Component } - * - */ - public ProteinType.Component createProteinTypeComponent() { - return new ProteinType.Component(); - } - - /** - * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} - * - */ - @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright") - public JAXBElement createCopyright(String value) { - return new JAXBElement(_Copyright_QNAME, String.class, null, value); - } +public class ObjectFactory +{ + + private final static QName _Copyright_QNAME = new QName( + "http://uniprot.org/uniprot", "copyright"); + + /** + * Create a new ObjectFactory that can be used to create new instances of + * schema derived classes for package: jalview.xml.binding.uniprot + * + */ + public ObjectFactory() + { + } + + /** + * Create an instance of {@link SourceDataType } + * + */ + public SourceDataType createSourceDataType() + { + return new SourceDataType(); + } + + /** + * Create an instance of {@link IsoformType } + * + */ + public IsoformType createIsoformType() + { + return new IsoformType(); + } + + /** + * Create an instance of {@link CommentType } + * + */ + public CommentType createCommentType() + { + return new CommentType(); + } + + /** + * Create an instance of {@link CommentType.Conflict } + * + */ + public CommentType.Conflict createCommentTypeConflict() + { + return new CommentType.Conflict(); + } + + /** + * Create an instance of {@link OrganismType } + * + */ + public OrganismType createOrganismType() + { + return new OrganismType(); + } + + /** + * Create an instance of {@link ProteinType } + * + */ + public ProteinType createProteinType() + { + return new ProteinType(); + } + + /** + * Create an instance of {@link Entry } + * + */ + public Entry createEntry() + { + return new Entry(); + } + + /** + * Create an instance of {@link GeneType } + * + */ + public GeneType createGeneType() + { + return new GeneType(); + } + + /** + * Create an instance of {@link GeneLocationType } + * + */ + public GeneLocationType createGeneLocationType() + { + return new GeneLocationType(); + } + + /** + * Create an instance of {@link ReferenceType } + * + */ + public ReferenceType createReferenceType() + { + return new ReferenceType(); + } + + /** + * Create an instance of {@link DbReferenceType } + * + */ + public DbReferenceType createDbReferenceType() + { + return new DbReferenceType(); + } + + /** + * Create an instance of {@link ProteinExistenceType } + * + */ + public ProteinExistenceType createProteinExistenceType() + { + return new ProteinExistenceType(); + } + + /** + * Create an instance of {@link KeywordType } + * + */ + public KeywordType createKeywordType() + { + return new KeywordType(); + } + + /** + * Create an instance of {@link FeatureType } + * + */ + public FeatureType createFeatureType() + { + return new FeatureType(); + } + + /** + * Create an instance of {@link EvidenceType } + * + */ + public EvidenceType createEvidenceType() + { + return new EvidenceType(); + } + + /** + * Create an instance of {@link SequenceType } + * + */ + public SequenceType createSequenceType() + { + return new SequenceType(); + } + + /** + * Create an instance of {@link Uniprot } + * + */ + public Uniprot createUniprot() + { + return new Uniprot(); + } + + /** + * Create an instance of {@link StatusType } + * + */ + public StatusType createStatusType() + { + return new StatusType(); + } + + /** + * Create an instance of {@link PositionType } + * + */ + public PositionType createPositionType() + { + return new PositionType(); + } + + /** + * Create an instance of {@link ConsortiumType } + * + */ + public ConsortiumType createConsortiumType() + { + return new ConsortiumType(); + } + + /** + * Create an instance of {@link GeneNameType } + * + */ + public GeneNameType createGeneNameType() + { + return new GeneNameType(); + } + + /** + * Create an instance of {@link LocationType } + * + */ + public LocationType createLocationType() + { + return new LocationType(); + } + + /** + * Create an instance of {@link CitationType } + * + */ + public CitationType createCitationType() + { + return new CitationType(); + } + + /** + * Create an instance of {@link PropertyType } + * + */ + public PropertyType createPropertyType() + { + return new PropertyType(); + } + + /** + * Create an instance of {@link PhysiologicalReactionType } + * + */ + public PhysiologicalReactionType createPhysiologicalReactionType() + { + return new PhysiologicalReactionType(); + } + + /** + * Create an instance of {@link CofactorType } + * + */ + public CofactorType createCofactorType() + { + return new CofactorType(); + } + + /** + * Create an instance of {@link EvidencedStringType } + * + */ + public EvidencedStringType createEvidencedStringType() + { + return new EvidencedStringType(); + } + + /** + * Create an instance of {@link PersonType } + * + */ + public PersonType createPersonType() + { + return new PersonType(); + } + + /** + * Create an instance of {@link ImportedFromType } + * + */ + public ImportedFromType createImportedFromType() + { + return new ImportedFromType(); + } + + /** + * Create an instance of {@link EventType } + * + */ + public EventType createEventType() + { + return new EventType(); + } + + /** + * Create an instance of {@link InteractantType } + * + */ + public InteractantType createInteractantType() + { + return new InteractantType(); + } + + /** + * Create an instance of {@link NameListType } + * + */ + public NameListType createNameListType() + { + return new NameListType(); + } + + /** + * Create an instance of {@link ReactionType } + * + */ + public ReactionType createReactionType() + { + return new ReactionType(); + } + + /** + * Create an instance of {@link SourceType } + * + */ + public SourceType createSourceType() + { + return new SourceType(); + } + + /** + * Create an instance of {@link MoleculeType } + * + */ + public MoleculeType createMoleculeType() + { + return new MoleculeType(); + } + + /** + * Create an instance of {@link OrganismNameType } + * + */ + public OrganismNameType createOrganismNameType() + { + return new OrganismNameType(); + } + + /** + * Create an instance of {@link SubcellularLocationType } + * + */ + public SubcellularLocationType createSubcellularLocationType() + { + return new SubcellularLocationType(); + } + + /** + * Create an instance of {@link SourceDataType.Strain } + * + */ + public SourceDataType.Strain createSourceDataTypeStrain() + { + return new SourceDataType.Strain(); + } + + /** + * Create an instance of {@link SourceDataType.Plasmid } + * + */ + public SourceDataType.Plasmid createSourceDataTypePlasmid() + { + return new SourceDataType.Plasmid(); + } + + /** + * Create an instance of {@link SourceDataType.Transposon } + * + */ + public SourceDataType.Transposon createSourceDataTypeTransposon() + { + return new SourceDataType.Transposon(); + } + + /** + * Create an instance of {@link SourceDataType.Tissue } + * + */ + public SourceDataType.Tissue createSourceDataTypeTissue() + { + return new SourceDataType.Tissue(); + } + + /** + * Create an instance of {@link IsoformType.Name } + * + */ + public IsoformType.Name createIsoformTypeName() + { + return new IsoformType.Name(); + } + + /** + * Create an instance of {@link IsoformType.Sequence } + * + */ + public IsoformType.Sequence createIsoformTypeSequence() + { + return new IsoformType.Sequence(); + } + + /** + * Create an instance of {@link CommentType.Absorption } + * + */ + public CommentType.Absorption createCommentTypeAbsorption() + { + return new CommentType.Absorption(); + } + + /** + * Create an instance of {@link CommentType.Kinetics } + * + */ + public CommentType.Kinetics createCommentTypeKinetics() + { + return new CommentType.Kinetics(); + } + + /** + * Create an instance of {@link CommentType.PhDependence } + * + */ + public CommentType.PhDependence createCommentTypePhDependence() + { + return new CommentType.PhDependence(); + } + + /** + * Create an instance of {@link CommentType.RedoxPotential } + * + */ + public CommentType.RedoxPotential createCommentTypeRedoxPotential() + { + return new CommentType.RedoxPotential(); + } + + /** + * Create an instance of {@link CommentType.TemperatureDependence } + * + */ + public CommentType.TemperatureDependence createCommentTypeTemperatureDependence() + { + return new CommentType.TemperatureDependence(); + } + + /** + * Create an instance of {@link CommentType.Link } + * + */ + public CommentType.Link createCommentTypeLink() + { + return new CommentType.Link(); + } + + /** + * Create an instance of {@link CommentType.Disease } + * + */ + public CommentType.Disease createCommentTypeDisease() + { + return new CommentType.Disease(); + } + + /** + * Create an instance of {@link CommentType.Conflict.Sequence } + * + */ + public CommentType.Conflict.Sequence createCommentTypeConflictSequence() + { + return new CommentType.Conflict.Sequence(); + } + + /** + * Create an instance of {@link OrganismType.Lineage } + * + */ + public OrganismType.Lineage createOrganismTypeLineage() + { + return new OrganismType.Lineage(); + } + + /** + * Create an instance of {@link ProteinType.RecommendedName } + * + */ + public ProteinType.RecommendedName createProteinTypeRecommendedName() + { + return new ProteinType.RecommendedName(); + } + + /** + * Create an instance of {@link ProteinType.AlternativeName } + * + */ + public ProteinType.AlternativeName createProteinTypeAlternativeName() + { + return new ProteinType.AlternativeName(); + } + + /** + * Create an instance of {@link ProteinType.SubmittedName } + * + */ + public ProteinType.SubmittedName createProteinTypeSubmittedName() + { + return new ProteinType.SubmittedName(); + } + + /** + * Create an instance of {@link ProteinType.Domain } + * + */ + public ProteinType.Domain createProteinTypeDomain() + { + return new ProteinType.Domain(); + } + + /** + * Create an instance of {@link ProteinType.Component } + * + */ + public ProteinType.Component createProteinTypeComponent() + { + return new ProteinType.Component(); + } + + /** + * Create an instance of {@link JAXBElement }{@code <}{@link String + * }{@code >}} + * + */ + @XmlElementDecl( + namespace = "http://uniprot.org/uniprot", + name = "copyright") + public JAXBElement createCopyright(String value) + { + return new JAXBElement(_Copyright_QNAME, String.class, null, + value); + } } diff --git a/src/jalview/xml/binding/uniprot/OrganismNameType.java b/src/jalview/xml/binding/uniprot/OrganismNameType.java index bc5c8c5..f2964dc 100644 --- a/src/jalview/xml/binding/uniprot/OrganismNameType.java +++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -14,13 +13,15 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; import javax.xml.bind.annotation.XmlValue; - /** * Describes different types of source organism names. * - *

Java class for organismNameType complex type. + *

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

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

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

  * <complexType name="organismNameType">
@@ -45,62 +46,60 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismNameType", propOrder = {
-    "value"
-})
-public class OrganismNameType {
+@XmlType(name = "organismNameType", propOrder = { "value" })
+public class OrganismNameType
+{
+
+  @XmlValue
+  protected String value;
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/OrganismType.java b/src/jalview/xml/binding/uniprot/OrganismType.java
index bb76add..033e498 100644
--- a/src/jalview/xml/binding/uniprot/OrganismType.java
+++ b/src/jalview/xml/binding/uniprot/OrganismType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Describes the source organism.
  * 
- * 

