*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.beans.PropertyChangeEvent;
import java.io.File;
import java.io.FileWriter;
+import java.io.IOException;
import java.io.PrintWriter;
import java.net.URL;
import java.util.ArrayList;
import jalview.schemes.ColourSchemes;
import jalview.schemes.ResidueColourScheme;
import jalview.schemes.TCoffeeColourScheme;
+import jalview.util.HttpUtils;
import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
*/
void init()
{
-// setBackground(Color.white); // BH 2019
-
+ // setBackground(Color.white); // BH 2019
+
if (!Jalview.isHeadlessMode())
{
progressBar = new ProgressBar(this.statusPanel, this.statusBar);
}
}
});
- if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ if (Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("devel") > -1
- || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase()
+ || Cache.getDefault("VERSION", "DEVELOPMENT").toLowerCase(Locale.ROOT)
.indexOf("test") > -1)
{
formatMenu.add(vsel);
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, 1);
+ alignPanel.getSeqPanel().moveCursor(0, 1, evt.isShiftDown());
}
break;
}
if (viewport.cursorMode)
{
- alignPanel.getSeqPanel().moveCursor(0, -1);
+ alignPanel.getSeqPanel().moveCursor(0, -1,evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(-1, 0);
+ alignPanel.getSeqPanel().moveCursor(-1, 0, evt.isShiftDown());
}
break;
}
else
{
- alignPanel.getSeqPanel().moveCursor(1, 0);
+ alignPanel.getSeqPanel().moveCursor(1, 0, evt.isShiftDown());
}
break;
Desktop.instance.closeAssociatedWindows();
FileLoader loader = new FileLoader();
- DataSourceType protocol = fileName.startsWith("http:")
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(fileName)
? DataSourceType.URL
: DataSourceType.FILE;
loader.LoadFile(viewport, fileName, protocol, currentFileFormat);
if (fileObject == null)
{
- DataSourceType protocol = (fileName.startsWith("http:")
- ? DataSourceType.URL
- : DataSourceType.FILE);
+ DataSourceType protocol = HttpUtils.startsWithHttpOrHttps(
+ fileName) ? DataSourceType.URL : DataSourceType.FILE;
newframe = loader.LoadFileWaitTillLoaded(fileName, protocol,
currentFileFormat);
}
public void save_actionPerformed(ActionEvent e)
{
if (fileName == null || (currentFileFormat == null)
- || fileName.startsWith("http"))
+ || HttpUtils.startsWithHttpOrHttps(fileName))
{
saveAs_actionPerformed();
}
if (!lastSaveSuccessful)
{
- JvOptionPane.showInternalMessageDialog(this, MessageManager
- .formatMessage("label.couldnt_save_file", new Object[]
- { lastFilenameSaved }),
- MessageManager.getString("label.error_saving_file"),
- JvOptionPane.WARNING_MESSAGE);
+ if (!Platform.isHeadless())
+ {
+ JvOptionPane.showInternalMessageDialog(this, MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }),
+ MessageManager.getString("label.error_saving_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ else
+ {
+ Cache.log.error(MessageManager
+ .formatMessage("label.couldnt_save_file", new Object[]
+ { lastFilenameSaved }));
+ }
}
else
{
String shortName = title;
if (shortName.indexOf(File.separatorChar) > -1)
{
- shortName = shortName.substring(
- shortName.lastIndexOf(File.separatorChar) + 1);
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
}
- lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file, shortName);
-
+ lastSaveSuccessful = new Jalview2XML().saveAlignment(this, file,
+ shortName);
+
statusBar.setText(MessageManager.formatMessage(
"label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format }));
-
+ { file, format }));
+
return;
}
{
// create backupfiles object and get new temp filename destination
boolean doBackup = BackupFiles.getEnabled();
- BackupFiles backupfiles = doBackup ? new BackupFiles(file) : null;
+ BackupFiles backupfiles = null;
+ if (doBackup)
+ {
+ Cache.log.trace(
+ "ALIGNFRAME making backupfiles object for " + file);
+ backupfiles = new BackupFiles(file);
+ }
try
{
- String tempFilePath = doBackup ? backupfiles.getTempFilePath() : file;
- PrintWriter out = new PrintWriter(
- new FileWriter(tempFilePath));
+ String tempFilePath = doBackup ? backupfiles.getTempFilePath()
+ : file;
+ Cache.log.trace("ALIGNFRAME setting PrintWriter");
+ PrintWriter out = new PrintWriter(new FileWriter(tempFilePath));
+
+ if (backupfiles != null)
+ {
+ Cache.log.trace("ALIGNFRAME about to write to temp file "
+ + backupfiles.getTempFilePath());
+ }
out.print(output);
+ Cache.log.trace("ALIGNFRAME about to close file");
out.close();
+ Cache.log.trace("ALIGNFRAME closed file");
AlignFrame.this.setTitle(file);
statusBar.setText(MessageManager.formatMessage(
- "label.successfully_saved_to_file_in_format", new Object[]
- { fileName, format.getName() }));
+ "label.successfully_saved_to_file_in_format",
+ new Object[]
+ { fileName, format.getName() }));
lastSaveSuccessful = true;
+ } catch (IOException e)
+ {
+ lastSaveSuccessful = false;
+ Cache.log.error(
+ "ALIGNFRAME Something happened writing the temp file");
+ Cache.log.error(e.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(e));
} catch (Exception ex)
{
lastSaveSuccessful = false;
- ex.printStackTrace();
+ Cache.log.error(
+ "ALIGNFRAME Something unexpected happened writing the temp file");
+ Cache.log.error(ex.getMessage());
+ Cache.log.debug(Cache.getStackTraceString(ex));
}
if (doBackup)
{
backupfiles.setWriteSuccess(lastSaveSuccessful);
+ Cache.log.debug("ALIGNFRAME writing temp file was "
+ + (lastSaveSuccessful ? "" : "NOT ") + "successful");
// do the backup file roll and rename the temp file to actual file
+ Cache.log.trace(
+ "ALIGNFRAME about to rollBackupsAndRenameTempFile");
lastSaveSuccessful = backupfiles.rollBackupsAndRenameTempFile();
+ Cache.log.debug(
+ "ALIGNFRAME performed rollBackupsAndRenameTempFile "
+ + (lastSaveSuccessful ? "" : "un")
+ + "successfully");
}
}
}
final JalviewFileChooser chooser = new JalviewFileChooser(
jalview.bin.Cache.getProperty("LAST_DIRECTORY"));
chooser.setFileView(new JalviewFileView());
- String tooltip = MessageManager.getString("label.load_jalview_annotations");
+ String tooltip = MessageManager
+ .getString("label.load_jalview_annotations");
chooser.setDialogTitle(tooltip);
chooser.setToolTipText(tooltip);
chooser.setResponseHandler(0, new Runnable()
}
/**
- * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection or the sequence under cursor in keyboard mode
+ * Calls AlignmentI.moveSelectedSequencesByOne with current sequence selection
+ * or the sequence under cursor in keyboard mode
*
* @param up
* or down (if !up)
if (sg == null)
{
- if (viewport.cursorMode)
+ if (viewport.cursorMode)
{
sg = new SequenceGroup();
- sg.addSequence(viewport.getAlignment()
- .getSequenceAt(alignPanel.getSeqPanel().seqCanvas.cursorY),false);
- } else {
+ sg.addSequence(viewport.getAlignment().getSequenceAt(
+ alignPanel.getSeqPanel().seqCanvas.cursorY), false);
+ }
+ else
+ {
return;
}
}
-
+
if (sg.getSize() < 1)
{
- return;
+ return;
}
-
+
// TODO: JAL-3733 - add an event to the undo buffer for this !
-
+
viewport.getAlignment().moveSelectedSequencesByOne(sg,
viewport.getHiddenRepSequences(), up);
alignPanel.paintAlignment(true, false);
return;
}
- Runnable okAction = new Runnable()
- {
- @Override
- public void run()
- {
- SequenceI[] cut = sg.getSequences()
- .toArray(new SequenceI[sg.getSize()]);
-
- addHistoryItem(new EditCommand(
- MessageManager.getString("label.cut_sequences"), Action.CUT,
- cut, sg.getStartRes(), sg.getEndRes() - sg.getStartRes() + 1,
- viewport.getAlignment()));
-
- viewport.setSelectionGroup(null);
- viewport.sendSelection();
- viewport.getAlignment().deleteGroup(sg);
-
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
- if (viewport.getAlignment().getHeight() < 1)
- {
- try
- {
- AlignFrame.this.setClosed(true);
- } catch (Exception ex)
- {
- }
- }
- }};
+ Runnable okAction = new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ SequenceI[] cut = sg.getSequences()
+ .toArray(new SequenceI[sg.getSize()]);
+
+ addHistoryItem(new EditCommand(
+ MessageManager.getString("label.cut_sequences"), Action.CUT,
+ cut, sg.getStartRes(),
+ sg.getEndRes() - sg.getStartRes() + 1,
+ viewport.getAlignment()));
+
+ viewport.setSelectionGroup(null);
+ viewport.sendSelection();
+ viewport.getAlignment().deleteGroup(sg);
+
+ viewport.firePropertyChange("alignment", null,
+ viewport.getAlignment().getSequences());
+ if (viewport.getAlignment().getHeight() < 1)
+ {
+ try
+ {
+ AlignFrame.this.setClosed(true);
+ } catch (Exception ex)
+ {
+ }
+ }
+ }
+ };
/*
* If the cut affects all sequences, prompt for confirmation
*/
- boolean wholeHeight = sg.getSize() == viewport.getAlignment().getHeight();
+ boolean wholeHeight = sg.getSize() == viewport.getAlignment()
+ .getHeight();
boolean wholeWidth = (((sg.getEndRes() - sg.getStartRes())
+ 1) == viewport.getAlignment().getWidth()) ? true : false;
- if (wholeHeight && wholeWidth)
- {
- JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
- dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
- Object[] options = new Object[] { MessageManager.getString("action.ok"),
- MessageManager.getString("action.cancel") };
- dialog.showDialog(MessageManager.getString("warn.delete_all"),
- MessageManager.getString("label.delete_all"),
- JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
- options, options[0]);
- } else
- {
- okAction.run();
- }
+ if (wholeHeight && wholeWidth)
+ {
+ JvOptionPane dialog = JvOptionPane.newOptionDialog(Desktop.desktop);
+ dialog.setResponseHandler(0, okAction); // 0 = OK_OPTION
+ Object[] options = new Object[] {
+ MessageManager.getString("action.ok"),
+ MessageManager.getString("action.cancel") };
+ dialog.showDialog(MessageManager.getString("warn.delete_all"),
+ MessageManager.getString("label.delete_all"),
+ JvOptionPane.DEFAULT_OPTION, JvOptionPane.PLAIN_MESSAGE, null,
+ options, options[0]);
+ }
+ else
+ {
+ okAction.run();
+ }
}
/**
column, viewport.getAlignment());
}
- setStatus(MessageManager
- .formatMessage("label.removed_columns", new String[]
+ setStatus(MessageManager.formatMessage("label.removed_columns",
+ new String[]
{ Integer.valueOf(trimRegion.getSize()).toString() }));
addHistoryItem(trimRegion);
addHistoryItem(removeGapCols);
- setStatus(MessageManager
- .formatMessage("label.removed_empty_columns", new Object[]
+ setStatus(MessageManager.formatMessage("label.removed_empty_columns",
+ new Object[]
{ Integer.valueOf(removeGapCols.getSize()).toString() }));
// This is to maintain viewport position on first residue
@Override
public void findMenuItem_actionPerformed(ActionEvent e)
{
- new Finder(alignPanel);
+ new Finder(alignPanel, false, null);
}
/**
if (viewport.getViewName() == null)
{
- viewport.setViewName(MessageManager
- .getString("label.view_name_original"));
+ viewport.setViewName(
+ MessageManager.getString("label.view_name_original"));
}
/*
viewport.setGatherViewsHere(true);
}
tabbedPane.setSelectedIndex(tabbedPane.getTabCount() - 1);
+
+ /*
+ * finally if new view has acquired an Overview window (because
+ * Preferences option to open Overview is selected), set its title
+ */
+ OverviewPanel ov = newap.overviewPanel;
+ if (ov != null)
+ {
+ String ttl = getOverviewTitle();
+ ((JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, ov))
+ .setTitle(ttl);
+ }
+
return newap;
}
JLabel textLabel = new JLabel();
textLabel.setText(content);
textLabel.setBackground(Color.WHITE);
-
+
pane = new JPanel(new BorderLayout());
((JPanel) pane).setOpaque(true);
pane.setBackground(Color.WHITE);
}
/**
- * DOCUMENT ME!