Java class for organismType complex type. + *

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

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

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

  * <complexType name="organismType">
@@ -52,190 +53,203 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "organismType", propOrder = {
-    "name",
-    "dbReference",
-    "lineage"
-})
-public class OrganismType {
-
-    @XmlElement(required = true)
-    protected List name;
-    @XmlElement(required = true)
-    protected List dbReference;
-    protected OrganismType.Lineage lineage;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getName().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link OrganismNameType } - * - * - */ - public List getName() { - if (name == null) { - name = new ArrayList(); - } - return this.name; +@XmlType( + name = "organismType", + propOrder = + { "name", "dbReference", "lineage" }) +public class OrganismType +{ + + @XmlElement(required = true) + protected List name; + + @XmlElement(required = true) + protected List dbReference; + + protected OrganismType.Lineage lineage; + + @XmlAttribute(name = "evidence") + protected List evidence; + + /** + * Gets the value of the name property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

- * For example, to add a new item, do as follows: - *

-     *    getDbReference().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link DbReferenceType } + * + * + */ + public List getDbReference() + { + if (dbReference == null) + { + dbReference = new ArrayList(); } - - /** - * Gets the value of the lineage property. - * - * @return - * possible object is - * {@link OrganismType.Lineage } - * - */ - public OrganismType.Lineage getLineage() { - return lineage; + return this.dbReference; + } + + /** + * Gets the value of the lineage property. + * + * @return possible object is {@link OrganismType.Lineage } + * + */ + public OrganismType.Lineage getLineage() + { + return lineage; + } + + /** + * Sets the value of the lineage property. + * + * @param value + * allowed object is {@link OrganismType.Lineage } + * + */ + public void setLineage(OrganismType.Lineage value) + { + this.lineage = value; + } + + /** + * Gets the value of the evidence property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "taxon" }) + public static class Lineage + { - /** - * Sets the value of the lineage property. - * - * @param value - * allowed object is - * {@link OrganismType.Lineage } - * - */ - public void setLineage(OrganismType.Lineage value) { - this.lineage = value; - } + @XmlElement(required = true) + protected List taxon; /** - * Gets the value of the evidence property. + * Gets the value of the taxon property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getEvidence().add(newItem);
+     * getTaxon().add(newItem);
      * 
* * *

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

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "taxon" - }) - public static class Lineage { - - @XmlElement(required = true) - protected List taxon; - - /** - * Gets the value of the taxon property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getTaxon().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getTaxon() { - if (taxon == null) { - taxon = new ArrayList(); - } - return this.taxon; - } - - } + } } diff --git a/src/jalview/xml/binding/uniprot/PersonType.java b/src/jalview/xml/binding/uniprot/PersonType.java index 1354092..66a5161 100644 --- a/src/jalview/xml/binding/uniprot/PersonType.java +++ b/src/jalview/xml/binding/uniprot/PersonType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for personType complex type. + *

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

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

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

  * <complexType name="personType">
@@ -33,33 +34,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "personType")
-public class PersonType {
+public class PersonType
+{
 
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
+  @XmlAttribute(name = "name", required = true)
+  protected String name;
 
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getName() {
-        return name;
-    }
+  /**
+   * Gets the value of the name property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getName()
+  {
+    return name;
+  }
 
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setName(String value) {
-        this.name = value;
-    }
+  /**
+   * Sets the value of the name property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setName(String value)
+  {
+    this.name = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
index e674452..9e805f0 100644
--- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
+++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
  * Describes a physiological reaction.
  * 
- * 

Java class for physiologicalReactionType complex type. + *

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

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

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

  * <complexType name="physiologicalReactionType">
@@ -48,93 +49,94 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "physiologicalReactionType", propOrder = {
-    "dbReference"
-})
-public class PhysiologicalReactionType {
+@XmlType(name = "physiologicalReactionType", propOrder = { "dbReference" })
+public class PhysiologicalReactionType
+{
 
-    @XmlElement(required = true)
-    protected DbReferenceType dbReference;
-    @XmlAttribute(name = "direction", required = true)
-    protected String direction;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+  @XmlElement(required = true)
+  protected DbReferenceType dbReference;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  @XmlAttribute(name = "direction", required = true)
+  protected String direction;
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
 
-    /**
-     * Gets the value of the direction property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getDirection() {
-        return direction;
-    }
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
 
-    /**
-     * Sets the value of the direction property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setDirection(String value) {
-        this.direction = value;
-    }
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
+
+  /**
+   * Gets the value of the direction property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getDirection()
+  {
+    return direction;
+  }
+
+  /**
+   * Sets the value of the direction property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setDirection(String value)
+  {
+    this.direction = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } } diff --git a/src/jalview/xml/binding/uniprot/PositionType.java b/src/jalview/xml/binding/uniprot/PositionType.java index a00d698..8eebd3d 100644 --- a/src/jalview/xml/binding/uniprot/PositionType.java +++ b/src/jalview/xml/binding/uniprot/PositionType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.math.BigInteger; @@ -17,11 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for positionType complex type. + *

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

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

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

  * <complexType name="positionType">
@@ -49,95 +50,101 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "positionType")
-public class PositionType {
+public class PositionType
+{
 
-    @XmlAttribute(name = "position")
-    @XmlSchemaType(name = "unsignedLong")
-    protected BigInteger position;
-    @XmlAttribute(name = "status")
-    protected String status;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+  @XmlAttribute(name = "position")
+  @XmlSchemaType(name = "unsignedLong")
+  protected BigInteger position;
 
-    /**
-     * Gets the value of the position property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getPosition() {
-        return position;
-    }
+  @XmlAttribute(name = "status")
+  protected String status;
 
-    /**
-     * Sets the value of the position property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setPosition(BigInteger value) {
-        this.position = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
 
-    /**
-     * Gets the value of the status property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getStatus() {
-        if (status == null) {
-            return "certain";
-        } else {
-            return status;
-        }
-    }
+  /**
+   * Gets the value of the position property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getPosition()
+  {
+    return position;
+  }
+
+  /**
+   * Sets the value of the position property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setPosition(BigInteger value)
+  {
+    this.position = value;
+  }
 
-    /**
-     * Sets the value of the status property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setStatus(String value) {
-        this.status = value;
+  /**
+   * Gets the value of the status property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getStatus()
+  {
+    if (status == null)
+    {
+      return "certain";
     }
+    else
+    {
+      return status;
+    }
+  }
+
+  /**
+   * Sets the value of the status property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setStatus(String value)
+  {
+    this.status = value;
+  }
 
-    /**
-     * Gets the value of the evidence property.
-     * 
-     * 

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

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } } diff --git a/src/jalview/xml/binding/uniprot/PropertyType.java b/src/jalview/xml/binding/uniprot/PropertyType.java index c9f169c..a701b99 100644 --- a/src/jalview/xml/binding/uniprot/PropertyType.java +++ b/src/jalview/xml/binding/uniprot/PropertyType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -13,11 +12,13 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for propertyType complex type. + *

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

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

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

  * <complexType name="propertyType">
@@ -34,59 +35,59 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "propertyType")
-public class PropertyType {
+public class PropertyType
+{
+
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
+  @XmlAttribute(name = "value", required = true)
+  protected String value;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
index c34a0f5..5b914d0 100644
--- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,14 +12,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the evidence for the protein's existence.
- *             Equivalent to the flat file PE-line.
+ * Describes the evidence for the protein's existence. Equivalent to the flat
+ * file PE-line.
  * 
- * 

Java class for proteinExistenceType complex type. + *

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

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

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

  * <complexType name="proteinExistenceType">
@@ -46,33 +47,33 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "proteinExistenceType")
-public class ProteinExistenceType {
+public class ProteinExistenceType
+{
 
-    @XmlAttribute(name = "type", required = true)
-    protected String type;
+  @XmlAttribute(name = "type", required = true)
+  protected String type;
 
-    /**
-     * Gets the value of the type property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getType() {
-        return type;
-    }
+  /**
+   * Gets the value of the type property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getType()
+  {
+    return type;
+  }
 
-    /**
-     * Sets the value of the type property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setType(String value) {
-        this.type = value;
-    }
+  /**
+   * Sets the value of the type property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setType(String value)
+  {
+    this.type = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/ProteinType.java b/src/jalview/xml/binding/uniprot/ProteinType.java
index 7b106fb..d35b45f 100644
--- a/src/jalview/xml/binding/uniprot/ProteinType.java
+++ b/src/jalview/xml/binding/uniprot/ProteinType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,14 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the names for the protein and parts thereof.
- *             Equivalent to the flat file DE-line.
+ * Describes the names for the protein and parts thereof. Equivalent to the flat
+ * file DE-line.
  * 
- * 

Java class for proteinType complex type. + *

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

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

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

  * <complexType name="proteinType">
@@ -57,66 +58,497 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "proteinType", propOrder = {
-    "recommendedName",
-    "alternativeName",
-    "submittedName",
-    "allergenName",
-    "biotechName",
-    "cdAntigenName",
-    "innName",
-    "domain",
-    "component"
-})
-public class ProteinType {
+@XmlType(
+  name = "proteinType",
+  propOrder =
+  { "recommendedName", "alternativeName", "submittedName", "allergenName",
+      "biotechName", "cdAntigenName", "innName", "domain", "component" })
+public class ProteinType
+{
+
+  protected ProteinType.RecommendedName recommendedName;
+
+  protected List alternativeName;
+
+  protected List submittedName;
+
+  protected EvidencedStringType allergenName;
+
+  protected EvidencedStringType biotechName;
+
+  protected List cdAntigenName;
+
+  protected List innName;
+
+  protected List domain;
+
+  protected List component;
+
+  /**
+   * Gets the value of the recommendedName property.
+   * 
+   * @return possible object is {@link ProteinType.RecommendedName }
+   * 
+   */
+  public ProteinType.RecommendedName getRecommendedName()
+  {
+    return recommendedName;
+  }
+
+  /**
+   * Sets the value of the recommendedName property.
+   * 
+   * @param value
+   *          allowed object is {@link ProteinType.RecommendedName }
+   * 
+   */
+  public void setRecommendedName(ProteinType.RecommendedName value)
+  {
+    this.recommendedName = value;
+  }
+
+  /**
+   * Gets the value of the alternativeName property.
+   * 
+   * 

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

+ * Objects of the following type(s) are allowed in the list + * {@link ProteinType.SubmittedName } + * + * + */ + public List getSubmittedName() + { + if (submittedName == null) + { + submittedName = new ArrayList(); + } + return this.submittedName; + } + + /** + * Gets the value of the allergenName property. + * + * @return possible object is {@link EvidencedStringType } + * + */ + public EvidencedStringType getAllergenName() + { + return allergenName; + } + + /** + * Sets the value of the allergenName property. + * + * @param value + * allowed object is {@link EvidencedStringType } + * + */ + public void setAllergenName(EvidencedStringType value) + { + this.allergenName = value; + } + + /** + * Gets the value of the biotechName property. + * + * @return possible object is {@link EvidencedStringType } + * + */ + public EvidencedStringType getBiotechName() + { + return biotechName; + } + + /** + * Sets the value of the biotechName property. + * + * @param value + * allowed object is {@link EvidencedStringType } + * + */ + public void setBiotechName(EvidencedStringType value) + { + this.biotechName = value; + } + + /** + * Gets the value of the cdAntigenName property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
+   *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" }) + public static class AlternativeName + { + + protected EvidencedStringType fullName; + + protected List shortName; + + protected List ecNumber; + + /** + * Gets the value of the fullName property. + * + * @return possible object is {@link EvidencedStringType } + * + */ + public EvidencedStringType getFullName() + { + return fullName; + } + + /** + * Sets the value of the fullName property. + * + * @param value + * allowed object is {@link EvidencedStringType } + * + */ + public void setFullName(EvidencedStringType value) + { + this.fullName = value; + } + + /** + * Gets the value of the shortName property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

+ * For example, to add a new item, do as follows: + * + *

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

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "recommendedName", "alternativeName", "submittedName", "allergenName", + "biotechName", "cdAntigenName", "innName" }) + public static class Component + { protected ProteinType.RecommendedName recommendedName; + protected List alternativeName; + protected List submittedName; + protected EvidencedStringType allergenName; + protected EvidencedStringType biotechName; + protected List cdAntigenName; + protected List innName; - protected List domain; - protected List component; /** * Gets the value of the recommendedName property. * - * @return - * possible object is - * {@link ProteinType.RecommendedName } - * + * @return possible object is {@link ProteinType.RecommendedName } + * */ - public ProteinType.RecommendedName getRecommendedName() { - return recommendedName; + public ProteinType.RecommendedName getRecommendedName() + { + return recommendedName; } /** * Sets the value of the recommendedName property. * * @param value - * allowed object is - * {@link ProteinType.RecommendedName } - * + * allowed object is {@link ProteinType.RecommendedName } + * */ - public void setRecommendedName(ProteinType.RecommendedName value) { - this.recommendedName = value; + public void setRecommendedName(ProteinType.RecommendedName value) + { + this.recommendedName = value; } /** * Gets the value of the alternativeName property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getAlternativeName().add(newItem);
+     * getAlternativeName().add(newItem);
      * 
* * @@ -126,26 +558,29 @@ public class ProteinType { * * */ - public List getAlternativeName() { - if (alternativeName == null) { - alternativeName = new ArrayList(); - } - return this.alternativeName; + public List getAlternativeName() + { + if (alternativeName == null) + { + alternativeName = new ArrayList(); + } + return this.alternativeName; } /** * Gets the value of the submittedName property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getSubmittedName().add(newItem);
+     * getSubmittedName().add(newItem);
      * 
* * @@ -155,74 +590,75 @@ public class ProteinType { * * */ - public List getSubmittedName() { - if (submittedName == null) { - submittedName = new ArrayList(); - } - return this.submittedName; + public List getSubmittedName() + { + if (submittedName == null) + { + submittedName = new ArrayList(); + } + return this.submittedName; } /** * Gets the value of the allergenName property. * - * @return - * possible object is - * {@link EvidencedStringType } - * + * @return possible object is {@link EvidencedStringType } + * */ - public EvidencedStringType getAllergenName() { - return allergenName; + public EvidencedStringType getAllergenName() + { + return allergenName; } /** * Sets the value of the allergenName property. * * @param value - * allowed object is - * {@link EvidencedStringType } - * + * allowed object is {@link EvidencedStringType } + * */ - public void setAllergenName(EvidencedStringType value) { - this.allergenName = value; + public void setAllergenName(EvidencedStringType value) + { + this.allergenName = value; } /** * Gets the value of the biotechName property. * - * @return - * possible object is - * {@link EvidencedStringType } - * + * @return possible object is {@link EvidencedStringType } + * */ - public EvidencedStringType getBiotechName() { - return biotechName; + public EvidencedStringType getBiotechName() + { + return biotechName; } /** * Sets the value of the biotechName property. * * @param value - * allowed object is - * {@link EvidencedStringType } - * + * allowed object is {@link EvidencedStringType } + * */ - public void setBiotechName(EvidencedStringType value) { - this.biotechName = value; + public void setBiotechName(EvidencedStringType value) + { + this.biotechName = value; } /** * Gets the value of the cdAntigenName property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getCdAntigenName().add(newItem);
+     * getCdAntigenName().add(newItem);
      * 
* * @@ -232,26 +668,29 @@ public class ProteinType { * * */ - public List getCdAntigenName() { - if (cdAntigenName == null) { - cdAntigenName = new ArrayList(); - } - return this.cdAntigenName; + public List getCdAntigenName() + { + if (cdAntigenName == null) + { + cdAntigenName = new ArrayList(); + } + return this.cdAntigenName; } /** * Gets the value of the innName property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getInnName().add(newItem);
+     * getInnName().add(newItem);
      * 
* * @@ -261,849 +700,472 @@ public class ProteinType { * * */ - public List getInnName() { - if (innName == null) { - innName = new ArrayList(); - } - return this.innName; + public List getInnName() + { + if (innName == null) + { + innName = new ArrayList(); + } + return this.innName; + } + + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType( + name = "", + propOrder = + { "recommendedName", "alternativeName", "submittedName", "allergenName", + "biotechName", "cdAntigenName", "innName" }) + public static class Domain + { + + protected ProteinType.RecommendedName recommendedName; + + protected List alternativeName; + + protected List submittedName; + + protected EvidencedStringType allergenName; + + protected EvidencedStringType biotechName; + + protected List cdAntigenName; + + protected List innName; + + /** + * Gets the value of the recommendedName property. + * + * @return possible object is {@link ProteinType.RecommendedName } + * + */ + public ProteinType.RecommendedName getRecommendedName() + { + return recommendedName; } /** - * Gets the value of the domain property. + * Sets the value of the recommendedName property. + * + * @param value + * allowed object is {@link ProteinType.RecommendedName } + * + */ + public void setRecommendedName(ProteinType.RecommendedName value) + { + this.recommendedName = value; + } + + /** + * Gets the value of the alternativeName property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getDomain().add(newItem);
+     * getAlternativeName().add(newItem);
      * 
* * *

* Objects of the following type(s) are allowed in the list - * {@link ProteinType.Domain } + * {@link ProteinType.AlternativeName } * * */ - public List getDomain() { - if (domain == null) { - domain = new ArrayList(); - } - return this.domain; + public List getAlternativeName() + { + if (alternativeName == null) + { + alternativeName = new ArrayList(); + } + return this.alternativeName; } /** - * Gets the value of the component property. + * Gets the value of the submittedName property. * *

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

* For example, to add a new item, do as follows: + * *

-     *    getComponent().add(newItem);
+     * getSubmittedName().add(newItem);
      * 
* * *

* Objects of the following type(s) are allowed in the list - * {@link ProteinType.Component } + * {@link ProteinType.SubmittedName } * * */ - public List getComponent() { - if (component == null) { - component = new ArrayList(); - } - return this.component; + public List getSubmittedName() + { + if (submittedName == null) + { + submittedName = new ArrayList(); + } + return this.submittedName; } + /** + * Gets the value of the allergenName property. + * + * @return possible object is {@link EvidencedStringType } + * + */ + public EvidencedStringType getAllergenName() + { + return allergenName; + } /** - *

Java class for anonymous complex type. + * Sets the value of the allergenName property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link EvidencedStringType } * - *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
-     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 
+ */ + public void setAllergenName(EvidencedStringType value) + { + this.allergenName = value; + } + + /** + * Gets the value of the biotechName property. * + * @return possible object is {@link EvidencedStringType } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "fullName", - "shortName", - "ecNumber" - }) - public static class AlternativeName { - - protected EvidencedStringType fullName; - protected List shortName; - protected List ecNumber; - - /** - * Gets the value of the fullName property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getFullName() { - return fullName; - } - - /** - * Sets the value of the fullName property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setFullName(EvidencedStringType value) { - this.fullName = value; - } - - /** - * Gets the value of the shortName property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getShortName().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getEcNumber().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getEcNumber() { - if (ecNumber == null) { - ecNumber = new ArrayList(); - } - return this.ecNumber; - } + public EvidencedStringType getBiotechName() + { + return biotechName; + } + /** + * Sets the value of the biotechName property. + * + * @param value + * allowed object is {@link EvidencedStringType } + * + */ + public void setBiotechName(EvidencedStringType value) + { + this.biotechName = value; } + /** + * Gets the value of the cdAntigenName property. + * + *

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

+ * For example, to add a new item, do as follows: + * + *

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

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

Java class for anonymous complex type. + * Gets the value of the innName property. * - *

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

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

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getInnName().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "recommendedName", - "alternativeName", - "submittedName", - "allergenName", - "biotechName", - "cdAntigenName", - "innName" - }) - public static class Component { - - protected ProteinType.RecommendedName recommendedName; - protected List alternativeName; - protected List submittedName; - protected EvidencedStringType allergenName; - protected EvidencedStringType biotechName; - protected List cdAntigenName; - protected List innName; - - /** - * Gets the value of the recommendedName property. - * - * @return - * possible object is - * {@link ProteinType.RecommendedName } - * - */ - public ProteinType.RecommendedName getRecommendedName() { - return recommendedName; - } - - /** - * Sets the value of the recommendedName property. - * - * @param value - * allowed object is - * {@link ProteinType.RecommendedName } - * - */ - public void setRecommendedName(ProteinType.RecommendedName value) { - this.recommendedName = value; - } - - /** - * Gets the value of the alternativeName property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getAlternativeName().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getSubmittedName().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link ProteinType.SubmittedName } - * - * - */ - public List getSubmittedName() { - if (submittedName == null) { - submittedName = new ArrayList(); - } - return this.submittedName; - } - - /** - * Gets the value of the allergenName property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getAllergenName() { - return allergenName; - } - - /** - * Sets the value of the allergenName property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setAllergenName(EvidencedStringType value) { - this.allergenName = value; - } - - /** - * Gets the value of the biotechName property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getBiotechName() { - return biotechName; - } - - /** - * Sets the value of the biotechName property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setBiotechName(EvidencedStringType value) { - this.biotechName = value; - } - - /** - * Gets the value of the cdAntigenName property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getCdAntigenName().add(newItem);
-         * 
- * - * - *