+ * Opens an Overview panel for the alignment, unless one is open already
*
* @param e
- * DOCUMENT ME!
*/
@Override
public void overviewMenuItem_actionPerformed(ActionEvent e)
{
+ boolean showHiddenRegions = Cache.getDefault(Preferences.SHOW_OV_HIDDEN_AT_START,
+ false);
+ openOverviewPanel(showHiddenRegions);
+ }
+
+ public OverviewPanel openOverviewPanel(boolean showHidden)
+ {
if (alignPanel.overviewPanel != null)
{
- return;
+ return alignPanel.overviewPanel;
}
-
JInternalFrame frame = new JInternalFrame();
- final OverviewPanel overview = new OverviewPanel(alignPanel);
+ final OverviewPanel overview = new OverviewPanel(alignPanel, showHidden);
frame.setContentPane(overview);
- Desktop.addInternalFrame(frame, MessageManager
- .formatMessage("label.overview_params", new Object[]
- { this.getTitle() }), true, frame.getWidth(), frame.getHeight(),
+ String overviewTitle = getOverviewTitle();
+ Desktop.addInternalFrame(frame, overviewTitle, true, frame.getWidth(), frame.getHeight(),
true, true);
frame.pack();
frame.setLayer(JLayeredPane.PALETTE_LAYER);
+ final AlignmentPanel thePanel = this.alignPanel;
frame.addInternalFrameListener(
new javax.swing.event.InternalFrameAdapter()
{
javax.swing.event.InternalFrameEvent evt)
{
overview.dispose();
- alignPanel.setOverviewPanel(null);
+ thePanel.setOverviewPanel(null);
}
});
if (getKeyListeners().length > 0)
}
alignPanel.setOverviewPanel(overview);
+
+ return overview;
+ }
+
+ /**
+ * Constructs a title for the Overview window including the alignment window's
+ * title, and view name (if applicable)
+ *
+ * @return
+ */
+ public String getOverviewTitle()
+ {
+ String overviewTitle = MessageManager
+ .formatMessage("label.overview_params", new Object[]
+ { this.getTitle() });
+ String viewName = alignPanel.getViewName();
+ if (viewName != null)
+ {
+ overviewTitle += (" " + viewName);
+ }
+ return overviewTitle;
}
@Override
* otherwise set the chosen colour scheme (or null for 'None')
*/
ColourSchemeI cs = ColourSchemes.getInstance().getColourScheme(name,
- viewport,
- viewport.getAlignment(), viewport.getHiddenRepSequences());
+ viewport, viewport.getAlignment(),
+ viewport.getHiddenRepSequences());
changeColour(cs);
}
Enumeration<String> labels = scoreSorts.keys();
while (labels.hasMoreElements())
{
- addSortByAnnotScoreMenuItem(sortByAnnotScore,
- labels.nextElement());
+ addSortByAnnotScoreMenuItem(sortByAnnotScore, labels.nextElement());
}
sortByAnnotScore.setVisible(scoreSorts.size() > 0);
scoreSorts.clear();
chooser.setToolTipText(
MessageManager.getString("label.load_tree_file"));
- chooser.setResponseHandler(0,new Runnable()
+ chooser.setResponseHandler(0, new Runnable()
{
@Override
public void run()
// Add any secondary structure prediction services
for (int i = 0, j = secstrpr.size(); i < j; i++)
{
- final ext.vamsas.ServiceHandle sh = secstrpr
- .get(i);
+ final ext.vamsas.ServiceHandle sh = secstrpr.get(i);
jalview.ws.WSMenuEntryProviderI impl = jalview.ws.jws1.Discoverer
.getServiceClient(sh);
int p = secstrmenu.getItemCount();
jws2servs.attachWSMenuEntry(webService, me);
for (Jws2Instance sv : jws2servs.getServices())
{
- if (sv.description.toLowerCase().contains("jpred"))
+ if (sv.description.toLowerCase(Locale.ROOT).contains("jpred"))
{
for (JMenuItem jmi : legacyItems)
{
if (protocol == DataSourceType.FILE)
{
File fl;
- if (file instanceof File) {
+ if (file instanceof File)
+ {
fl = (File) file;
Platform.cacheFileData(fl);
- } else {
+ }
+ else
+ {
fl = new File(fileName);
}
pdbfn = fl.getName();
}
private Rectangle lastFeatureSettingsBounds = null;
+
@Override
public void setFeatureSettingsGeometry(Rectangle bounds)
{
import java.io.File;
import java.util.ArrayList;
import java.util.List;
+import java.util.concurrent.CompletableFuture;
import javax.help.HelpSetException;
import javax.swing.JComboBox;
import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
import jalview.bin.Cache;
+import jalview.bin.MemorySetting;
import jalview.ext.pymol.PymolManager;
import jalview.gui.Help.HelpId;
import jalview.gui.StructureViewer.ViewerType;
* @author $author$
* @version $Revision$
*/
+/*
+ * for merge with Jalview-JS
+ public class Preferences extends GPreferences implements ApplicationSingletonI
+ */
public class Preferences extends GPreferences
{
public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
private static final int MAX_FONT_SIZE = 30;
+ private String previousProxyType;
+
+ private static Preferences INSTANCE = null; // add "final"
+
/**
* Holds name and link separated with | character. Sequence ID must be
* $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
/**
* Holds name and link separated with | character. Sequence IDS and Sequences
- * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
- * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
- * for first and second token specified after a pipe character at end |,|.
- * (TODO: proper escape for using | to separate ids or sequences
+ * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and $SEQUENCES$
+ * or $SEQUENCES=/.possible | chars ./=$ and separation character for first and
+ * second token specified after a pipe character at end |,|. (TODO: proper
+ * escape for using | to separate ids or sequences
*/
public static List<String> groupURLLinks;
private OptionsParam textOpt = new OptionsParam(
MessageManager.getString("action.text"), "Text");
+ // get singleton Preferences instance
+ public static Preferences getInstance()
+ {
+ if (INSTANCE == null || INSTANCE.frame == null
+ || INSTANCE.frame.isClosed())
+ {
+ INSTANCE = new Preferences();
+ }
+ return INSTANCE;
+
+ /*
+ * Replace code with the following for Jalvew-JS
+ Preferences INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
+ if (INSTANCE == null || INSTANCE.frame == null
+ || INSTANCE.frame.isClosed())
+ {
+ ApplicationSingletonProvider.remove(Preferences.class);
+ INSTANCE = ApplicationSingletonProvider.getInstance(Preferences.class);
+ }
+ return INSTANCE;
+ */
+ }
+
+ public static void openPreferences()
+ {
+ openPreferences(null, null);
+ }
+
+ public static void openPreferences(TabRef selectTab, String message)
+ {
+ Preferences p = getInstance();
+ if (selectTab != null)
+ p.selectTab(selectTab, message);
+ p.frame.show();
+ p.frame.moveToFront();
+ p.frame.grabFocus();
+ }
+
+ public void selectTab(TabRef selectTab, String message)
+ {
+ this.selectTab(selectTab);
+ if (message != null)
+ this.setMessage(message);
+ this.frame.show();
+ }
+
/**
* Creates a new Preferences object.
*/
- public Preferences()
+ private Preferences()
{
super();
frame = new JInternalFrame();
startupCheckbox
.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
- Cache.getDefault("www.jalview.org", "http://www.jalview.org")
- + "/examples/exampleFile_2_3.jar"));
+ Cache.getDefault("www.jalview.org", "https://www.jalview.org")
+ + "/examples/exampleFile_2_7.jvp"));
/*
* Set Colours tab defaults
* Set overview panel defaults
*/
gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+ OverviewCanvas.OVERVIEW_DEFAULT_GAP));
hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+ OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN));
useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
gapLabel.setEnabled(!useLegacyGap.isSelected());
gapColour.setEnabled(!useLegacyGap.isSelected());
/*
* Set Structure tab defaults
*/
- final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+ final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, true);
structFromPdb.setSelected(structSelected);
- useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
- useRnaView.setEnabled(structSelected);
- addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+ addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, true));
addSecondaryStructure.setEnabled(structSelected);
- addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+ addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, true));
addTempFactor.setEnabled(structSelected);
/*
{
if (validateViewerPath())
{
- Cache.setProperty(
- structViewer.getSelectedItem().equals(
- ViewerType.CHIMERAX.name()) ? CHIMERAX_PATH
- : CHIMERA_PATH,
- structureViewerPath.getText());
+ String path = structureViewerPath.getText();
+ try {
+ ViewerType type = ViewerType.valueOf(viewerType);
+ switch (type)
+ {
+ case JMOL:
+ break;
+ case CHIMERA:
+ Cache.setProperty(CHIMERA_PATH, path);
+ break;
+ case CHIMERAX:
+ Cache.setProperty(CHIMERAX_PATH, path);
+ break;
+ case PYMOL:
+ Cache.setProperty(PYMOL_PATH, path);
+ break;
+ }
+ } catch (IllegalArgumentException x)
+ {
+ Cache.log.error("Failed to set path - unknown viewer type",x);
+ }
}
}
});
}
}
- useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
- useProxy_actionPerformed(); // make sure useProxy is correctly initialised
- proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
- proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+ String proxyTypeString = Cache.getDefault("USE_PROXY", "false");
+ previousProxyType = proxyTypeString;
+ switch (proxyTypeString)
+ {
+ case Cache.PROXYTYPE_NONE:
+ proxyType.setSelected(noProxy.getModel(), true);
+ break;
+ case Cache.PROXYTYPE_SYSTEM:
+ proxyType.setSelected(systemProxy.getModel(), true);
+ break;
+ case Cache.PROXYTYPE_CUSTOM:
+ proxyType.setSelected(customProxy.getModel(), true);
+ break;
+ default:
+ Cache.log.warn(
+ "Incorrect PROXY_TYPE - should be 'none' (clear proxy properties), 'false' (system settings), 'true' (custom settings): "
+ + proxyTypeString);
+ }
+ proxyServerHttpTB.setText(Cache.getDefault("PROXY_SERVER", ""));
+ proxyPortHttpTB.setText(Cache.getDefault("PROXY_PORT", ""));
+ proxyServerHttpsTB.setText(Cache.getDefault("PROXY_SERVER_HTTPS", ""));
+ proxyPortHttpsTB.setText(Cache.getDefault("PROXY_PORT_HTTPS", ""));
+ proxyAuth.setSelected(Cache.getDefault("PROXY_AUTH", false));
+ proxyAuthUsernameTB
+ .setText(Cache.getDefault("PROXY_AUTH_USERNAME", ""));
+ // we are not storing or retrieving proxy password from .jalview_properties
+ proxyAuthPasswordPB.setText(Cache.proxyAuthPassword == null ? ""
+ : new String(Cache.proxyAuthPassword));
+ setCustomProxyEnabled();
+ applyProxyButtonEnabled(false);
defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
* Set Backups tab defaults
*/
loadLastSavedBackupsOptions();
+
+ /*
+ * Set Startup tab defaults
+ */
+
}
/**
return;
}
+ /*
+ * Set proxy settings first (to be before web services refresh)
+ */
+ saveProxySettings();
+
/*
* Save Visual settings
*/
Boolean.toString(addTempFactor.isSelected()));
Cache.applicationProperties.setProperty(ADD_SS_ANN,
Boolean.toString(addSecondaryStructure.isSelected()));
- Cache.applicationProperties.setProperty(USE_RNAVIEW,
- Boolean.toString(useRnaView.isSelected()));
Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
Boolean.toString(structFromPdb.isSelected()));
String viewer = structViewer.getSelectedItem().toString();
/*
* Save Connections settings
*/
+ // Proxy settings set first (to catch web services)
+
Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
jalview.util.BrowserLauncher.resetBrowser();
Cache.applicationProperties.setProperty("DEFAULT_URL",
sequenceUrlLinks.getPrimaryUrlId());
- Cache.applicationProperties.setProperty("USE_PROXY",
- Boolean.toString(useProxy.isSelected()));
-
- Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
-
- Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
-
- if (useProxy.isSelected())
- {
- System.setProperty("http.proxyHost", proxyServerTB.getText());
- System.setProperty("http.proxyPort", proxyPortTB.getText());
- }
- else
- {
- System.setProperty("http.proxyHost", "");
- System.setProperty("http.proxyPort", "");
- }
Cache.setProperty("VERSION_CHECK",
Boolean.toString(versioncheck.isSelected()));
if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
Cache.applicationProperties.setProperty(
BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
+ /*
+ * Save Memory Settings
+ */
+ Cache.applicationProperties.setProperty(
+ MemorySetting.CUSTOMISED_SETTINGS,
+ Boolean.toString(customiseMemorySetting.isSelected()));
+ Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMPC,
+ Integer.toString(jvmMemoryPercentSlider.getValue()));
+ Cache.applicationProperties.setProperty(MemorySetting.MEMORY_JVMMEMMAX,
+ jvmMemoryMaxTextField.getText());
+
+ /*
+ * save and close Preferences
+ */
+
Cache.saveProperties();
Desktop.instance.doConfigureStructurePrefs();
try
}
}
+ public void saveProxySettings()
+ {
+ String newProxyType = customProxy.isSelected() ? Cache.PROXYTYPE_CUSTOM
+ : noProxy.isSelected() ? Cache.PROXYTYPE_NONE
+ : Cache.PROXYTYPE_SYSTEM;
+ Cache.applicationProperties.setProperty("USE_PROXY", newProxyType);
+ Cache.setOrRemove("PROXY_SERVER", proxyServerHttpTB.getText());
+ Cache.setOrRemove("PROXY_PORT", proxyPortHttpTB.getText());
+ Cache.setOrRemove("PROXY_SERVER_HTTPS", proxyServerHttpsTB.getText());
+ Cache.setOrRemove("PROXY_PORT_HTTPS", proxyPortHttpsTB.getText());
+ Cache.setOrRemove("PROXY_AUTH",
+ Boolean.toString(proxyAuth.isSelected()));
+ Cache.setOrRemove("PROXY_AUTH_USERNAME", proxyAuthUsernameTB.getText());
+ Cache.proxyAuthPassword = proxyAuthPasswordPB.getPassword();
+ Cache.setProxyPropertiesFromPreferences(previousProxyType);
+ if (newProxyType.equals(Cache.PROXYTYPE_CUSTOM)
+ || !newProxyType.equals(previousProxyType))
+ {
+ // force a re-lookup of ws if proxytype is custom or has changed
+ wsPrefs.update++;
+ }
+ previousProxyType = newProxyType;
+ }
+
/**
- * Do any necessary validation before saving settings. Return focus to the
- * first tab which fails validation.
+ * Do any necessary validation before saving settings. Return focus to the first
+ * tab which fails validation.
*
* @return
*/
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
@Override
public void cancel_actionPerformed(ActionEvent e)
* DOCUMENT ME!
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
@Override
public void annotations_actionPerformed(ActionEvent e)
boolean enabled = useLegacyGap.isSelected();
if (enabled)
{
- gapColour.setBackground(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
+ gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_LEGACY_GAP);
}
else
{
- gapColour.setBackground(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+ gapColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_GAP);
}
gapColour.setEnabled(!enabled);
gapLabel.setEnabled(!enabled);
useLegacyGap.setSelected(false);
useLegacyGaps_actionPerformed(null);
showHiddenAtStart.setSelected(false);
- hiddenColour.setBackground(
- jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+ hiddenColour.setBackground(OverviewCanvas.OVERVIEW_DEFAULT_HIDDEN);
}
@Override
}
/**
- * Returns true if structure viewer path is to a valid executable, else shows
- * an error dialog. Does nothing if the path is empty, as is the case for Jmol
+ * Returns true if structure viewer path is to a valid executable, else shows an
+ * error dialog. Does nothing if the path is empty, as is the case for Jmol
* (built in to Jalview) or when Jalview is left to try default paths.
*/
private boolean validateViewerPath()
}
/**
- * If Chimera or ChimeraX or Pymol is selected, check it can be found on
- * default or user-specified path, if not show a warning/help dialog
+ * If Chimera or ChimeraX or Pymol is selected, check it can be found on default
+ * or user-specified path, if not show a warning/help dialog
*/
@Override
protected void structureViewer_actionPerformed(String selectedItem)
MessageManager.getString("label.viewer_missing")),
"", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
null, options, options[0]);
+
if (showHelp == JvOptionPane.NO_OPTION)
{
+ this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
try
{
Help.showHelpWindow(HelpId.StructureViewer);
e.printStackTrace();
}
}
+ else if (showHelp == JvOptionPane.OK_OPTION)
+ {
+ this.selectTab(Preferences.TabRef.STRUCTURE_TAB, null);
+ CompletableFuture<Void> cf = CompletableFuture.runAsync(() -> {
+ try
+ {
+ for (int i = 0; i < 3; i++)
+ {
+ structureViewerPath.setBackground(Color.PINK);
+ Thread.sleep(500);
+ structureViewerPath.setBackground(Color.WHITE);
+ Thread.sleep(500);
+ }
+ } catch (InterruptedException e)
+ {
+ }
+ });
+ }
}
}
import java.util.StringTokenizer;
import java.util.Vector;
+ import javax.swing.JInternalFrame;
import javax.swing.SwingUtilities;
import jalview.api.ComplexAlignFile;
import jalview.gui.AlignViewport;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
+ import jalview.gui.OverviewPanel;
import jalview.json.binding.biojson.v1.ColourSchemeMapper;
import jalview.project.Jalview2XML;
import jalview.schemes.ColourSchemeI;
.getFeatureColourScheme();
if (viewport != null)
{
- if (proxyColourScheme != null)
- {
- viewport.applyFeaturesStyle(proxyColourScheme);
- }
// append to existing alignment
viewport.addAlignment(al, title);
+ viewport.applyFeaturesStyle(proxyColourScheme);
}
else
{
// that perform queries to find the 'current working alignment'
Desktop.addInternalFrame(alignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ OverviewPanel ov = alignFrame.alignPanel.getOverviewPanel();
+ if (ov != null)
+ {
+ /*
+ * Overview automatically opened with alignment
+ * - set its title now alignFrame title has been set
+ */
+ String ttl = alignFrame.getOverviewTitle();
+ ((JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, ov))
+ .setTitle(ttl);
+ }
+
}
try
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import jalview.gui.Desktop;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
+ import jalview.gui.OverviewPanel;
import jalview.gui.PCAPanel;
import jalview.gui.PaintRefresher;
import jalview.gui.SplitFrame;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.Format;
+import jalview.util.HttpUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.util.StringUtils;
import jalview.xml.binding.jalview.JalviewModel.Viewport;
import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+ import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
import jalview.xml.binding.jalview.MapListType.MapListFrom;
// create backupfiles object and get new temp filename destination
boolean doBackup = BackupFiles.getEnabled();
BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
- FileOutputStream fos = new FileOutputStream(doBackup ?
- backupfiles.getTempFilePath() : jarFile);
+ FileOutputStream fos = new FileOutputStream(
+ doBackup ? backupfiles.getTempFilePath() : jarFile);
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
else
{
vamsasSeq = createVamsasSequence(id, jds);
-// vamsasSet.addSequence(vamsasSeq);
+ // vamsasSet.addSequence(vamsasSeq);
vamsasSet.getSequence().add(vamsasSeq);
vamsasSetIds.put(id, vamsasSeq);
seqRefIds.put(id, jds);
if (frames[f] instanceof StructureViewerBase)
{
StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
- matchedFile = saveStructureViewer(ap, jds, pdb, entry, viewIds,
- matchedFile, viewFrame);
+ matchedFile = saveStructureViewer(ap, jds, pdb, entry,
+ viewIds, matchedFile, viewFrame);
/*
* Only store each structure viewer's state once in the project
* jar. First time through only (storeDS==false)
}
else
{
- Cache.log.error("Failed to save viewer state for "
- +
- viewerType);
+ Cache.log.error(
+ "Failed to save viewer state for " + viewerType);
}
}
}
if (colourScheme instanceof jalview.schemes.UserColourScheme)
{
- jGroup.setColour(
- setUserColourScheme(colourScheme, userColours,
- object));
+ jGroup.setColour(setUserColourScheme(colourScheme,
+ userColours, object));
}
else
{
}
}
- //jms.setJGroup(groups);
+ // jms.setJGroup(groups);
Object group;
for (JGroup grp : groups)
{
view.setStartRes(vpRanges.getStartRes());
view.setStartSeq(vpRanges.getStartSeq());
+ OverviewPanel ov = ap.getOverviewPanel();
+ if (ov != null)
+ {
+ Overview overview = new Overview();
+ JInternalFrame frame = (JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, ov);
+ overview.setTitle(frame.getTitle());
+ Rectangle bounds = frame.getBounds();
+ overview.setXpos(bounds.x);
+ overview.setYpos(bounds.y);
+ overview.setWidth(bounds.width);
+ overview.setHeight(bounds.height);
+ overview.setShowHidden(ov.isShowHiddenRegions());
+ overview.setGapColour(ov.getCanvas().getGapColour().getRGB());
+ overview.setResidueColour(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(),
* save any filter for the feature type
*/
FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
- if (filter != null) {
- Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+ if (filter != null)
+ {
+ Iterator<FeatureMatcherI> filters = filter.getMatchers()
+ .iterator();
FeatureMatcherI firstFilter = filters.next();
- setting.setMatcherSet(Jalview2XML.marshalFilter(
- firstFilter, filters, filter.isAnded()));
+ setting.setMatcherSet(Jalview2XML.marshalFilter(firstFilter,
+ filters, filter.isAnded()));
}
/*
setting.setDisplay(
av.getFeaturesDisplayed().isVisible(featureType));
- float rorder = fr
- .getOrder(featureType);
+ float rorder = fr.getOrder(featureType);
if (rorder > -1)
{
setting.setOrder(rorder);
Group g = new Group();
g.setName(grp);
g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
- .booleanValue());
+ .booleanValue());
// fs.addGroup(g);
fs.getGroup().add(g);
groupsAdded.addElement(grp);
{
final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
final String pdbId = pdbentry.getId();
- if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId().toLowerCase()
- .startsWith(pdbId.toLowerCase())))
+ if (!pdbId.equals(entry.getId()) && !(entry.getId().length() > 4
+ && entry.getId().toLowerCase(Locale.ROOT)
+ .startsWith(pdbId.toLowerCase(Locale.ROOT))))
{
/*
* not interested in a binding to a different PDB entry here
{
if (calcIdParam.getVersion().equals("1.0"))
{
- final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+ final String[] calcIds = calcIdParam.getServiceURL()
+ .toArray(new String[0]);
Jws2Instance service = Jws2Discoverer.getDiscoverer()
.getPreferredServiceFor(calcIds);
if (service != null)
dbref.setSource(ref.getSource());
dbref.setVersion(ref.getVersion());
dbref.setAccessionId(ref.getAccessionId());
+ dbref.setCanonical(ref.isCanonical());
if (ref instanceof GeneLocus)
{
dbref.setLocus(true);
}
if (ref.hasMap())
{
- Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
- jds, recurse);
+ Mapping mp = createVamsasMapping(ref.getMap(), parentseq, jds,
+ recurse);
dbref.setMapping(mp);
}
vamsasSeq.getDBRef().add(dbref);
for (int i = 0; i < colours.length; i++)
{
Colour col = new Colour();
- col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
col.setRGB(jalview.util.Format.getHexString(colours[i]));
// jbucs.addColour(col);
jbucs.getColour().add(col);
return id;
}
- jalview.schemes.UserColourScheme getUserColourScheme(
- JalviewModel jm, String id)
+ jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
+ String id)
{
List<UserColours> uc = jm.getUserColours();
UserColours colours = null;
-/*
+ /*
for (int i = 0; i < uc.length; i++)
{
if (uc[i].getId().equals(id))
break;
}
}
-*/
+ */
for (UserColours c : uc)
{
if (c.getId().equals(id))
newColours = new java.awt.Color[23];
for (int i = 0; i < 23; i++)
{
- newColours[i] = new java.awt.Color(Integer.parseInt(
- colours.getUserColourScheme().getColour().get(i + 24)
- .getRGB(),
- 16));
+ newColours[i] = new java.awt.Color(
+ Integer.parseInt(colours.getUserColourScheme().getColour()
+ .get(i + 24).getRGB(), 16));
}
ucs.setLowerCaseColours(newColours);
}
return af;
}
- @SuppressWarnings("unused")
- private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
+ @SuppressWarnings("unused")
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final Object ofile) throws MalformedURLException
+ {
- // BH 2018 allow for bytes already attached to File object
- try {
- String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+ // BH 2018 allow for bytes already attached to File object
+ try
+ {
+ String file = (ofile instanceof File
+ ? ((File) ofile).getCanonicalPath()
+ : ofile.toString());
byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
: null;
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://")) {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider() {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException {
- if (bytes != null) {
-// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
- return new JarInputStream(new ByteArrayInputStream(bytes));
- }
- if (_url != null) {
-// System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
- return new JarInputStream(_url.openStream());
- } else {
-// System.out.println("Jalview2XML: opening file jarInputStream for " + file);
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename() {
- return file;
- }
- };
- } catch (IOException e) {
- e.printStackTrace();
- return null;
- }
- }
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ if (HttpUtils.startsWithHttpOrHttps(file))
+ {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider()
+ {
+
+ @Override
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ if (bytes != null)
+ {
+ // System.out.println("Jalview2XML: opening byte jarInputStream for
+ // bytes.length=" + bytes.length);
+ return new JarInputStream(new ByteArrayInputStream(bytes));
+ }
+ if (_url != null)
+ {
+ // System.out.println("Jalview2XML: opening url jarInputStream for "
+ // + _url);
+ return new JarInputStream(_url.openStream());
+ }
+ else
+ {
+ // System.out.println("Jalview2XML: opening file jarInputStream for
+ // " + file);
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ @Override
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ return null;
+ }
+ }
/**
* Recover jalview session from a jalview project archive. Caller may
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.createXMLStreamReader(jin);
javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<JalviewModel> jbe = um
- .unmarshal(streamReader, JalviewModel.class);
+ JAXBElement<JalviewModel> jbe = um.unmarshal(streamReader,
+ JalviewModel.class);
JalviewModel object = jbe.getValue();
if (true) // !skipViewport(object))
entryCount++;
}
} while (jarentry != null);
+ jin.close();
resolveFrefedSequences();
} catch (IOException ex)
{
AlignFrame loadFromObject(JalviewModel jalviewModel, String file,
boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
- SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+ SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet()
+ .get(0);
List<Sequence> vamsasSeqs = vamsasSet.getSequence();
// JalviewModelSequence jms = object.getJalviewModelSequence();
if (tmpSeq.getStart() != jseq.getStart()
|| tmpSeq.getEnd() != jseq.getEnd())
{
- System.err.println(
- String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
- tmpSeq.getName(), tmpSeq.getStart(),
- tmpSeq.getEnd(), jseq.getStart(),
- jseq.getEnd()));
+ System.err.println(String.format(
+ "Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+ tmpSeq.getName(), tmpSeq.getStart(), tmpSeq.getEnd(),
+ jseq.getStart(), jseq.getEnd()));
}
}
else
else
{
// defer to later
- frefedSequence.add(
- newAlcodMapRef(map.getDnasq(), cf, mapping));
+ frefedSequence
+ .add(newAlcodMapRef(map.getDnasq(), cf, mapping));
}
}
}
jaa.setCalcId(annotation.getCalcId());
if (annotation.getProperty().size() > 0)
{
- for (Annotation.Property prop : annotation
- .getProperty())
+ for (Annotation.Property prop : annotation.getProperty())
{
jaa.setProperty(prop.getName(), prop.getValue());
}
sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
// attributes with a default in the schema are never null
- sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
- sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
- sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+ sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+ sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+ sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
if (jGroup.getConsThreshold() != null
&& jGroup.getConsThreshold().intValue() != 0)
if (addAnnotSchemeGroup)
{
// reconstruct the annotation colourscheme
- sg.setColourScheme(constructAnnotationColour(
- jGroup.getAnnotationColours(), null, al, jalviewModel, false));
+ sg.setColourScheme(
+ constructAnnotationColour(jGroup.getAnnotationColours(),
+ null, al, jalviewModel, false));
}
}
}
}
/*
- * Load any trees, PDB structures and viewers
+ * Load any trees, PDB structures and viewers, Overview
*
* Not done if flag is false (when this method is used for New View)
*/
loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
+ loadOverview(view, af);
}
// and finally return.