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

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

- * For example, to add a new item, do as follows: - *

-         *    getInnName().add(newItem);
-         * 
- * - * - *

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

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+   *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "fullName", "shortName", "ecNumber" }) + public static class RecommendedName + { + + @XmlElement(required = true) + protected EvidencedStringType fullName; + + protected List shortName; + + protected List ecNumber; + + /** + * Gets the value of the fullName property. + * + * @return possible object is {@link EvidencedStringType } + * + */ + public EvidencedStringType getFullName() + { + return fullName; } + /** + * Sets the value of the fullName property. + * + * @param value + * allowed object is {@link EvidencedStringType } + * + */ + public void setFullName(EvidencedStringType value) + { + this.fullName = value; + } /** - *

Java class for anonymous complex type. + * Gets the value of the shortName property. * - *

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

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

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getShortName().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "recommendedName", - "alternativeName", - "submittedName", - "allergenName", - "biotechName", - "cdAntigenName", - "innName" - }) - public static class Domain { - - protected ProteinType.RecommendedName recommendedName; - protected List alternativeName; - protected List submittedName; - protected EvidencedStringType allergenName; - protected EvidencedStringType biotechName; - protected List cdAntigenName; - protected List innName; - - /** - * Gets the value of the recommendedName property. - * - * @return - * possible object is - * {@link ProteinType.RecommendedName } - * - */ - public ProteinType.RecommendedName getRecommendedName() { - return recommendedName; - } - - /** - * Sets the value of the recommendedName property. - * - * @param value - * allowed object is - * {@link ProteinType.RecommendedName } - * - */ - public void setRecommendedName(ProteinType.RecommendedName value) { - this.recommendedName = value; - } - - /** - * Gets the value of the alternativeName property. - * - *

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

- * For example, to add a new item, do as follows: - *

-         *    getAlternativeName().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link ProteinType.AlternativeName } - * - * - */ - public List getAlternativeName() { - if (alternativeName == null) { - alternativeName = new ArrayList(); - } - return this.alternativeName; - } - - /** - * Gets the value of the submittedName property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the submittedName property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getSubmittedName().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link ProteinType.SubmittedName } - * - * - */ - public List getSubmittedName() { - if (submittedName == null) { - submittedName = new ArrayList(); - } - return this.submittedName; - } - - /** - * Gets the value of the allergenName property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getAllergenName() { - return allergenName; - } - - /** - * Sets the value of the allergenName property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setAllergenName(EvidencedStringType value) { - this.allergenName = value; - } - - /** - * Gets the value of the biotechName property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getBiotechName() { - return biotechName; - } - - /** - * Sets the value of the biotechName property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setBiotechName(EvidencedStringType value) { - this.biotechName = value; - } - - /** - * Gets the value of the cdAntigenName property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the cdAntigenName property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getCdAntigenName().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getCdAntigenName() { - if (cdAntigenName == null) { - cdAntigenName = new ArrayList(); - } - return this.cdAntigenName; - } - - /** - * Gets the value of the innName property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the innName property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getInnName().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getInnName() { - if (innName == null) { - innName = new ArrayList(); - } - return this.innName; - } - + public List getShortName() + { + if (shortName == null) + { + shortName = new ArrayList(); + } + return this.shortName; } - /** - *

Java class for anonymous complex type. + * Gets the value of the ecNumber property. + * + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the ecNumber property. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getEcNumber().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "fullName", - "shortName", - "ecNumber" - }) - public static class RecommendedName { - - @XmlElement(required = true) - protected EvidencedStringType fullName; - protected List shortName; - protected List ecNumber; - - /** - * Gets the value of the fullName property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getFullName() { - return fullName; - } - - /** - * Sets the value of the fullName property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setFullName(EvidencedStringType value) { - this.fullName = value; - } - - /** - * Gets the value of the shortName property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the shortName property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getShortName().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getShortName() { - if (shortName == null) { - shortName = new ArrayList(); - } - return this.shortName; - } - - /** - * Gets the value of the ecNumber property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the ecNumber property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getEcNumber().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getEcNumber() { - if (ecNumber == null) { - ecNumber = new ArrayList(); - } - return this.ecNumber; - } + public List getEcNumber() + { + if (ecNumber == null) + { + ecNumber = new ArrayList(); + } + return this.ecNumber; + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + *

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
+   *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
+   *       </sequence>
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "fullName", "ecNumber" }) + public static class SubmittedName + { + + @XmlElement(required = true) + protected EvidencedStringType fullName; + + protected List ecNumber; + /** + * Gets the value of the fullName property. + * + * @return possible object is {@link EvidencedStringType } + * + */ + public EvidencedStringType getFullName() + { + return fullName; } + /** + * Sets the value of the fullName property. + * + * @param value + * allowed object is {@link EvidencedStringType } + * + */ + public void setFullName(EvidencedStringType value) + { + this.fullName = value; + } /** - *

Java class for anonymous complex type. + * Gets the value of the ecNumber property. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the ecNumber property. + * + *

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
-     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-     *       </sequence>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     * getEcNumber().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "fullName", - "ecNumber" - }) - public static class SubmittedName { - - @XmlElement(required = true) - protected EvidencedStringType fullName; - protected List ecNumber; - - /** - * Gets the value of the fullName property. - * - * @return - * possible object is - * {@link EvidencedStringType } - * - */ - public EvidencedStringType getFullName() { - return fullName; - } - - /** - * Sets the value of the fullName property. - * - * @param value - * allowed object is - * {@link EvidencedStringType } - * - */ - public void setFullName(EvidencedStringType value) { - this.fullName = value; - } - - /** - * Gets the value of the ecNumber property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the ecNumber property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getEcNumber().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getEcNumber() { - if (ecNumber == null) { - ecNumber = new ArrayList(); - } - return this.ecNumber; - } - + public List getEcNumber() + { + if (ecNumber == null) + { + ecNumber = new ArrayList(); + } + return this.ecNumber; } + } + } diff --git a/src/jalview/xml/binding/uniprot/ReactionType.java b/src/jalview/xml/binding/uniprot/ReactionType.java index 8d9d51d..2260842 100644 --- a/src/jalview/xml/binding/uniprot/ReactionType.java +++ b/src/jalview/xml/binding/uniprot/ReactionType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,13 +15,15 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** * Describes a chemical reaction. * - *

Java class for reactionType complex type. + *

+ * Java class for reactionType complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType name="reactionType">
@@ -41,99 +42,103 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "reactionType", propOrder = {
-    "text",
-    "dbReference"
-})
-public class ReactionType {
+@XmlType(name = "reactionType", propOrder = { "text", "dbReference" })
+public class ReactionType
+{
 
-    @XmlElement(required = true)
-    protected String text;
-    @XmlElement(required = true)
-    protected List dbReference;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
+  @XmlElement(required = true)
+  protected String text;
 
-    /**
-     * Gets the value of the text property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getText() {
-        return text;
-    }
+  @XmlElement(required = true)
+  protected List dbReference;
 
-    /**
-     * Sets the value of the text property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setText(String value) {
-        this.text = value;
-    }
+  @XmlAttribute(name = "evidence")
+  protected List evidence;
+
+  /**
+   * Gets the value of the text property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getText()
+  {
+    return text;
+  }
+
+  /**
+   * Sets the value of the text property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setText(String value)
+  {
+    this.text = value;
+  }
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * 

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the dbReference property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getDbReference().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link DbReferenceType } - * - * - */ - public List getDbReference() { - if (dbReference == null) { - dbReference = new ArrayList(); - } - return this.dbReference; + /** + * Gets the value of the dbReference property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the dbReference property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getDbReference().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link DbReferenceType } + * + * + */ + public List getDbReference() + { + if (dbReference == null) + { + dbReference = new ArrayList(); } + return this.dbReference; + } - /** - * Gets the value of the evidence property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the evidence property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; + /** + * Gets the value of the evidence property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the evidence property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getEvidence().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } } diff --git a/src/jalview/xml/binding/uniprot/ReferenceType.java b/src/jalview/xml/binding/uniprot/ReferenceType.java index e5f9fde..2f7daa3 100644 --- a/src/jalview/xml/binding/uniprot/ReferenceType.java +++ b/src/jalview/xml/binding/uniprot/ReferenceType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,14 +15,16 @@ import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlType; - /** - * Describes a citation and a summary of its content. - * Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines. + * Describes a citation and a summary of its content. Equivalent to the flat + * file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines. * - *

Java class for referenceType complex type. + *

+ * Java class for referenceType complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType name="referenceType">
@@ -43,151 +44,156 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "referenceType", propOrder = {
-    "citation",
-    "scope",
-    "source"
-})
-public class ReferenceType {
-
-    @XmlElement(required = true)
-    protected CitationType citation;
-    @XmlElement(required = true)
-    protected List scope;
-    protected SourceDataType source;
-    @XmlAttribute(name = "evidence")
-    protected List evidence;
-    @XmlAttribute(name = "key", required = true)
-    protected String key;
-
-    /**
-     * Gets the value of the citation property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link CitationType }
-     *     
-     */
-    public CitationType getCitation() {
-        return citation;
-    }
+@XmlType(
+  name = "referenceType",
+  propOrder =
+  { "citation", "scope", "source" })
+public class ReferenceType
+{
 
-    /**
-     * Sets the value of the citation property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link CitationType }
-     *     
-     */
-    public void setCitation(CitationType value) {
-        this.citation = value;
-    }
+  @XmlElement(required = true)
+  protected CitationType citation;
 