return af;
}
/**
+ * Load Overview window, restoring colours, 'show hidden regions' flag, title
+ * and geometry as saved
+ *
+ * @param view
+ * @param af
+ */
+ protected void loadOverview(Viewport view, AlignFrame af)
+ {
+ Overview overview = view.getOverview();
+ if (overview != null)
+ {
+ OverviewPanel overviewPanel = af
+ .openOverviewPanel(overview.isShowHidden());
+ JInternalFrame frame = (JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, overviewPanel);
+ frame.setTitle(overview.getTitle());
+ frame.setBounds(overview.getXpos(), overview.getYpos(),
+ overview.getWidth(), overview.getHeight());
+ Color gap = new Color(overview.getGapColour());
+ Color residue = new Color(overview.getResidueColour());
+ Color hidden = new Color(overview.getHiddenColour());
+ overviewPanel.getCanvas().setColours(gap, residue, hidden);
+ }
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
* @param av
* @param ap
*/
- protected void loadTrees(JalviewModel jm, Viewport view,
- AlignFrame af, AlignViewport av, AlignmentPanel ap)
+ protected void loadTrees(JalviewModel jm, Viewport view, AlignFrame af,
+ AlignViewport av, AlignmentPanel ap)
{
// TODO result of automated refactoring - are all these parameters needed?
try
for (int s = 0; s < structureStateCount; s++)
{
// check to see if we haven't already created this structure view
- final StructureState structureState = pdbid
- .getStructureState().get(s);
+ final StructureState structureState = pdbid.getStructureState()
+ .get(s);
String sviewid = (structureState.getViewId() == null) ? null
: structureState.getViewId() + uniqueSetSuffix;
jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
colourByViewer &= structureState.isColourByJmol();
jmoldat.setColourByViewer(colourByViewer);
- if (jmoldat.getStateData().length() < structureState
- .getValue()/*Content()*/.length())
+ if (jmoldat.getStateData().length() < structureState.getValue()
+ /*Content()*/.length())
{
jmoldat.setStateData(structureState.getValue());// Content());
}
} catch (IllegalArgumentException | NullPointerException e)
{
// TODO JAL-3619 show error dialog / offer an alternative viewer
- Cache.log.error(
- "Invalid structure viewer type: " + type);
+ Cache.log.error("Invalid structure viewer type: " + type);
}
}
}
AlignFrame loadViewport(String file, List<JSeq> JSEQ,
- List<SequenceI> hiddenSeqs, AlignmentI al,
- JalviewModel jm, Viewport view, String uniqueSeqSetId,
- String viewId, List<JvAnnotRow> autoAlan)
+ List<SequenceI> hiddenSeqs, AlignmentI al, JalviewModel jm,
+ Viewport view, String uniqueSeqSetId, String viewId,
+ List<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
- safeInt(view.getHeight()), uniqueSeqSetId, viewId)
-// {
-//
-// @Override
-// protected void processKeyEvent(java.awt.event.KeyEvent e) {
-// System.out.println("Jalview2XML AF " + e);
-// super.processKeyEvent(e);
-//
-// }
-//
-// }
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+ // {
+ //
+ // @Override
+ // protected void processKeyEvent(java.awt.event.KeyEvent e) {
+ // System.out.println("Jalview2XML AF " + e);
+ // super.processKeyEvent(e);
+ //
+ // }
+ //
+ // }
;
af.setFileName(file, FileFormat.Jalview);
viewport.setColourText(safeBoolean(view.isShowColourText()));
- viewport
- .setConservationSelected(
- safeBoolean(view.isConservationSelected()));
+ viewport.setConservationSelected(
+ safeBoolean(view.isConservationSelected()));
viewport.setIncrement(safeInt(view.getConsThreshold()));
viewport.setShowJVSuffix(safeBoolean(view.isShowFullId()));
viewport.setRightAlignIds(safeBoolean(view.isRightAlignIds()));
af.changeColour(cs);
viewport.setColourAppliesToAllGroups(true);
- viewport
- .setShowSequenceFeatures(
- safeBoolean(view.isShowSequenceFeatures()));
+ viewport.setShowSequenceFeatures(
+ safeBoolean(view.isShowSequenceFeatures()));
viewport.setCentreColumnLabels(view.isCentreColumnLabels());
viewport.setIgnoreGapsConsensus(view.isIgnoreGapsinConsensus(), null);
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
- String[] renderOrder = new String[jm.getFeatureSettings()
- .getSetting().size()];
+ String[] renderOrder = new String[jm.getFeatureSettings().getSetting()
+ .size()];
Map<String, FeatureColourI> featureColours = new Hashtable<>();
Map<String, Float> featureOrder = new Hashtable<>();
- for (int fs = 0; fs < jm.getFeatureSettings()
- .getSetting().size(); fs++)
+ for (int fs = 0; fs < jm.getFeatureSettings().getSetting()
+ .size(); fs++)
{
Setting setting = jm.getFeatureSettings().getSetting().get(fs);
String featureType = setting.getType();
.getMatcherSet();
if (filters != null)
{
- FeatureMatcherSetI filter = Jalview2XML
- .parseFilter(featureType, filters);
+ FeatureMatcherSetI filter = Jalview2XML.parseFilter(featureType,
+ filters);
if (!filter.isEmpty())
{
fr.setFeatureFilter(featureType, filter);
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
FeatureColourI gc = new FeatureColour(maxColour, minColour,
- maxColour,
- noValueColour, min, max);
+ maxColour, noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
gc.setAttributeName(setting.getAttributeName().toArray(
}
else
{
- featureColours.put(featureType,
- new FeatureColour(maxColour));
+ featureColours.put(featureType, new FeatureColour(maxColour));
}
renderOrder[fs] = featureType;
if (setting.getOrder() != null)
{
splitFrameCandidates.put(view, af);
}
+
return af;
}
}
}
}
+
/**
*
* @param vamsasSeq
{
entry.setMap(addMapping(dr.getMapping()));
}
+ entry.setCanonical(dr.isCanonical());
datasetSequence.addDBRef(entry);
}
}
* @param af
* @param jprovider
*/
- protected void createStructureViewer(
- ViewerType viewerType, final Entry<String, StructureViewerModel> viewerData,
+ protected void createStructureViewer(ViewerType viewerType,
+ final Entry<String, StructureViewerModel> viewerData,
AlignFrame af, jarInputStreamProvider jprovider)
{
final StructureViewerModel viewerModel = viewerData.getValue();
{
String viewerJarEntryName = getViewerJarEntryName(
viewerModel.getViewId());
- sessionFilePath = copyJarEntry(jprovider,
- viewerJarEntryName,
+ sessionFilePath = copyJarEntry(jprovider, viewerJarEntryName,
"viewerSession", ".tmp");
}
final String sessionPath = sessionFilePath;
addNewStructureViewer(sview);
} catch (OutOfMemoryError ex)
{
- new OOMWarning("Restoring structure view for "
- + viewerType,
+ new OOMWarning("Restoring structure view for " + viewerType,
(OutOfMemoryError) ex.getCause());
if (sview != null && sview.isVisible())
{
String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
filedat = oldFiles.get(new File(reformatedOldFilename));
}
- rewritten
- .append(Platform.escapeBackslashes(filedat.getFilePath()));
+ rewritten.append(Platform.escapeBackslashes(filedat.getFilePath()));
rewritten.append("\"");
cp = ecp + 1; // advance beyond last \" and set cursor so we can
// look for next file statement.
* @param fcol
* @return
*/
- public static Colour marshalColour(
- String featureType, FeatureColourI fcol)
+ public static Colour marshalColour(String featureType,
+ FeatureColourI fcol)
{
Colour col = new Colour();
if (fcol.isSimpleColour())
boolean and)
{
jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
-
+
if (filters.hasNext())
{
/*
}
result.setMatchCondition(matcherModel);
}
-
+
return result;
}
* @param matcherSetModel
* @return
*/
- public static FeatureMatcherSetI parseFilter(
- String featureType,
+ public static FeatureMatcherSetI parseFilter(String featureType,
jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel)
{
FeatureMatcherSetI result = new FeatureMatcherSet();
featureType, e.getMessage()));
// return as much as was parsed up to the error
}
-
+
return result;
}
* @throws IllegalStateException
* if AND and OR conditions are mixed
*/
- protected static void parseFilterConditions(
- FeatureMatcherSetI matcherSet,
+ protected static void parseFilterConditions(FeatureMatcherSetI matcherSet,
jalview.xml.binding.jalview.FeatureMatcherSet matcherSetModel,
boolean and)
{
else if (filterBy == FilterBy.BY_SCORE)
{
matchCondition = FeatureMatcher.byScore(cond, pattern);
-
+
}
else if (filterBy == FilterBy.BY_ATTRIBUTE)
{
matchCondition = FeatureMatcher.byAttribute(cond, pattern,
attNames);
}
-
+
/*
* note this throws IllegalStateException if AND-ing to a
* previously OR-ed compound condition, or vice versa
public static FeatureColourI parseColour(Colour colourModel)
{
FeatureColourI colour = null;
-
+
if (colourModel.getMax() != null)
{
Color mincol = null;
Color maxcol = null;
Color noValueColour = null;
-
+
try
{
mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
{
Cache.log.warn("Couldn't parse out graduated feature color.", e);
}
-
+
NoValueColour noCol = colourModel.getNoValueColour();
if (noCol == NoValueColour.MIN)
{
{
noValueColour = maxcol;
}
-
+
colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
colour = new FeatureColour(color);
}
-
+
return colour;
}
}
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2018.09.14 at 02:46:00 PM BST
++// Generated on: 2022.02.07 at 04:45:21 PM GMT
//
/**
-- * <p>Java class for EntrySetType complex type.
++ * <p>Java class for EntrySetType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="EntrySetType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence maxOccurs="unbounded">
-- * <element name="entry" type="{}EntryType"/>
-- * </sequence>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="EntrySetType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence maxOccurs="unbounded"&gt;
++ * &lt;element name="entry" type="{}EntryType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the entry property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the entry property.
++ * This is why there is not a <CODE>set</CODE> method for the entry property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEntry().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EntryType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2018.09.14 at 02:46:00 PM BST
++// Generated on: 2022.02.07 at 04:45:21 PM GMT
//
/**
-- * <p>Java class for EntryType complex type.
++ * <p>Java class for EntryType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="EntryType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="secondaryAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="projectAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- * <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- * <element name="keyword" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="reference" maxOccurs="unbounded" minOccurs="0">
-- * <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>
-- * </element>
-- * <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="feature" maxOccurs="unbounded" minOccurs="0">
-- * <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>
-- * </element>
-- * <element name="assembly" minOccurs="0">
-- * <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>
-- * </element>
-- * <element name="contig" minOccurs="0">
-- * <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>
-- * </element>
-- * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- * </sequence>
-- * <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="entryVersion" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- * <attribute name="dataClass" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="taxonomicDivision" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="moleculeType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="sequenceLength" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- * <attribute name="topology" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="circular"/>
-- * <enumeration value="linear"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="firstPublic" type="{http://www.w3.org/2001/XMLSchema}date" />
-- * <attribute name="firstPublicRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- * <attribute name="lastUpdated" type="{http://www.w3.org/2001/XMLSchema}date" />
-- * <attribute name="lastUpdatedRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="EntryType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="secondaryAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="projectAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="keyword" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="reference" maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/&gt;
++ * &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="submission"/&gt;
++ * &lt;enumeration value="book"/&gt;
++ * &lt;enumeration value="article"/&gt;
++ * &lt;enumeration value="patent"/&gt;
++ * &lt;enumeration value="thesis"/&gt;
++ * &lt;enumeration value="unpublished"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="feature" maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="lineage" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" maxOccurs="unbounded"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="assembly" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="range" maxOccurs="unbounded"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="contig" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;choice maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;element name="range"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="gap"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/choice&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="entryVersion" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="dataClass" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="taxonomicDivision" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="moleculeType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="sequenceLength" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="topology" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="circular"/&gt;
++ * &lt;enumeration value="linear"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="firstPublic" type="{http://www.w3.org/2001/XMLSchema}date" /&gt;
++ * &lt;attribute name="firstPublicRelease" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="lastUpdated" type="{http://www.w3.org/2001/XMLSchema}date" /&gt;
++ * &lt;attribute name="lastUpdatedRelease" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the secondaryAccession property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property.
++ * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getSecondaryAccession().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the projectAccession property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
++ * This is why there is not a <CODE>set</CODE> method for the projectAccession property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getProjectAccession().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the keyword property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the keyword property.
++ * This is why there is not a <CODE>set</CODE> method for the keyword property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getKeyword().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the reference property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the reference property.
++ * This is why there is not a <CODE>set</CODE> method for the reference property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getReference().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Reference }
*
/**
* Gets the value of the xref property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the xref property.
++ * This is why there is not a <CODE>set</CODE> method for the xref property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getXref().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link XrefType }
*
/**
* Gets the value of the feature property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the feature property.
++ * This is why there is not a <CODE>set</CODE> method for the feature property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getFeature().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Feature }
*
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="range" maxOccurs="unbounded"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the range property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the range property.
++ * This is why there is not a <CODE>set</CODE> method for the range property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getRange().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Assembly.Range }
*
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;choice maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;element name="range"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="gap"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/choice&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the rangeOrGap property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
++ * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getRangeOrGap().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Contig.Range }
* {@link EntryType.Contig.Gap }
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="lineage" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" maxOccurs="unbounded"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the xref property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the xref property.
++ * This is why there is not a <CODE>set</CODE> method for the xref property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getXref().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link XrefType }
*
/**
* Gets the value of the qualifier property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the qualifier property.
++ * This is why there is not a <CODE>set</CODE> method for the qualifier property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getQualifier().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Feature.Qualifier }
*
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="lineage" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" maxOccurs="unbounded"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" maxOccurs="unbounded"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the taxon property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the taxon property.
++ * This is why there is not a <CODE>set</CODE> method for the taxon property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getTaxon().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/&gt;
++ * &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="submission"/&gt;
++ * &lt;enumeration value="book"/&gt;
++ * &lt;enumeration value="article"/&gt;
++ * &lt;enumeration value="patent"/&gt;
++ * &lt;enumeration value="thesis"/&gt;
++ * &lt;enumeration value="unpublished"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the author property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the author property.
++ * This is why there is not a <CODE>set</CODE> method for the author property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getAuthor().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the applicant property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the applicant property.
++ * This is why there is not a <CODE>set</CODE> method for the applicant property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getApplicant().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the xref property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the xref property.
++ * This is why there is not a <CODE>set</CODE> method for the xref property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getXref().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link XrefType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2018.09.14 at 02:46:00 PM BST
++// Generated on: 2022.02.07 at 04:45:21 PM GMT
//
* This object contains factory methods for each
* Java content interface and Java element interface
* generated in the jalview.xml.binding.embl package.
-- * <p>An ObjectFactory allows you to programatically
++ * <p>An ObjectFactory allows you to programatically
* construct new instances of the Java representation
* for XML content. The Java representation of XML
* content can consist of schema derived interfaces
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2018.09.14 at 02:46:00 PM BST
++// Generated on: 2022.02.07 at 04:45:21 PM GMT
//
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <choice>
-- * <element name="entrySet" type="{}EntrySetType"/>
-- * <element name="entry" type="{}EntryType"/>
-- * </choice>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;choice&gt;
++ * &lt;element name="entrySet" type="{}EntrySetType"/&gt;
++ * &lt;element name="entry" type="{}EntryType"/&gt;
++ * &lt;/choice&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2018.09.14 at 02:46:00 PM BST
++// Generated on: 2022.02.07 at 04:45:21 PM GMT
//
/**
* Database cross-reference.
*
-- * <p>Java class for XrefType complex type.
++ * <p>Java class for XrefType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="XrefType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <attribute name="db" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="secondaryId" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="XrefType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="db" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="secondaryId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the alcodon property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodon property.
+ * This is why there is not a <CODE>set</CODE> method for the alcodon property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAlcodon().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AlcodonFrame.Alcodon }
*
/**
* Gets the value of the alcodMap property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
+ * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAlcodMap().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AlcodonFrame.AlcodMap }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
* Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
*
*
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="thresholdLine" minOccurs="0">
- * <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>
- * </element>
- * <element name="property" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
- * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * <attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- * <attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="thresholdLine" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" /&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the annotationElement property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
+ * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAnnotationElement().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AnnotationElement }
*
/**
* Gets the value of the property property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getProperty().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Annotation.Property }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for AnnotationColourScheme complex type.
+ * <p>Java class for AnnotationColourScheme complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="AnnotationColourScheme">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- * <attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="AnnotationColourScheme"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="secondaryStructure" minOccurs="0">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <length value="1"/>
- * </restriction>
- * </simpleType>
- * </element>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
- * </sequence>
- * <attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="secondaryStructure" minOccurs="0"&gt;
+ * &lt;simpleType&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;length value="1"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for DoubleMatrix complex type.
+ * <p>Java class for DoubleMatrix complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="DoubleMatrix">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- * <element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- * </sequence>
- * <attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="DoubleMatrix"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the row property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the row property.
+ * This is why there is not a <CODE>set</CODE> method for the row property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getRow().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link DoubleVector }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for DoubleVector complex type.
+ * <p>Java class for DoubleVector complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="DoubleVector">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="DoubleVector"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the v property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the v property.
+ * This is why there is not a <CODE>set</CODE> method for the v property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getV().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Double }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for feature complex type.
+ * <p>Java class for feature complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="feature">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="otherData" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * </sequence>
- * <attribute name="begin" 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="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="feature"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the otherData property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the otherData property.
+ * This is why there is not a <CODE>set</CODE> method for the otherData property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getOtherData().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Feature.OtherData }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for FeatureMatcher complex type.
+ * <p>Java class for FeatureMatcher complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="FeatureMatcher">
- * <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="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attribute name="by" type="{www.jalview.org/colours}FilterBy" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="FeatureMatcher"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAttributeName().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
* A feature match condition, which may be simple or compound
*
- * <p>Java class for FeatureMatcherSet complex type.
+ * <p>Java class for FeatureMatcherSet complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="FeatureMatcherSet">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <choice>
- * <element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
- * <element name="compoundMatcher">
- * <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>
- * </element>
- * </choice>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="FeatureMatcherSet"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;choice&gt;
+ * &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/&gt;
+ * &lt;element name="compoundMatcher"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/choice&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the matcherSet property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
+ * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getMatcherSet().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link FeatureMatcherSet }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for FilterBy.
+ * <p>Java class for FilterBy.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * <simpleType name="FilterBy">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="byLabel"/>
- * <enumeration value="byScore"/>
- * <enumeration value="byAttribute"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="FilterBy"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="byLabel"/&gt;
+ * &lt;enumeration value="byScore"/&gt;
+ * &lt;enumeration value="byAttribute"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2020.12.10 at 03:00:06 PM GMT
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for JalviewModel complex type.
+ * <p>Java class for JalviewModel complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="JalviewModel">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- * <sequence>
- * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- * <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="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>
- * </element>
- * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * <element name="tree" maxOccurs="unbounded" minOccurs="0">
- * <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="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>
- * </element>
- * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * <element name="FeatureSettings" minOccurs="0">
- * <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>
- * </element>
- * </sequence>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="JalviewModel"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
+ * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
+ * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
++ * &lt;element name="overview" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
++ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
++ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt;
+ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="FeatureSettings" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the jSeq property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+ * This is why there is not a <CODE>set</CODE> method for the jSeq property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getJSeq().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq }
*
/**
* Gets the value of the jGroup property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+ * This is why there is not a <CODE>set</CODE> method for the jGroup property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getJGroup().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JGroup }
*
/**
* Gets the value of the viewport property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the viewport property.
+ * This is why there is not a <CODE>set</CODE> method for the viewport property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getViewport().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport }
*
/**
* Gets the value of the userColours property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the userColours property.
+ * This is why there is not a <CODE>set</CODE> method for the userColours property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getUserColours().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.UserColours }
*
/**
* Gets the value of the tree property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getTree().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Tree }
*
/**
* Gets the value of the pcaViewer property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+ * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getPcaViewer().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the setting property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the setting property.
+ * This is why there is not a <CODE>set</CODE> method for the setting property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSetting().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Setting }
*
/**
* Gets the value of the group property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the group property.
+ * This is why there is not a <CODE>set</CODE> method for the group property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getGroup().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Group }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAttributeName().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
+ * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the seq property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the seq property.
+ * This is why there is not a <CODE>set</CODE> method for the seq property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSeq().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the features property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the features property.
+ * This is why there is not a <CODE>set</CODE> method for the features property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getFeatures().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Feature }
*
/**
* Gets the value of the pdbids property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ * This is why there is not a <CODE>set</CODE> method for the pdbids property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getPdbids().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.Pdbids }
*
/**
* Gets the value of the hiddenSequences property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getHiddenSequences().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
* Gets the value of the rnaViewer property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getRnaViewer().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.RnaViewer }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org}pdbentry"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the structureState property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the structureState property.
+ * This is why there is not a <CODE>set</CODE> method for the structureState property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getStructureState().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.Pdbids.StructureState }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;simpleContent&gt;
+ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/simpleContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the secondaryStructure property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSecondaryStructure().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMin"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="seqPointMax"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
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 xpos;
@XmlAttribute(name = "ypos")
protected Integer ypos;
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
/**
* Gets the value of the sequencePoint property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+ * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequencePoint().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.SequencePoint }
*
/**
* Gets the value of the axis property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the axis property.
+ * This is why there is not a <CODE>set</CODE> method for the axis property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAxis().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.Axis }
*
}
/**
- * Gets the value of the includeGaps property.