-    /**
-     * Gets the value of the scope property.
-     * 
-     * 

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the scope property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getScope().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link String } - * - * - */ - public List getScope() { - if (scope == null) { - scope = new ArrayList(); - } - return this.scope; - } + @XmlElement(required = true) + protected List scope; - /** - * Gets the value of the source property. - * - * @return - * possible object is - * {@link SourceDataType } - * - */ - public SourceDataType getSource() { - return source; - } + protected SourceDataType source; - /** - * Sets the value of the source property. - * - * @param value - * allowed object is - * {@link SourceDataType } - * - */ - public void setSource(SourceDataType value) { - this.source = value; - } + @XmlAttribute(name = "evidence") + protected List evidence; - /** - * Gets the value of the evidence property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the evidence property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getEvidence().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + @XmlAttribute(name = "key", required = true) + protected String key; + + /** + * Gets the value of the citation property. + * + * @return possible object is {@link CitationType } + * + */ + public CitationType getCitation() + { + return citation; + } - /** - * Gets the value of the key property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getKey() { - return key; + /** + * Sets the value of the citation property. + * + * @param value + * allowed object is {@link CitationType } + * + */ + public void setCitation(CitationType value) + { + this.citation = value; + } + + /** + * Gets the value of the scope property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the scope property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getScope().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link String } + * + * + */ + public List getScope() + { + if (scope == null) + { + scope = new ArrayList(); } + return this.scope; + } + + /** + * Gets the value of the source property. + * + * @return possible object is {@link SourceDataType } + * + */ + public SourceDataType getSource() + { + return source; + } - /** - * Sets the value of the key property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setKey(String value) { - this.key = value; + /** + * Sets the value of the source property. + * + * @param value + * allowed object is {@link SourceDataType } + * + */ + public void setSource(SourceDataType value) + { + this.source = value; + } + + /** + * Gets the value of the evidence property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the evidence property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getEvidence().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * + */ + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); } + return this.evidence; + } + + /** + * Gets the value of the key property. + * + * @return possible object is {@link String } + * + */ + public String getKey() + { + return key; + } + + /** + * Sets the value of the key property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setKey(String value) + { + this.key = value; + } } diff --git a/src/jalview/xml/binding/uniprot/SequenceType.java b/src/jalview/xml/binding/uniprot/SequenceType.java index 49cd130..42d8c58 100644 --- a/src/jalview/xml/binding/uniprot/SequenceType.java +++ b/src/jalview/xml/binding/uniprot/SequenceType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import javax.xml.bind.annotation.XmlAccessType; @@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlType; import javax.xml.bind.annotation.XmlValue; import javax.xml.datatype.XMLGregorianCalendar; - /** - *

Java class for sequenceType complex type. + *

+ * Java class for sequenceType complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType name="sequenceType">
@@ -48,195 +49,202 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sequenceType", propOrder = {
-    "value"
-})
-public class SequenceType {
-
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "length", required = true)
-    protected int length;
-    @XmlAttribute(name = "mass", required = true)
-    protected int mass;
-    @XmlAttribute(name = "checksum", required = true)
-    protected String checksum;
-    @XmlAttribute(name = "modified", required = true)
-    @XmlSchemaType(name = "date")
-    protected XMLGregorianCalendar modified;
-    @XmlAttribute(name = "version", required = true)
-    protected int version;
-    @XmlAttribute(name = "precursor")
-    protected Boolean precursor;
-    @XmlAttribute(name = "fragment")
-    protected String fragment;
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
-
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
-
-    /**
-     * Gets the value of the length property.
-     * 
-     */
-    public int getLength() {
-        return length;
-    }
-
-    /**
-     * Sets the value of the length property.
-     * 
-     */
-    public void setLength(int value) {
-        this.length = value;
-    }
-
-    /**
-     * Gets the value of the mass property.
-     * 
-     */
-    public int getMass() {
-        return mass;
-    }
-
-    /**
-     * Sets the value of the mass property.
-     * 
-     */
-    public void setMass(int value) {
-        this.mass = value;
-    }
-
-    /**
-     * Gets the value of the checksum property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getChecksum() {
-        return checksum;
-    }
-
-    /**
-     * Sets the value of the checksum property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setChecksum(String value) {
-        this.checksum = value;
-    }
-
-    /**
-     * Gets the value of the modified property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public XMLGregorianCalendar getModified() {
-        return modified;
-    }
-
-    /**
-     * Sets the value of the modified property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link XMLGregorianCalendar }
-     *     
-     */
-    public void setModified(XMLGregorianCalendar value) {
-        this.modified = value;
-    }
-
-    /**
-     * Gets the value of the version property.
-     * 
-     */
-    public int getVersion() {
-        return version;
-    }
-
-    /**
-     * Sets the value of the version property.
-     * 
-     */
-    public void setVersion(int value) {
-        this.version = value;
-    }
-
-    /**
-     * Gets the value of the precursor property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link Boolean }
-     *     
-     */
-    public Boolean isPrecursor() {
-        return precursor;
-    }
-
-    /**
-     * Sets the value of the precursor property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link Boolean }
-     *     
-     */
-    public void setPrecursor(Boolean value) {
-        this.precursor = value;
-    }
-
-    /**
-     * Gets the value of the fragment property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getFragment() {
-        return fragment;
-    }
-
-    /**
-     * Sets the value of the fragment property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setFragment(String value) {
-        this.fragment = value;
-    }
+@XmlType(name = "sequenceType", propOrder = { "value" })
+public class SequenceType
+{
+
+  @XmlValue
+  protected String value;
+
+  @XmlAttribute(name = "length", required = true)
+  protected int length;
+
+  @XmlAttribute(name = "mass", required = true)
+  protected int mass;
+
+  @XmlAttribute(name = "checksum", required = true)
+  protected String checksum;
+
+  @XmlAttribute(name = "modified", required = true)
+  @XmlSchemaType(name = "date")
+  protected XMLGregorianCalendar modified;
+
+  @XmlAttribute(name = "version", required = true)
+  protected int version;
+
+  @XmlAttribute(name = "precursor")
+  protected Boolean precursor;
+
+  @XmlAttribute(name = "fragment")
+  protected String fragment;
+
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
+
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
+
+  /**
+   * Gets the value of the length property.
+   * 
+   */
+  public int getLength()
+  {
+    return length;
+  }
+
+  /**
+   * Sets the value of the length property.
+   * 
+   */
+  public void setLength(int value)
+  {
+    this.length = value;
+  }
+
+  /**
+   * Gets the value of the mass property.
+   * 
+   */
+  public int getMass()
+  {
+    return mass;
+  }
+
+  /**
+   * Sets the value of the mass property.
+   * 
+   */
+  public void setMass(int value)
+  {
+    this.mass = value;
+  }
+
+  /**
+   * Gets the value of the checksum property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getChecksum()
+  {
+    return checksum;
+  }
+
+  /**
+   * Sets the value of the checksum property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setChecksum(String value)
+  {
+    this.checksum = value;
+  }
+
+  /**
+   * Gets the value of the modified property.
+   * 
+   * @return possible object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public XMLGregorianCalendar getModified()
+  {
+    return modified;
+  }
+
+  /**
+   * Sets the value of the modified property.
+   * 
+   * @param value
+   *          allowed object is {@link XMLGregorianCalendar }
+   * 
+   */
+  public void setModified(XMLGregorianCalendar value)
+  {
+    this.modified = value;
+  }
+
+  /**
+   * Gets the value of the version property.
+   * 
+   */
+  public int getVersion()
+  {
+    return version;
+  }
+
+  /**
+   * Sets the value of the version property.
+   * 
+   */
+  public void setVersion(int value)
+  {
+    this.version = value;
+  }
+
+  /**
+   * Gets the value of the precursor property.
+   * 
+   * @return possible object is {@link Boolean }
+   * 
+   */
+  public Boolean isPrecursor()
+  {
+    return precursor;
+  }
+
+  /**
+   * Sets the value of the precursor property.
+   * 
+   * @param value
+   *          allowed object is {@link Boolean }
+   * 
+   */
+  public void setPrecursor(Boolean value)
+  {
+    this.precursor = value;
+  }
+
+  /**
+   * Gets the value of the fragment property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getFragment()
+  {
+    return fragment;
+  }
+
+  /**
+   * Sets the value of the fragment property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setFragment(String value)
+  {
+    this.fragment = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SourceDataType.java b/src/jalview/xml/binding/uniprot/SourceDataType.java
index 9796260..5fa8cd6 100644
--- a/src/jalview/xml/binding/uniprot/SourceDataType.java
+++ b/src/jalview/xml/binding/uniprot/SourceDataType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -18,14 +17,16 @@ import javax.xml.bind.annotation.XmlElements;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
- * Describes the source of the sequence according to the citation.
- *             Equivalent to the flat file RC-line.
+ * Describes the source of the sequence according to the citation. Equivalent to
+ * the flat file RC-line.
  * 
- * 

Java class for sourceDataType complex type. + *

+ * Java class for sourceDataType complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType name="sourceDataType">
@@ -77,385 +78,401 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceDataType", propOrder = {
-    "strainOrPlasmidOrTransposon"
-})
-public class SourceDataType {
-
-    @XmlElements({
-        @XmlElement(name = "strain", type = SourceDataType.Strain.class),
-        @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
-        @XmlElement(name = "transposon", type = SourceDataType.Transposon.class),
-        @XmlElement(name = "tissue", type = SourceDataType.Tissue.class)
-    })
-    protected List strainOrPlasmidOrTransposon;
+@XmlType(
+  name = "sourceDataType",
+  propOrder =
+  { "strainOrPlasmidOrTransposon" })
+public class SourceDataType
+{
+
+  @XmlElements({
+      @XmlElement(name = "strain", type = SourceDataType.Strain.class),
+      @XmlElement(name = "plasmid", type = SourceDataType.Plasmid.class),
+      @XmlElement(
+        name = "transposon",
+        type = SourceDataType.Transposon.class),
+      @XmlElement(name = "tissue", type = SourceDataType.Tissue.class) })
+  protected List strainOrPlasmidOrTransposon;
+
+  /**
+   * Gets the value of the strainOrPlasmidOrTransposon property.
+   * 
+   * 

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the strainOrPlasmidOrTransposon property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getStrainOrPlasmidOrTransposon().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link SourceDataType.Strain } {@link SourceDataType.Plasmid } + * {@link SourceDataType.Transposon } {@link SourceDataType.Tissue } + * + * + */ + public List getStrainOrPlasmidOrTransposon() + { + if (strainOrPlasmidOrTransposon == null) + { + strainOrPlasmidOrTransposon = new ArrayList(); + } + return this.strainOrPlasmidOrTransposon; + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + *

+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "value" }) + public static class Plasmid + { + + @XmlValue + protected String value; + + @XmlAttribute(name = "evidence") + protected List evidence; + + /** + * Gets the value of the value property. + * + * @return possible object is {@link String } + * + */ + public String getValue() + { + return value; + } /** - * Gets the value of the strainOrPlasmidOrTransposon property. + * Sets the value of the value property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setValue(String value) + { + this.value = value; + } + + /** + * Gets the value of the evidence property. * *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the strainOrPlasmidOrTransposon property. + * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the evidence property. * *

* For example, to add a new item, do as follows: + * *

-     *    getStrainOrPlasmidOrTransposon().add(newItem);
+     * getEvidence().add(newItem);
      * 
* * *