+ * Gets the value of the width property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isIncludeGaps() {
- return includeGaps;
+ public Integer getWidth() {
+ return width;
}
/**
- * Sets the value of the includeGaps property.
+ * Sets the value of the width property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
+ public void setWidth(Integer value) {
+ this.width = value;
}
/**
- * Gets the value of the matchGaps property.
+ * Gets the value of the height property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isMatchGaps() {
- return matchGaps;
+ public Integer getHeight() {
+ return height;
}
/**
- * Sets the value of the matchGaps property.
+ * Sets the value of the height property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
+ public void setHeight(Integer value) {
+ this.height = value;
}
/**
- * Gets the value of the includeGappedColumns property.
+ * Gets the value of the xpos property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
+ public Integer getXpos() {
+ return xpos;
}
/**
- * Sets the value of the includeGappedColumns property.
+ * Sets the value of the xpos property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
+ public void setXpos(Integer value) {
+ this.xpos = value;
}
/**
- * Gets the value of the denominateByShortestLength property.
+ * Gets the value of the ypos property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
+ public Integer getYpos() {
+ return ypos;
}
/**
- * Sets the value of the denominateByShortestLength property.
+ * Sets the value of the ypos property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = value;
+ public void setYpos(Integer value) {
+ this.ypos = value;
}
/**
- * Gets the value of the width property.
+ * Gets the value of the includeGaps property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getWidth() {
- return width;
+ public Boolean isIncludeGaps() {
+ return includeGaps;
}
/**
- * Sets the value of the width property.
+ * Sets the value of the includeGaps property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setWidth(Integer value) {
- this.width = value;
+ public void setIncludeGaps(Boolean value) {
+ this.includeGaps = value;
}
/**
- * Gets the value of the height property.
+ * Gets the value of the matchGaps property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getHeight() {
- return height;
+ public Boolean isMatchGaps() {
+ return matchGaps;
}
/**
- * Sets the value of the height property.
+ * Sets the value of the matchGaps property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setHeight(Integer value) {
- this.height = value;
+ public void setMatchGaps(Boolean value) {
+ this.matchGaps = value;
}
/**
- * Gets the value of the xpos property.
+ * Gets the value of the includeGappedColumns property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getXpos() {
- return xpos;
+ public Boolean isIncludeGappedColumns() {
+ return includeGappedColumns;
}
/**
- * Sets the value of the xpos property.
+ * Sets the value of the includeGappedColumns property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setXpos(Integer value) {
- this.xpos = value;
+ public void setIncludeGappedColumns(Boolean value) {
+ this.includeGappedColumns = value;
}
/**
- * Gets the value of the ypos property.
+ * Gets the value of the denominateByShortestLength property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getYpos() {
- return ypos;
+ public Boolean isDenominateByShortestLength() {
+ return denominateByShortestLength;
}
/**
- * Sets the value of the ypos property.
+ * Sets the value of the denominateByShortestLength property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setYpos(Integer value) {
- this.ypos = value;
+ public void setDenominateByShortestLength(Boolean value) {
+ this.denominateByShortestLength = value;
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attGroup ref="{www.jalview.org}position"/&gt;
+ * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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="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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence minOccurs="0"&gt;
+ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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="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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
+ * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
++ * &lt;element name="overview" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
++ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
++ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
+ * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
+ * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
+ * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
@XmlType(name = "", propOrder = {
"annotationColours",
"hiddenColumns",
- "calcIdParam"
+ "calcIdParam",
+ "overview"
})
public static class Viewport {
protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
@XmlElement(namespace = "www.jalview.org")
protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+ @XmlElement(namespace = "www.jalview.org")
+ protected JalviewModel.Viewport.Overview overview;
@XmlAttribute(name = "conservationSelected")
protected Boolean conservationSelected;
@XmlAttribute(name = "pidSelected")
/**
* Gets the value of the hiddenColumns property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getHiddenColumns().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.HiddenColumns }
*
/**
* Gets the value of the calcIdParam property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getCalcIdParam().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.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
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
+ * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
}
+
+ /**
- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
+ *
- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
- * <pre>
- * <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>
- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
++ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
++ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden() {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value) {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getResidueColour() {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value) {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGapColour() {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value) {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHiddenColour() {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value) {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
+
}
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for JalviewUserColours complex type.
+ * <p>Java class for JalviewUserColours complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="JalviewUserColours">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="colour" 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"/>
- * </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>
- * </element>
- * <element name="filter" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * </sequence>
- * <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="JalviewUserColours"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the colour property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the colour property.
+ * This is why there is not a <CODE>set</CODE> method for the colour property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getColour().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewUserColours.Colour }
*
/**
* Gets the value of the filter property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the filter property.
+ * This is why there is not a <CODE>set</CODE> method for the filter property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getFilter().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewUserColours.Filter }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
+ * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
+ * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
+ * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAttributeName().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
* This effectively represents a java.util.MapList object
*
*
- * <p>Java class for mapListType complex type.
+ * <p>Java class for mapListType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="mapListType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * <element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * </sequence>
- * <attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- * <attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="mapListType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the mapListFrom property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
+ * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getMapListFrom().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link MapListType.MapListFrom }
*
/**
* Gets the value of the mapListTo property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
+ * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getMapListTo().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link MapListType.MapListTo }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
* to the sequence set (which will mean they are then added to the alignment too).
*
*
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
- * <sequence>
- * <choice minOccurs="0">
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
- * <element name="dseqFor">
- * <simpleType>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * </restriction>
- * </simpleType>
- * </element>
- * </choice>
- * </sequence>
- * <attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType"&gt;
+ * &lt;sequence&gt;
+ * &lt;choice minOccurs="0"&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&gt;
+ * &lt;element name="dseqFor"&gt;
+ * &lt;simpleType&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * &lt;/element&gt;
+ * &lt;/choice&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for NoValueColour.
+ * <p>Java class for NoValueColour.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * <simpleType name="NoValueColour">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="None"/>
- * <enumeration value="Min"/>
- * <enumeration value="Max"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="NoValueColour"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="None"/&gt;
+ * &lt;enumeration value="Min"/&gt;
+ * &lt;enumeration value="Max"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2020.12.10 at 10:15:41 AM GMT
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
* This object contains factory methods for each
* Java content interface and Java element interface
* generated in the jalview.xml.binding.jalview package.
- * <p>An ObjectFactory allows you to programatically
+ * <p>An ObjectFactory allows you to programatically
* construct new instances of the Java representation
* for XML content. The Java representation of XML
* content can consist of schema derived interfaces
@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");
+ private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
/**
* Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
}
/**
- * Create an instance of {@link AlcodonFrame }
- *
- */
- public AlcodonFrame createAlcodonFrame() {
- return new AlcodonFrame();
- }
-
- /**
* Create an instance of {@link MapListType }
*
*/
}
/**
+ * Create an instance of {@link AlcodonFrame }
+ *
+ */
+ public AlcodonFrame createAlcodonFrame() {
+ return new AlcodonFrame();
+ }
+
+ /**
* Create an instance of {@link Annotation }
*
*/
}
/**
- * Create an instance of {@link DoubleMatrix }
- *
- */
- public DoubleMatrix createDoubleMatrix() {
- return new DoubleMatrix();
- }
-
- /**
* Create an instance of {@link AnnotationColourScheme }
*
*/
}
/**
- * 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 }
+ * Create an instance of {@link DoubleMatrix }
*
*/
- public AnnotationElement createAnnotationElement() {
- return new AnnotationElement();
+ public DoubleMatrix createDoubleMatrix() {
+ return new DoubleMatrix();
}
/**
}
/**
+ * Create an instance of {@link AlcodonFrame.Alcodon }
+ *
+ */
+ public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+ return new AlcodonFrame.Alcodon();
+ }
+
+ /**
+ * Create an instance of {@link AlcodonFrame.AlcodMap }
+ *
+ */
+ public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+ return new AlcodonFrame.AlcodMap();
+ }
+
+ /**
+ * Create an instance of {@link AnnotationElement }
+ *
+ */
+ public AnnotationElement createAnnotationElement() {
+ return new AnnotationElement();
+ }
+
+ /**
* Create an instance of {@link Annotation.ThresholdLine }
*
*/
}
/**
+ * 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 }
*
*/
}
/**
- * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
- *
- */
- @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
- public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
- return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
- }
-
- /**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
*
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
*/
@XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
}
/**
- * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+ * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
*
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
*/
@XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
}
+ /**
+ * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+ *
+ * @param value
+ * Java instance representing xml element's value.
+ * @return
+ * the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+ */
+ @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+ public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
+ return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+ }
+
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
* The results of a PCA calculation
*
*
- * <p>Java class for PcaDataType complex type.
+ * <p>Java class for PcaDataType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="PcaDataType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * <element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * <element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="PcaDataType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for pdbentry complex type.
+ * <p>Java class for pdbentry complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="pdbentry">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence maxOccurs="unbounded" minOccurs="0">
- * <element name="property" maxOccurs="unbounded" minOccurs="0">
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" 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>
- * </element>
- * </sequence>
- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="pdbentry"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;element name="property" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the property property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the property property.
+ * This is why there is not a <CODE>set</CODE> method for the property property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getProperty().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Pdbentry.Property }
*
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <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>
- * </pre>
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
- * <sequence>
- * <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
- * <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" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </element>
- * </sequence>
- * <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/extension&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the dbRef property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the dbRef property.
+ * This is why there is not a <CODE>set</CODE> method for the dbRef property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getDBRef().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Sequence.DBRef }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <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" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
protected String accessionId;
@XmlAttribute(name = "locus")
protected Boolean locus;
+ @XmlAttribute(name = "canonical")
+ protected Boolean canonical;
/**
* Gets the value of the mapping property.
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;
+ }
+
}
}
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
- * <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
- * <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>
- * </element>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&gt;
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * &lt;/element&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the sequence property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequence property.
+ * This is why there is not a <CODE>set</CODE> method for the sequence property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequence().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Sequence }
*
/**
* Gets the value of the annotation property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the annotation property.
+ * This is why there is not a <CODE>set</CODE> method for the annotation property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAnnotation().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Annotation }
*
/**
* Gets the value of the sequenceSetProperties property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequenceSetProperties().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link SequenceSet.SequenceSetProperties }
*
/**
* Gets the value of the alcodonFrame property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
+ * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAlcodonFrame().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link AlcodonFrame }
*
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <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>
- * </pre>
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for SequenceType complex type.
+ * <p>Java class for SequenceType complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="SequenceType">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * </sequence>
- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="SequenceType"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for ThresholdType.
+ * <p>Java class for ThresholdType.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * <simpleType name="ThresholdType">
- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
- * <enumeration value="NONE"/>
- * <enumeration value="ABOVE"/>
- * <enumeration value="BELOW"/>
- * </restriction>
- * </simpleType>
- * </pre>
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <pre>
+ * &lt;simpleType name="ThresholdType"&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
+ * &lt;enumeration value="NONE"/&gt;
+ * &lt;enumeration value="ABOVE"/&gt;
+ * &lt;enumeration value="BELOW"/&gt;
+ * &lt;/restriction&gt;
+ * &lt;/simpleType&gt;
+ * </pre>
*
*/
@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for VAMSAS complex type.
+ * <p>Java class for VAMSAS complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="VAMSAS">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- * <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
- * </sequence>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="VAMSAS"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the tree property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getTree().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the sequenceSet property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
+ * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequenceSet().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link SequenceSet }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2019.06.07 at 02:21:15 PM BST
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
/**
- * <p>Java class for WebServiceParameterSet complex type.
+ * <p>Java class for WebServiceParameterSet complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * <complexType name="WebServiceParameterSet">
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence>
- * <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- * <element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
- * <element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
- * </sequence>
- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <pre>
+ * &lt;complexType name="WebServiceParameterSet"&gt;
+ * &lt;complexContent&gt;
+ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
+ * &lt;sequence&gt;
+ * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
+ * &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/&gt;
+ * &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
+ * &lt;/sequence&gt;
+ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
+ * &lt;/restriction&gt;
+ * &lt;/complexContent&gt;
+ * &lt;/complexType&gt;
+ * </pre>
*
*
*/
/**
* Gets the value of the serviceURL property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
+ * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getServiceURL().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
- // Generated on: 2021.08.30 at 11:05:22 AM BST
-// Generated on: 2020.12.10 at 03:00:06 PM GMT
++// Generated on: 2022.02.07 at 04:44:47 PM GMT
//
@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes different types of citations.
* Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines.
*
-- * <p>Java class for citationType complex type.
++ * <p>Java class for citationType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="citationType">
-- * <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="editorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/>
-- * <element name="authorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/>
-- * <element name="locator" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/>
-- * </sequence>
-- * <attribute name="type" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="book"/>
-- * <enumeration value="journal article"/>
-- * <enumeration value="online journal article"/>
-- * <enumeration value="patent"/>
-- * <enumeration value="submission"/>
-- * <enumeration value="thesis"/>
-- * <enumeration value="unpublished observations"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="date">
-- * <simpleType>
-- * <union memberTypes=" {http://www.w3.org/2001/XMLSchema}date {http://www.w3.org/2001/XMLSchema}gYearMonth {http://www.w3.org/2001/XMLSchema}gYear">
-- * </union>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="volume" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="first" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="last" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="publisher" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="city" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="db" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="number" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="institute" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="country" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="citationType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="editorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/&gt;
++ * &lt;element name="authorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/&gt;
++ * &lt;element name="locator" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="book"/&gt;
++ * &lt;enumeration value="journal article"/&gt;
++ * &lt;enumeration value="online journal article"/&gt;
++ * &lt;enumeration value="patent"/&gt;
++ * &lt;enumeration value="submission"/&gt;
++ * &lt;enumeration value="thesis"/&gt;
++ * &lt;enumeration value="unpublished observations"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="date"&gt;
++ * &lt;simpleType&gt;
++ * &lt;union memberTypes=" {http://www.w3.org/2001/XMLSchema}date {http://www.w3.org/2001/XMLSchema}gYearMonth {http://www.w3.org/2001/XMLSchema}gYear"&gt;
++ * &lt;/union&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="volume" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="first" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="last" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="publisher" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="city" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="db" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="number" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="institute" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="country" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the dbReference property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
++ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getDbReference().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link DbReferenceType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes a cofactor.
*
-- * <p>Java class for cofactorType complex type.
++ * <p>Java class for cofactorType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="cofactorType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-- * </sequence>
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="cofactorType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes different types of general annotations.
* Equivalent to the flat file CC-line.
*
-- * <p>Java class for commentType complex type.
++ * <p>Java class for commentType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="commentType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/>
-- * <choice minOccurs="0">
-- * <group ref="{http://uniprot.org/uniprot}bpcCommentGroup"/>
-- * <sequence>
-- * <element name="reaction" type="{http://uniprot.org/uniprot}reactionType"/>
-- * <element name="physiologicalReaction" type="{http://uniprot.org/uniprot}physiologicalReactionType" maxOccurs="2" minOccurs="0"/>
-- * </sequence>
-- * <sequence>
-- * <element name="cofactor" type="{http://uniprot.org/uniprot}cofactorType" maxOccurs="unbounded"/>
-- * </sequence>
-- * <sequence>
-- * <element name="subcellularLocation" type="{http://uniprot.org/uniprot}subcellularLocationType" maxOccurs="unbounded"/>
-- * </sequence>
-- * <element name="conflict">
-- * <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>
-- * </element>
-- * <sequence>
-- * <element name="link" maxOccurs="unbounded" minOccurs="0">
-- * <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>
-- * </element>
-- * </sequence>
-- * <sequence>
-- * <element name="event" type="{http://uniprot.org/uniprot}eventType" maxOccurs="4"/>
-- * <element name="isoform" type="{http://uniprot.org/uniprot}isoformType" maxOccurs="unbounded" minOccurs="0"/>
-- * </sequence>
-- * <sequence>
-- * <element name="interactant" type="{http://uniprot.org/uniprot}interactantType" maxOccurs="2" minOccurs="2"/>
-- * <element name="organismsDiffer" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
-- * <element name="experiments" type="{http://www.w3.org/2001/XMLSchema}int"/>
-- * </sequence>
-- * <element name="disease">
-- * <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>
-- * </element>
-- * </choice>
-- * <element name="location" type="{http://uniprot.org/uniprot}locationType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- * </sequence>
-- * <attribute name="type" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="allergen"/>
-- * <enumeration value="alternative products"/>
-- * <enumeration value="biotechnology"/>
-- * <enumeration value="biophysicochemical properties"/>
-- * <enumeration value="catalytic activity"/>
-- * <enumeration value="caution"/>
-- * <enumeration value="cofactor"/>
-- * <enumeration value="developmental stage"/>
-- * <enumeration value="disease"/>
-- * <enumeration value="domain"/>
-- * <enumeration value="disruption phenotype"/>
-- * <enumeration value="activity regulation"/>
-- * <enumeration value="function"/>
-- * <enumeration value="induction"/>
-- * <enumeration value="miscellaneous"/>
-- * <enumeration value="pathway"/>
-- * <enumeration value="pharmaceutical"/>
-- * <enumeration value="polymorphism"/>
-- * <enumeration value="PTM"/>
-- * <enumeration value="RNA editing"/>
-- * <enumeration value="similarity"/>
-- * <enumeration value="subcellular location"/>
-- * <enumeration value="sequence caution"/>
-- * <enumeration value="subunit"/>
-- * <enumeration value="tissue specificity"/>
-- * <enumeration value="toxic dose"/>
-- * <enumeration value="online information"/>
-- * <enumeration value="mass spectrometry"/>
-- * <enumeration value="interaction"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="locationType" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="mass" type="{http://www.w3.org/2001/XMLSchema}float" />
-- * <attribute name="error" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="method" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="commentType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/&gt;
++ * &lt;choice minOccurs="0"&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}bpcCommentGroup"/&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="reaction" type="{http://uniprot.org/uniprot}reactionType"/&gt;
++ * &lt;element name="physiologicalReaction" type="{http://uniprot.org/uniprot}physiologicalReactionType" maxOccurs="2" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="cofactor" type="{http://uniprot.org/uniprot}cofactorType" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="subcellularLocation" type="{http://uniprot.org/uniprot}subcellularLocationType" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;element name="conflict"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="sequence" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="resource" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="EMBL-CDS"/&gt;
++ * &lt;enumeration value="EMBL"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="frameshift"/&gt;
++ * &lt;enumeration value="erroneous initiation"/&gt;
++ * &lt;enumeration value="erroneous termination"/&gt;
++ * &lt;enumeration value="erroneous gene model prediction"/&gt;
++ * &lt;enumeration value="erroneous translation"/&gt;
++ * &lt;enumeration value="miscellaneous discrepancy"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="link" maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="event" type="{http://uniprot.org/uniprot}eventType" maxOccurs="4"/&gt;
++ * &lt;element name="isoform" type="{http://uniprot.org/uniprot}isoformType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="interactant" type="{http://uniprot.org/uniprot}interactantType" maxOccurs="2" minOccurs="2"/&gt;
++ * &lt;element name="organismsDiffer" type="{http://www.w3.org/2001/XMLSchema}boolean"/&gt;
++ * &lt;element name="experiments" type="{http://www.w3.org/2001/XMLSchema}int"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;element name="disease"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/choice&gt;
++ * &lt;element name="location" type="{http://uniprot.org/uniprot}locationType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="allergen"/&gt;
++ * &lt;enumeration value="alternative products"/&gt;
++ * &lt;enumeration value="biotechnology"/&gt;
++ * &lt;enumeration value="biophysicochemical properties"/&gt;
++ * &lt;enumeration value="catalytic activity"/&gt;
++ * &lt;enumeration value="caution"/&gt;
++ * &lt;enumeration value="cofactor"/&gt;
++ * &lt;enumeration value="developmental stage"/&gt;
++ * &lt;enumeration value="disease"/&gt;
++ * &lt;enumeration value="domain"/&gt;
++ * &lt;enumeration value="disruption phenotype"/&gt;
++ * &lt;enumeration value="activity regulation"/&gt;
++ * &lt;enumeration value="function"/&gt;
++ * &lt;enumeration value="induction"/&gt;
++ * &lt;enumeration value="miscellaneous"/&gt;
++ * &lt;enumeration value="pathway"/&gt;
++ * &lt;enumeration value="pharmaceutical"/&gt;
++ * &lt;enumeration value="polymorphism"/&gt;
++ * &lt;enumeration value="PTM"/&gt;
++ * &lt;enumeration value="RNA editing"/&gt;
++ * &lt;enumeration value="similarity"/&gt;
++ * &lt;enumeration value="subcellular location"/&gt;
++ * &lt;enumeration value="sequence caution"/&gt;
++ * &lt;enumeration value="subunit"/&gt;
++ * &lt;enumeration value="tissue specificity"/&gt;
++ * &lt;enumeration value="toxic dose"/&gt;
++ * &lt;enumeration value="online information"/&gt;
++ * &lt;enumeration value="mass spectrometry"/&gt;
++ * &lt;enumeration value="interaction"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="locationType" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="mass" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
++ * &lt;attribute name="error" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="method" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the physiologicalReaction property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the physiologicalReaction property.
++ * This is why there is not a <CODE>set</CODE> method for the physiologicalReaction property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getPhysiologicalReaction().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link PhysiologicalReactionType }
*
/**
* Gets the value of the cofactor property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the cofactor property.
++ * This is why there is not a <CODE>set</CODE> method for the cofactor property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getCofactor().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link CofactorType }
*
/**
* Gets the value of the subcellularLocation property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property.
++ * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getSubcellularLocation().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link SubcellularLocationType }
*
/**
* Gets the value of the link property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the link property.
++ * This is why there is not a <CODE>set</CODE> method for the link property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getLink().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link CommentType.Link }
*
/**
* Gets the value of the event property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the event property.
++ * This is why there is not a <CODE>set</CODE> method for the event property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvent().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EventType }
*
/**
* Gets the value of the isoform property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the isoform property.
++ * This is why there is not a <CODE>set</CODE> method for the isoform property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getIsoform().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link IsoformType }
*
/**
* Gets the value of the interactant property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the interactant property.
++ * This is why there is not a <CODE>set</CODE> method for the interactant property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getInteractant().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link InteractantType }
*
/**
* Gets the value of the location property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the location property.
++ * This is why there is not a <CODE>set</CODE> method for the location property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getLocation().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link LocationType }
*
/**
* Gets the value of the text property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the text property.
++ * This is why there is not a <CODE>set</CODE> method for the text property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getText().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/&gt;
++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the text property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the text property.
++ * This is why there is not a <CODE>set</CODE> method for the text property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getText().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="sequence" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="resource" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="EMBL-CDS"/&gt;
++ * &lt;enumeration value="EMBL"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="frameshift"/&gt;
++ * &lt;enumeration value="erroneous initiation"/&gt;
++ * &lt;enumeration value="erroneous termination"/&gt;
++ * &lt;enumeration value="erroneous gene model prediction"/&gt;
++ * &lt;enumeration value="erroneous translation"/&gt;
++ * &lt;enumeration value="miscellaneous discrepancy"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="resource" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="EMBL-CDS"/&gt;
++ * &lt;enumeration value="EMBL"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
-- *
-- * <p>The following schema fragment specifies the expected content contained within this class.
-- *
-- * <pre>
-- * <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>
-- * </pre>
++ * <p>Java class for anonymous complex type.
++ *
++ * <p>The following schema fragment specifies the expected content contained within this class.
++ *
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the km property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the km property.
++ * This is why there is not a <CODE>set</CODE> method for the km property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getKM().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the vmax property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the vmax property.
++ * This is why there is not a <CODE>set</CODE> method for the vmax property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getVmax().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the text property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the text property.
++ * This is why there is not a <CODE>set</CODE> method for the text property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getText().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the text property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the text property.
++ * This is why there is not a <CODE>set</CODE> method for the text property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getText().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the text property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the text property.
++ * This is why there is not a <CODE>set</CODE> method for the text property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getText().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the text property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the text property.
++ * This is why there is not a <CODE>set</CODE> method for the text property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getText().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes the authors of a citation when these are represented by a consortium.
* Equivalent to the flat file RG-line.
*
-- * <p>Java class for consortiumType complex type.
++ * <p>Java class for consortiumType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="consortiumType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="consortiumType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Equivalent to the flat file DR-line.
*
*
-- * <p>Java class for dbReferenceType complex type.
++ * <p>Java class for dbReferenceType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="dbReferenceType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/>
-- * <element name="property" type="{http://uniprot.org/uniprot}propertyType" maxOccurs="unbounded" minOccurs="0"/>
-- * </sequence>
-- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="dbReferenceType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/&gt;
++ * &lt;element name="property" type="{http://uniprot.org/uniprot}propertyType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the property property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the property property.