- * Objects of the following type(s) are allowed in the list - * {@link SourceDataType.Strain } - * {@link SourceDataType.Plasmid } - * {@link SourceDataType.Transposon } - * {@link SourceDataType.Tissue } + * Objects of the following type(s) are allowed in the list {@link Integer } * * */ - public List getStrainOrPlasmidOrTransposon() { - if (strainOrPlasmidOrTransposon == null) { - strainOrPlasmidOrTransposon = new ArrayList(); - } - return this.strainOrPlasmidOrTransposon; + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); + } + return this.evidence; } + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + *

+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "value" }) + public static class Strain + { + + @XmlValue + protected String value; + + @XmlAttribute(name = "evidence") + protected List evidence; /** - *

Java class for anonymous complex type. + * Gets the value of the value property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link String } * - *

-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
-     * 
+ */ + public String getValue() + { + return value; + } + + /** + * Sets the value of the value property. * + * @param value + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "value" - }) - public static class Plasmid { - - @XmlValue - protected String value; - @XmlAttribute(name = "evidence") - protected List evidence; - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - /** - * Gets the value of the evidence property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the evidence property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getEvidence().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } - + public void setValue(String value) + { + this.value = value; } - /** - *

Java class for anonymous complex type. + * Gets the value of the evidence property. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the evidence property. + * + *

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
+     * getEvidence().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "value" - }) - public static class Strain { - - @XmlValue - protected String value; - @XmlAttribute(name = "evidence") - protected List evidence; - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - /** - * Gets the value of the evidence property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the evidence property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getEvidence().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); + } + return this.evidence; + } + + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + *

+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "value" }) + public static class Tissue + { + + @XmlValue + protected String value; + + @XmlAttribute(name = "evidence") + protected List evidence; + /** + * Gets the value of the value property. + * + * @return possible object is {@link String } + * + */ + public String getValue() + { + return value; } + /** + * Sets the value of the value property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setValue(String value) + { + this.value = value; + } /** - *

Java class for anonymous complex type. + * Gets the value of the evidence property. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the evidence property. + * + *

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
+     * getEvidence().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "value" - }) - public static class Tissue { - - @XmlValue - protected String value; - @XmlAttribute(name = "evidence") - protected List evidence; - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - /** - * Gets the value of the evidence property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the evidence property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getEvidence().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); + } + return this.evidence; + } + } + + /** + *

+ * Java class for anonymous complex type. + * + *

+ * The following schema fragment specifies the expected content contained + * within this class. + * + *

+   * <complexType>
+   *   <simpleContent>
+   *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+   *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
+   *     </extension>
+   *   </simpleContent>
+   * </complexType>
+   * 
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "value" }) + public static class Transposon + { + + @XmlValue + protected String value; + + @XmlAttribute(name = "evidence") + protected List evidence; + + /** + * Gets the value of the value property. + * + * @return possible object is {@link String } + * + */ + public String getValue() + { + return value; } + /** + * Sets the value of the value property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setValue(String value) + { + this.value = value; + } /** - *

Java class for anonymous complex type. + * Gets the value of the evidence property. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * This accessor method returns a reference to the live list, not a + * snapshot. Therefore any modification you make to the returned list will + * be present inside the JAXB object. This is why there is not a + * set method for the evidence property. + * + *

+ * For example, to add a new item, do as follows: * *

-     * <complexType>
-     *   <simpleContent>
-     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-     *     </extension>
-     *   </simpleContent>
-     * </complexType>
+     * getEvidence().add(newItem);
      * 
* * + *

+ * Objects of the following type(s) are allowed in the list {@link Integer } + * + * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "value" - }) - public static class Transposon { - - @XmlValue - protected String value; - @XmlAttribute(name = "evidence") - protected List evidence; - - /** - * Gets the value of the value property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getValue() { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setValue(String value) { - this.value = value; - } - - /** - * Gets the value of the evidence property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the evidence property. - * - *

- * For example, to add a new item, do as follows: - *

-         *    getEvidence().add(newItem);
-         * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Integer } - * - * - */ - public List getEvidence() { - if (evidence == null) { - evidence = new ArrayList(); - } - return this.evidence; - } - + public List getEvidence() + { + if (evidence == null) + { + evidence = new ArrayList(); + } + return this.evidence; } + } + } diff --git a/src/jalview/xml/binding/uniprot/SourceType.java b/src/jalview/xml/binding/uniprot/SourceType.java index 9293a64..4500112 100644 --- a/src/jalview/xml/binding/uniprot/SourceType.java +++ b/src/jalview/xml/binding/uniprot/SourceType.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.math.BigInteger; @@ -14,13 +13,17 @@ import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlType; - /** - * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry). + * Describes the source of the data using a database cross-reference (or a 'ref' + * attribute when the source cannot be found in a public data source, such as + * PubMed, and is cited only within the UniProtKB entry). * - *

Java class for sourceType complex type. + *

+ * Java class for sourceType complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType name="sourceType">
@@ -38,61 +41,59 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "sourceType", propOrder = {
-    "dbReference"
-})
-public class SourceType {
+@XmlType(name = "sourceType", propOrder = { "dbReference" })
+public class SourceType
+{
+
+  protected DbReferenceType dbReference;
 
-    protected DbReferenceType dbReference;
-    @XmlAttribute(name = "ref")
-    protected BigInteger ref;
+  @XmlAttribute(name = "ref")
+  protected BigInteger ref;
 
-    /**
-     * Gets the value of the dbReference property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public DbReferenceType getDbReference() {
-        return dbReference;
-    }
+  /**
+   * Gets the value of the dbReference property.
+   * 
+   * @return possible object is {@link DbReferenceType }
+   * 
+   */
+  public DbReferenceType getDbReference()
+  {
+    return dbReference;
+  }
 
-    /**
-     * Sets the value of the dbReference property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link DbReferenceType }
-     *     
-     */
-    public void setDbReference(DbReferenceType value) {
-        this.dbReference = value;
-    }
+  /**
+   * Sets the value of the dbReference property.
+   * 
+   * @param value
+   *          allowed object is {@link DbReferenceType }
+   * 
+   */
+  public void setDbReference(DbReferenceType value)
+  {
+    this.dbReference = value;
+  }
 
-    /**
-     * Gets the value of the ref property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link BigInteger }
-     *     
-     */
-    public BigInteger getRef() {
-        return ref;
-    }
+  /**
+   * Gets the value of the ref property.
+   * 
+   * @return possible object is {@link BigInteger }
+   * 
+   */
+  public BigInteger getRef()
+  {
+    return ref;
+  }
 
-    /**
-     * Sets the value of the ref property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link BigInteger }
-     *     
-     */
-    public void setRef(BigInteger value) {
-        this.ref = value;
-    }
+  /**
+   * Sets the value of the ref property.
+   * 
+   * @param value
+   *          allowed object is {@link BigInteger }
+   * 
+   */
+  public void setRef(BigInteger value)
+  {
+    this.ref = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/StatusType.java b/src/jalview/xml/binding/uniprot/StatusType.java
index dd3308b..551c67a 100644
--- a/src/jalview/xml/binding/uniprot/StatusType.java
+++ b/src/jalview/xml/binding/uniprot/StatusType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,13 +13,15 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 import javax.xml.bind.annotation.XmlValue;
 
-
 /**
  * Indicates whether the name of a plasmid is known or unknown.
  * 
- * 

Java class for statusType complex type. + *

+ * Java class for statusType complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType name="statusType">
@@ -42,66 +43,67 @@ import javax.xml.bind.annotation.XmlValue;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "statusType", propOrder = {
-    "value"
-})
-public class StatusType {
+@XmlType(name = "statusType", propOrder = { "value" })
+public class StatusType
+{
 
-    @XmlValue
-    protected String value;
-    @XmlAttribute(name = "status")
-    protected String status;
+  @XmlValue
+  protected String value;
 
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getValue() {
-        return value;
-    }
+  @XmlAttribute(name = "status")
+  protected String status;
 
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setValue(String value) {
-        this.value = value;
-    }
+  /**
+   * Gets the value of the value property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getValue()
+  {
+    return value;
+  }
 
-    /**
-     * Gets the value of the status property.
-     * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
-     */
-    public String getStatus() {
-        if (status == null) {
-            return "known";
-        } else {
-            return status;
-        }
-    }
+  /**
+   * Sets the value of the value property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setValue(String value)
+  {
+    this.value = value;
+  }
 
-    /**
-     * Sets the value of the status property.
-     * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setStatus(String value) {
-        this.status = value;
+  /**
+   * Gets the value of the status property.
+   * 
+   * @return possible object is {@link String }
+   * 
+   */
+  public String getStatus()
+  {
+    if (status == null)
+    {
+      return "known";
+    }
+    else
+    {
+      return status;
     }
+  }
+
+  /**
+   * Sets the value of the status property.
+   * 
+   * @param value
+   *          allowed object is {@link String }
+   * 
+   */
+  public void setStatus(String value)
+  {
+    this.status = value;
+  }
 
 }
diff --git a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
index 97522e2..c9dbdf8 100644
--- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
+++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.03.17 at 05:31:46 PM GMT 
 //
 
-
 package jalview.xml.binding.uniprot;
 
 import java.util.ArrayList;
@@ -15,13 +14,16 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
-
 /**
- * Describes the subcellular location and optionally the topology and orientation of a molecule.
+ * Describes the subcellular location and optionally the topology and
+ * orientation of a molecule.
  * 
- * 

Java class for subcellularLocationType complex type. + *

+ * Java class for subcellularLocationType complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType name="subcellularLocationType">
@@ -40,103 +42,114 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "subcellularLocationType", propOrder = {
-    "location",
-    "topology",
-    "orientation"
-})
-public class SubcellularLocationType {
+@XmlType(
+  name = "subcellularLocationType",
+  propOrder =
+  { "location", "topology", "orientation" })
+public class SubcellularLocationType
+{
+
+  @XmlElement(required = true)
+  protected List location;
+
+  protected List topology;
 
-    @XmlElement(required = true)
-    protected List location;
-    protected List topology;
-    protected List orientation;
+  protected List orientation;
 
-    /**
-     * Gets the value of the location property.
-     * 
-     * 

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the location property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getLocation().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getLocation() { - if (location == null) { - location = new ArrayList(); - } - return this.location; + /** + * Gets the value of the location property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the location property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getLocation().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * + */ + public List getLocation() + { + if (location == null) + { + location = new ArrayList(); } + return this.location; + } - /** - * Gets the value of the topology property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the topology property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getTopology().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getTopology() { - if (topology == null) { - topology = new ArrayList(); - } - return this.topology; + /** + * Gets the value of the topology property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the topology property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getTopology().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * + */ + public List getTopology() + { + if (topology == null) + { + topology = new ArrayList(); } + return this.topology; + } - /** - * Gets the value of the orientation property. - * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the orientation property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getOrientation().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link EvidencedStringType } - * - * - */ - public List getOrientation() { - if (orientation == null) { - orientation = new ArrayList(); - } - return this.orientation; + /** + * Gets the value of the orientation property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the orientation property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getOrientation().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link EvidencedStringType } + * + * + */ + public List getOrientation() + { + if (orientation == null) + { + orientation = new ArrayList(); } + return this.orientation; + } } diff --git a/src/jalview/xml/binding/uniprot/Uniprot.java b/src/jalview/xml/binding/uniprot/Uniprot.java index 14f96df..a2f8c6b 100644 --- a/src/jalview/xml/binding/uniprot/Uniprot.java +++ b/src/jalview/xml/binding/uniprot/Uniprot.java @@ -5,7 +5,6 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // - package jalview.xml.binding.uniprot; import java.util.ArrayList; @@ -16,11 +15,13 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; - /** - *

Java class for anonymous complex type. + *

+ * Java class for anonymous complex type. * - *

The following schema fragment specifies the expected content contained within this class. + *

+ * The following schema fragment specifies the expected content contained within + * this class. * *

  * <complexType>
@@ -38,68 +39,68 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = {
-    "entry",
-    "copyright"
-})
+@XmlType(name = "", propOrder = { "entry", "copyright" })
 @XmlRootElement(name = "uniprot")
-public class Uniprot {
+public class Uniprot
+{
 
-    @XmlElement(required = true)
-    protected List entry;
-    protected String copyright;
+  @XmlElement(required = true)
+  protected List entry;
 
-    /**
-     * Gets the value of the entry property.
-     * 
-     * 

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the entry property. - * - *

- * For example, to add a new item, do as follows: - *

-     *    getEntry().add(newItem);
-     * 
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Entry } - * - * - */ - public List getEntry() { - if (entry == null) { - entry = new ArrayList(); - } - return this.entry; - } + protected String copyright; - /** - * Gets the value of the copyright property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getCopyright() { - return copyright; + /** + * Gets the value of the entry property. + * + *

+ * This accessor method returns a reference to the live list, not a snapshot. + * Therefore any modification you make to the returned list will be present + * inside the JAXB object. This is why there is not a set method + * for the entry property. + * + *

+ * For example, to add a new item, do as follows: + * + *

+   * getEntry().add(newItem);
+   * 
+ * + * + *

+ * Objects of the following type(s) are allowed in the list {@link Entry } + * + * + */ + public List getEntry() + { + if (entry == null) + { + entry = new ArrayList(); } + return this.entry; + } - /** - * Sets the value of the copyright property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setCopyright(String value) { - this.copyright = value; - } + /** + * Gets the value of the copyright property. + * + * @return possible object is {@link String } + * + */ + public String getCopyright() + { + return copyright; + } + + /** + * Sets the value of the copyright property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setCopyright(String value) + { + this.copyright = value; + } } diff --git a/src/jalview/xml/binding/uniprot/package-info.java b/src/jalview/xml/binding/uniprot/package-info.java index a7bc67c..0b60eaa 100644 --- a/src/jalview/xml/binding/uniprot/package-info.java +++ b/src/jalview/xml/binding/uniprot/package-info.java @@ -5,5 +5,7 @@ // Generated on: 2023.03.17 at 05:31:46 PM GMT // -@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) +@javax.xml.bind.annotation.XmlSchema( + namespace = "http://uniprot.org/uniprot", + elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) package jalview.xml.binding.uniprot; diff --git a/src/mc_view/PDBChain.java b/src/mc_view/PDBChain.java index 6d02630..5b209d0 100755 --- a/src/mc_view/PDBChain.java +++ b/src/mc_view/PDBChain.java @@ -717,8 +717,8 @@ public class PDBChain // Useful for debugging mappings - adds annotation for mapped position float min = -1, max = 0; Annotation[] an = new Annotation[sq.getEnd() - sq.getStart() + 1]; - for (int i = sq.getStart(), j = sq.getEnd(), - k = 0; i <= j; i++, k++) + for (int i = sq.getStart(), j = sq + .getEnd(), k = 0; i <= j; i++, k++) { int prn = mapping.getPDBResNum(k + 1); diff --git a/test/jalview/analysis/AlignmentUtilsTests.java b/test/jalview/analysis/AlignmentUtilsTests.java index 4baa384..c526fa1 100644 --- a/test/jalview/analysis/AlignmentUtilsTests.java +++ b/test/jalview/analysis/AlignmentUtilsTests.java @@ -2630,7 +2630,8 @@ public class AlignmentUtilsTests assertNotNull( "No contact matrix recovered after reference annotation transfer", cl); - // semantics of sequence associated contact list is slightly tricky - column 3 in alignment should have data + // semantics of sequence associated contact list is slightly tricky - column + // 3 in alignment should have data cl = al.getContactListFor(alan, 3); assertNotNull( "Contact matrix should have data for last position in sequence", diff --git a/test/jalview/analysis/AverageDistanceEngineTest.java b/test/jalview/analysis/AverageDistanceEngineTest.java index 6d9ab50..f7688b5 100644 --- a/test/jalview/analysis/AverageDistanceEngineTest.java +++ b/test/jalview/analysis/AverageDistanceEngineTest.java @@ -32,66 +32,78 @@ import jalview.ws.datamodel.alphafold.PAEContactMatrix; public class AverageDistanceEngineTest { - @BeforeClass(alwaysRun = true) - public void setUpJvOptionPane() + @BeforeClass(alwaysRun = true) + public void setUpJvOptionPane() + { + JvOptionPane.setInteractiveMode(false); + JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + } + + @BeforeMethod(alwaysRun = true) + public void loadProperties() + { + Cache.loadProperties("test/jalview/bin/TestProps.jvprops"); + } + + @Test + public void testUPGMAEngine() throws Exception + { + AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded( + "examples/test_fab41.result/sample.a3m", DataSourceType.FILE); + AlignmentI seqs = af.getViewport().getAlignment(); + SequenceI target = seqs.getSequenceAt(0); + File testPAE = new File( + "examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json"); + List pae_obj = (List) Platform + .parseJSON(new FileInputStream(testPAE)); + if (pae_obj == null) { - JvOptionPane.setInteractiveMode(false); - JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION); + Assert.fail("JSON PAE file did not parse properly."); } + ContactMatrixI matrix = new PAEContactMatrix(target, + (Map) pae_obj.get(0)); + AlignmentAnnotation aa = target.addContactList(matrix); + System.out.println("Matrix has max=" + matrix.getMax() + " and min=" + + matrix.getMin()); + long start = System.currentTimeMillis(); + AverageDistanceEngine clusterer = new AverageDistanceEngine( + af.getViewport(), null, matrix); + System.out.println("built a tree in " + + (System.currentTimeMillis() - start) * 0.001 + " seconds."); + StringBuffer sb = new StringBuffer(); + System.out.println("Newick string\n" + + new jalview.io.NewickFile(clusterer.getTopNode(), true, true) + .print()); - @BeforeMethod(alwaysRun = true) - public void loadProperties() + double height = clusterer.findHeight(clusterer.getTopNode()); + // compute height fraction to cut + // PAE matrixes are absolute measure in angstrom, so + // cluster all regions within threshold (e.g. 2A) - if height above + // threshold. Otherwise all nodes are in one cluster + double thr = .2; + List groups; + if (height > thr) { - Cache.loadProperties("test/jalview/bin/TestProps.jvprops"); + float cut = (float) (thr / height); + System.out.println("Threshold " + cut + " for height=" + height); + groups = clusterer.groupNodes(cut); } - @Test - public void testUPGMAEngine() throws Exception + else { - AlignFrame af = new FileLoader(false).LoadFileWaitTillLoaded("examples/test_fab41.result/sample.a3m",DataSourceType.FILE); - AlignmentI seqs = af.getViewport().getAlignment(); - SequenceI target = seqs.getSequenceAt(0); - File testPAE = new File("examples/test_fab41.result/test_fab41_predicted_aligned_error_v1.json"); - List pae_obj = (List) Platform.parseJSON(new FileInputStream(testPAE)); - if (pae_obj == null) - { - Assert.fail("JSON PAE file did not parse properly."); - } - ContactMatrixI matrix = new PAEContactMatrix(target, - (Map) pae_obj.get(0)); - AlignmentAnnotation aa = target.addContactList(matrix); - System.out.println("Matrix has max="+matrix.getMax()+" and min="+matrix.getMin()); - long start = System.currentTimeMillis(); - AverageDistanceEngine clusterer = new AverageDistanceEngine(af.getViewport(), null, matrix); - System.out.println("built a tree in "+(System.currentTimeMillis()-start)*0.001+" seconds."); - StringBuffer sb = new StringBuffer(); - System.out.println("Newick string\n"+ new jalview.io.NewickFile(clusterer.getTopNode(),true,true).print()); - - double height = clusterer.findHeight(clusterer.getTopNode()); - // compute height fraction to cut - // PAE matrixes are absolute measure in angstrom, so - // cluster all regions within threshold (e.g. 2A) - if height above threshold. Otherwise all nodes are in one cluster - double thr=.2; - List groups; - if (height>thr) - { - float cut = (float) (thr/height); - System.out.println("Threshold "+cut+" for height="+height); - groups = clusterer.groupNodes(cut); - } else{ - groups=new ArrayList(); - groups.add(clusterer.getTopNode()); - } - int n=1; - for (BinaryNode root:groups) + groups = new ArrayList(); + groups.add(clusterer.getTopNode()); + } + int n = 1; + for (BinaryNode root : groups) + { + System.out.println("Cluster " + n++); + for (BinaryNode leaf : clusterer.findLeaves(root)) { - System.out.println("Cluster "+n++); - for (BinaryNode leaf:clusterer.findLeaves(root)) - { - System.out.print(" "+leaf.getName()); - } - System.out.println("\\"); + System.out.print(" " + leaf.getName()); } - + System.out.println("\\"); } + } + } diff --git a/test/jalview/datamodel/AlignmentTest.java b/test/jalview/datamodel/AlignmentTest.java index 92db223..1c27420 100644 --- a/test/jalview/datamodel/AlignmentTest.java +++ b/test/jalview/datamodel/AlignmentTest.java @@ -1591,7 +1591,8 @@ public class AlignmentTest // ? } - @Test(groups = {"Functional"}) + + @Test(groups = { "Functional" }) public void testEquals() { SequenceI seq1 = new Sequence("seq1", "ABCDEF--"); @@ -1599,6 +1600,6 @@ public class AlignmentTest SequenceI seq3 = new Sequence("seq2", "-PQR"); AlignmentI a = new Alignment(new SequenceI[] { seq1, seq2, seq3 }); a.setDataset(null); - assertEquals(a.getDataset(),a.getDataset()); + assertEquals(a.getDataset(), a.getDataset()); } } diff --git a/test/jalview/datamodel/ContactRangeTest.java b/test/jalview/datamodel/ContactRangeTest.java index 431834c..8bde11e 100644 --- a/test/jalview/datamodel/ContactRangeTest.java +++ b/test/jalview/datamodel/ContactRangeTest.java @@ -3,13 +3,14 @@ package jalview.datamodel; import org.testng.Assert; import org.testng.annotations.Test; -public class ContactRangeTest { +public class ContactRangeTest +{ @Test public void testContactRangeBean() { ContactRange cr = new ContactRange(); - cr.update(5, 15, 6, 0.2, 12, 1.5,3.7); + cr.update(5, 15, 6, 0.2, 12, 1.5, 3.7); Assert.assertEquals(5, cr.getFrom_column()); Assert.assertEquals(15, cr.getTo_column()); Assert.assertEquals(6, cr.getMinPos()); diff --git a/test/jalview/gui/AlignmentPanelTest.java b/test/jalview/gui/AlignmentPanelTest.java index 2d7e3dc..c1896bc 100644 --- a/test/jalview/gui/AlignmentPanelTest.java +++ b/test/jalview/gui/AlignmentPanelTest.java @@ -291,41 +291,43 @@ public class AlignmentPanelTest Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString()); assertEquals(115, af.alignPanel.getVisibleIdWidth(false)); } - + @Test(groups = "Functional") public void testSetOverviewTitle() { OverviewPanel ov1 = this.af.openOverviewPanel(true); String alignFrameTitle = af.getTitle(); assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle); - + /* * on New View, existing overview should get " Original" added to title * and new view's overview should get " View 1" added */ af.newView_actionPerformed(null); - assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original"); + assertEquals(ov1.getTitle(), + "Overview " + alignFrameTitle + " Original"); OverviewPanel ov2 = this.af.openOverviewPanel(true); assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1"); } - + @Test(groups = "Functional") public void testSetOverviewTitle_automaticOverview() { - Cache.setProperty("SHOW_OVERVIEW", "true"); + Cache.setProperty("SHOW_OVERVIEW", "true"); AlignFrame alignFrame = new FileLoader().LoadFileWaitTillLoaded( "examples/uniref50.fa", DataSourceType.FILE); OverviewPanel ov1 = alignFrame.alignPanel.getOverviewPanel(); assertNotNull(ov1); String alignFrameTitle = alignFrame.getTitle(); assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle); - + /* * on New View, existing overview should get " Original" added to title * and new view's automatic overview should have " View 1" added */ alignFrame.newView_actionPerformed(null); - assertEquals(ov1.getTitle(), "Overview " + alignFrameTitle + " Original"); + assertEquals(ov1.getTitle(), + "Overview " + alignFrameTitle + " Original"); OverviewPanel ov2 = alignFrame.alignPanel.getOverviewPanel(); assertNotNull(ov2); assertEquals(ov2.getTitle(), "Overview " + alignFrameTitle + " View 1"); diff --git a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java index 16f4b7e..c21add1 100644 --- a/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java +++ b/test/jalview/gui/structurechooser/StructureChooserQuerySourceTest.java @@ -250,8 +250,7 @@ public class StructureChooserQuerySourceTest } @SuppressWarnings("deprecation") - @Test(groups = - { "Functional" }) + @Test(groups = { "Functional" }) public void buildPDBQueryTest() { System.out.println("seq >>>> " + seq); @@ -299,8 +298,7 @@ public class StructureChooserQuerySourceTest } @SuppressWarnings("deprecation") - @Test(groups = - { "Functional" }) + @Test(groups = { "Functional" }) public void buildThreeDBQueryTest() { System.out.println("seq >>>> " + upSeq); diff --git a/test/jalview/io/CrossRef2xmlTests.java b/test/jalview/io/CrossRef2xmlTests.java index 0189ef2..c46477a 100644 --- a/test/jalview/io/CrossRef2xmlTests.java +++ b/test/jalview/io/CrossRef2xmlTests.java @@ -418,7 +418,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase cra_views2.add(af2.getViewport().getAlignPanel()); cra_views2.add(((jalview.gui.AlignViewport) af2 .getViewport().getCodingComplement()) - .getAlignPanel()); + .getAlignPanel()); } else @@ -426,7 +426,7 @@ public class CrossRef2xmlTests extends Jalview2xmlBase // bottom view, then top cra_views2.add(((jalview.gui.AlignViewport) af2 .getViewport().getCodingComplement()) - .getAlignPanel()); + .getAlignPanel()); cra_views2.add(af2.getViewport().getAlignPanel()); } Assert.assertEquals(cra_views2.size(), 2); diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java index 6b2982d..10f368a 100644 --- a/test/jalview/io/StockholmFileTest.java +++ b/test/jalview/io/StockholmFileTest.java @@ -136,27 +136,30 @@ public class StockholmFileTest "Couldn't find Uniprot DBRef on re-imported sequence."); } + @Test(groups = { "Functional" }) public void descriptionLineOutput() throws Exception { // quick test that sequence description is exported & reimported SequenceI sq = new Sequence("FER2_SPIOL", "AASSDDDFFF"); - String expected_descr="This is a description !@&^%@£@"; + String expected_descr = "This is a description !@&^%@£@"; sq.setDescription(expected_descr); AppletFormatAdapter af = new AppletFormatAdapter(); String toStockholm = af.formatSequences(FileFormat.Stockholm, new Alignment(new SequenceI[] { sq }), false); System.out.println(toStockholm); - + // bleh - java.util.Regex sucks - assertTrue(toStockholm.contains(expected_descr),"Couldn't locate expected description srting in generated Stockholm file."); - + assertTrue(toStockholm.contains(expected_descr), + "Couldn't locate expected description srting in generated Stockholm file."); + AlignmentI fromStockholm = af.readFile(toStockholm, DataSourceType.PASTE, FileFormat.Stockholm); SequenceI importedSeq = fromStockholm.getSequenceAt(0); - assertEquals( "Description did not get reimported.",expected_descr,importedSeq.getDescription()); + assertEquals("Description did not get reimported.", expected_descr, + importedSeq.getDescription()); } /** diff --git a/test/jalview/project/Jalview2xmlTests.java b/test/jalview/project/Jalview2xmlTests.java index af52eda..d74cd31 100644 --- a/test/jalview/project/Jalview2xmlTests.java +++ b/test/jalview/project/Jalview2xmlTests.java @@ -245,9 +245,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase boolean diffseqcols = false, diffgseqcols = false; SequenceI[] sqs = af.getViewport().getAlignment().getSequencesArray(); - for (int p = 0, - pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { if (_rcs.findColour(sqs[0].getCharAt(p), p, sqs[0], null, 0f) != _rcs .findColour(sqs[5].getCharAt(p), p, sqs[5], null, 0f)) @@ -266,9 +265,8 @@ public class Jalview2xmlTests extends Jalview2xmlBase assertTrue(__rcs.isSeqAssociated(), "Group Annotation colourscheme wasn't sequence associated"); - for (int p = 0, - pSize = af.getViewport().getAlignment().getWidth(); p < pSize - && (!diffseqcols || !diffgseqcols); p++) + for (int p = 0, pSize = af.getViewport().getAlignment() + .getWidth(); p < pSize && (!diffseqcols || !diffgseqcols); p++) { if (_rgcs.findColour(sqs[1].getCharAt(p), p, sqs[1], null, 0f) != _rgcs.findColour(sqs[2].getCharAt(p), p, sqs[2], null, diff --git a/test/jalview/renderer/OverviewRendererTest.java b/test/jalview/renderer/OverviewRendererTest.java index cdb69e3..829eec5 100644 --- a/test/jalview/renderer/OverviewRendererTest.java +++ b/test/jalview/renderer/OverviewRendererTest.java @@ -47,8 +47,8 @@ public class OverviewRendererTest public void testGetColumnColourFromSequence() { // gapColour, residueColour, hiddenColour - OverviewResColourFinder cf = new OverviewResColourFinder( - Color.PINK, Color.white, Color.green); + OverviewResColourFinder cf = new OverviewResColourFinder(Color.PINK, + Color.white, Color.green); Sequence seq1 = new Sequence("seq1", "PQ-RL-"); Sequence seq2 = new Sequence("seq2", "FVE"); AlignmentI al = new Alignment(new SequenceI[] { seq1, seq2 }); diff --git a/test/jalview/renderer/OverviewResColourFinderTest.java b/test/jalview/renderer/OverviewResColourFinderTest.java index 028777e..1c9daea 100644 --- a/test/jalview/renderer/OverviewResColourFinderTest.java +++ b/test/jalview/renderer/OverviewResColourFinderTest.java @@ -186,7 +186,8 @@ public class OverviewResColourFinderTest av.getResidueShading(), groups, seq, 2, null)); // use legacy colouring - rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red); + rcf = new OverviewResColourFinder(Color.white, Color.lightGray, + Color.red); // G in group specified as magenta in Zappo assertEquals(Color.magenta, rcf.getResidueColour(false, @@ -237,7 +238,8 @@ public class OverviewResColourFinderTest assertEquals(OverviewCanvas.OVERVIEW_DEFAULT_GAP, c); // legacy colouring set explicitly via constructor - rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red); + rcf = new OverviewResColourFinder(Color.white, Color.lightGray, + Color.red); shader = new ResidueShader(); // residues light gray @@ -273,7 +275,8 @@ public class OverviewResColourFinderTest assertEquals(Color.blue, c); // legacy colouring with colour scheme - rcf = new OverviewResColourFinder(Color.white, Color.lightGray, Color.red); + rcf = new OverviewResColourFinder(Color.white, Color.lightGray, + Color.red); // M residue pink c = rcf.getBoxColour(shader, seq, 0); diff --git a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java index 637bbf4..3d8313d 100644 --- a/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java +++ b/test/jalview/renderer/seqfeatures/FeatureColourFinderTest.java @@ -169,7 +169,8 @@ public class FeatureColourFinderTest @Test(groups = "Functional") public void testFindFeatureColour_nestedFeatures() { - SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120, 0f, null); + SequenceFeature sf1 = new SequenceFeature("domain", "peptide", 1, 120, + 0f, null); seq.addSequenceFeature(sf1); SequenceFeature sf2 = new SequenceFeature("domain", "binding", 10, 20, 0f, null);