++ * This is why there is not a <CODE>set</CODE> method for the property property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getProperty().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link PropertyType }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="accession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-- * <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-- * <element name="protein" type="{http://uniprot.org/uniprot}proteinType"/>
-- * <element name="gene" type="{http://uniprot.org/uniprot}geneType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="organism" type="{http://uniprot.org/uniprot}organismType"/>
-- * <element name="organismHost" type="{http://uniprot.org/uniprot}organismType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="geneLocation" type="{http://uniprot.org/uniprot}geneLocationType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="reference" type="{http://uniprot.org/uniprot}referenceType" maxOccurs="unbounded"/>
-- * <element name="comment" type="{http://uniprot.org/uniprot}commentType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="proteinExistence" type="{http://uniprot.org/uniprot}proteinExistenceType"/>
-- * <element name="keyword" type="{http://uniprot.org/uniprot}keywordType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="feature" type="{http://uniprot.org/uniprot}featureType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="evidence" type="{http://uniprot.org/uniprot}evidenceType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="sequence" type="{http://uniprot.org/uniprot}sequenceType"/>
-- * </sequence>
-- * <attribute name="dataset" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="Swiss-Prot"/>
-- * <enumeration value="TrEMBL"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="created" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
-- * <attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
-- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="accession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
++ * &lt;element name="protein" type="{http://uniprot.org/uniprot}proteinType"/&gt;
++ * &lt;element name="gene" type="{http://uniprot.org/uniprot}geneType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="organism" type="{http://uniprot.org/uniprot}organismType"/&gt;
++ * &lt;element name="organismHost" type="{http://uniprot.org/uniprot}organismType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="geneLocation" type="{http://uniprot.org/uniprot}geneLocationType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="reference" type="{http://uniprot.org/uniprot}referenceType" maxOccurs="unbounded"/&gt;
++ * &lt;element name="comment" type="{http://uniprot.org/uniprot}commentType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="proteinExistence" type="{http://uniprot.org/uniprot}proteinExistenceType"/&gt;
++ * &lt;element name="keyword" type="{http://uniprot.org/uniprot}keywordType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="feature" type="{http://uniprot.org/uniprot}featureType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="evidence" type="{http://uniprot.org/uniprot}evidenceType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="sequence" type="{http://uniprot.org/uniprot}sequenceType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="dataset" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="Swiss-Prot"/&gt;
++ * &lt;enumeration value="TrEMBL"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="created" use="required" type="{http://www.w3.org/2001/XMLSchema}date" /&gt;
++ * &lt;attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the accession property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the accession property.
++ * This is why there is not a <CODE>set</CODE> method for the accession property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getAccession().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the name property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the name property.
++ * This is why there is not a <CODE>set</CODE> method for the name property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the gene property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the gene property.
++ * This is why there is not a <CODE>set</CODE> method for the gene property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getGene().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link GeneType }
*
/**
* Gets the value of the organismHost property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the organismHost property.
++ * This is why there is not a <CODE>set</CODE> method for the organismHost property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getOrganismHost().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link OrganismType }
*
/**
* Gets the value of the geneLocation property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the geneLocation property.
++ * This is why there is not a <CODE>set</CODE> method for the geneLocation property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getGeneLocation().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link GeneLocationType }
*
/**
* Gets the value of the reference property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the reference property.
++ * This is why there is not a <CODE>set</CODE> method for the reference property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getReference().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ReferenceType }
*
/**
* Gets the value of the comment property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the comment property.
++ * This is why there is not a <CODE>set</CODE> method for the comment property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getComment().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link CommentType }
*
/**
* Gets the value of the dbReference property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
++ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getDbReference().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link DbReferenceType }
*
/**
* Gets the value of the keyword property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the keyword property.
++ * This is why there is not a <CODE>set</CODE> method for the keyword property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getKeyword().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link KeywordType }
*
/**
* Gets the value of the feature property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the feature property.
++ * This is why there is not a <CODE>set</CODE> method for the feature property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getFeature().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link FeatureType }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidenceType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes the type of events that cause alternative products.
*
-- * <p>Java class for eventType complex type.
++ * <p>Java class for eventType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="eventType">
-- * <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="alternative splicing"/>
-- * <enumeration value="alternative initiation"/>
-- * <enumeration value="alternative promoter"/>
-- * <enumeration value="ribosomal frameshifting"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="eventType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="alternative splicing"/&gt;
++ * &lt;enumeration value="alternative initiation"/&gt;
++ * &lt;enumeration value="alternative promoter"/&gt;
++ * &lt;enumeration value="ribosomal frameshifting"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes the evidence for an annotation.
* No flat file equivalent.
*
-- * <p>Java class for evidenceType complex type.
++ * <p>Java class for evidenceType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="evidenceType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="source" type="{http://uniprot.org/uniprot}sourceType" minOccurs="0"/>
-- * <element name="importedFrom" type="{http://uniprot.org/uniprot}importedFromType" minOccurs="0"/>
-- * </sequence>
-- * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="evidenceType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="source" type="{http://uniprot.org/uniprot}sourceType" minOccurs="0"/&gt;
++ * &lt;element name="importedFrom" type="{http://uniprot.org/uniprot}importedFromType" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for evidencedStringType complex type.
++ * <p>Java class for evidencedStringType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="evidencedStringType">
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * <attribute name="status">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="by similarity"/>
-- * <enumeration value="probable"/>
-- * <enumeration value="potential"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="evidencedStringType"&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;attribute name="status"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="by similarity"/&gt;
++ * &lt;enumeration value="probable"/&gt;
++ * &lt;enumeration value="potential"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes different types of sequence annotations.
* Equivalent to the flat file FT-line.
*
-- * <p>Java class for featureType complex type.
++ * <p>Java class for featureType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="featureType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- * <element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="location" type="{http://uniprot.org/uniprot}locationType"/>
-- * </sequence>
-- * <attribute name="type" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="active site"/>
-- * <enumeration value="binding site"/>
-- * <enumeration value="calcium-binding region"/>
-- * <enumeration value="chain"/>
-- * <enumeration value="coiled-coil region"/>
-- * <enumeration value="compositionally biased region"/>
-- * <enumeration value="cross-link"/>
-- * <enumeration value="disulfide bond"/>
-- * <enumeration value="DNA-binding region"/>
-- * <enumeration value="domain"/>
-- * <enumeration value="glycosylation site"/>
-- * <enumeration value="helix"/>
-- * <enumeration value="initiator methionine"/>
-- * <enumeration value="lipid moiety-binding region"/>
-- * <enumeration value="metal ion-binding site"/>
-- * <enumeration value="modified residue"/>
-- * <enumeration value="mutagenesis site"/>
-- * <enumeration value="non-consecutive residues"/>
-- * <enumeration value="non-terminal residue"/>
-- * <enumeration value="nucleotide phosphate-binding region"/>
-- * <enumeration value="peptide"/>
-- * <enumeration value="propeptide"/>
-- * <enumeration value="region of interest"/>
-- * <enumeration value="repeat"/>
-- * <enumeration value="non-standard amino acid"/>
-- * <enumeration value="sequence conflict"/>
-- * <enumeration value="sequence variant"/>
-- * <enumeration value="short sequence motif"/>
-- * <enumeration value="signal peptide"/>
-- * <enumeration value="site"/>
-- * <enumeration value="splice variant"/>
-- * <enumeration value="strand"/>
-- * <enumeration value="topological domain"/>
-- * <enumeration value="transit peptide"/>
-- * <enumeration value="transmembrane region"/>
-- * <enumeration value="turn"/>
-- * <enumeration value="unsure residue"/>
-- * <enumeration value="zinc finger region"/>
-- * <enumeration value="intramembrane region"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="status">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="by similarity"/>
-- * <enumeration value="probable"/>
-- * <enumeration value="potential"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="featureType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
++ * &lt;element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="location" type="{http://uniprot.org/uniprot}locationType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="active site"/&gt;
++ * &lt;enumeration value="binding site"/&gt;
++ * &lt;enumeration value="calcium-binding region"/&gt;
++ * &lt;enumeration value="chain"/&gt;
++ * &lt;enumeration value="coiled-coil region"/&gt;
++ * &lt;enumeration value="compositionally biased region"/&gt;
++ * &lt;enumeration value="cross-link"/&gt;
++ * &lt;enumeration value="disulfide bond"/&gt;
++ * &lt;enumeration value="DNA-binding region"/&gt;
++ * &lt;enumeration value="domain"/&gt;
++ * &lt;enumeration value="glycosylation site"/&gt;
++ * &lt;enumeration value="helix"/&gt;
++ * &lt;enumeration value="initiator methionine"/&gt;
++ * &lt;enumeration value="lipid moiety-binding region"/&gt;
++ * &lt;enumeration value="metal ion-binding site"/&gt;
++ * &lt;enumeration value="modified residue"/&gt;
++ * &lt;enumeration value="mutagenesis site"/&gt;
++ * &lt;enumeration value="non-consecutive residues"/&gt;
++ * &lt;enumeration value="non-terminal residue"/&gt;
++ * &lt;enumeration value="nucleotide phosphate-binding region"/&gt;
++ * &lt;enumeration value="peptide"/&gt;
++ * &lt;enumeration value="propeptide"/&gt;
++ * &lt;enumeration value="region of interest"/&gt;
++ * &lt;enumeration value="repeat"/&gt;
++ * &lt;enumeration value="non-standard amino acid"/&gt;
++ * &lt;enumeration value="sequence conflict"/&gt;
++ * &lt;enumeration value="sequence variant"/&gt;
++ * &lt;enumeration value="short sequence motif"/&gt;
++ * &lt;enumeration value="signal peptide"/&gt;
++ * &lt;enumeration value="site"/&gt;
++ * &lt;enumeration value="splice variant"/&gt;
++ * &lt;enumeration value="strand"/&gt;
++ * &lt;enumeration value="topological domain"/&gt;
++ * &lt;enumeration value="transit peptide"/&gt;
++ * &lt;enumeration value="transmembrane region"/&gt;
++ * &lt;enumeration value="turn"/&gt;
++ * &lt;enumeration value="unsure residue"/&gt;
++ * &lt;enumeration value="zinc finger region"/&gt;
++ * &lt;enumeration value="intramembrane region"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="status"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="by similarity"/&gt;
++ * &lt;enumeration value="probable"/&gt;
++ * &lt;enumeration value="potential"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the variation property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the variation property.
++ * This is why there is not a <CODE>set</CODE> method for the variation property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getVariation().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes non-nuclear gene locations (organelles and plasmids).
* Equivalent to the flat file OG-line.
*
-- * <p>Java class for geneLocationType complex type.
++ * <p>Java class for geneLocationType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="geneLocationType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="name" type="{http://uniprot.org/uniprot}statusType" maxOccurs="unbounded" minOccurs="0"/>
-- * </sequence>
-- * <attribute name="type" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="apicoplast"/>
-- * <enumeration value="chloroplast"/>
-- * <enumeration value="organellar chromatophore"/>
-- * <enumeration value="cyanelle"/>
-- * <enumeration value="hydrogenosome"/>
-- * <enumeration value="mitochondrion"/>
-- * <enumeration value="non-photosynthetic plastid"/>
-- * <enumeration value="nucleomorph"/>
-- * <enumeration value="plasmid"/>
-- * <enumeration value="plastid"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="geneLocationType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="name" type="{http://uniprot.org/uniprot}statusType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="apicoplast"/&gt;
++ * &lt;enumeration value="chloroplast"/&gt;
++ * &lt;enumeration value="organellar chromatophore"/&gt;
++ * &lt;enumeration value="cyanelle"/&gt;
++ * &lt;enumeration value="hydrogenosome"/&gt;
++ * &lt;enumeration value="mitochondrion"/&gt;
++ * &lt;enumeration value="non-photosynthetic plastid"/&gt;
++ * &lt;enumeration value="nucleomorph"/&gt;
++ * &lt;enumeration value="plasmid"/&gt;
++ * &lt;enumeration value="plastid"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the name property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the name property.
++ * This is why there is not a <CODE>set</CODE> method for the name property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link StatusType }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes different types of gene designations.
* Equivalent to the flat file GN-line.
*
-- * <p>Java class for geneNameType complex type.
++ * <p>Java class for geneNameType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="geneNameType">
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * <attribute name="type" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="primary"/>
-- * <enumeration value="synonym"/>
-- * <enumeration value="ordered locus"/>
-- * <enumeration value="ORF"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="geneNameType"&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="primary"/&gt;
++ * &lt;enumeration value="synonym"/&gt;
++ * &lt;enumeration value="ordered locus"/&gt;
++ * &lt;enumeration value="ORF"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes a gene.
* Equivalent to the flat file GN-line.
*
-- * <p>Java class for geneType complex type.
++ * <p>Java class for geneType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="geneType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="name" type="{http://uniprot.org/uniprot}geneNameType" maxOccurs="unbounded"/>
-- * </sequence>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="geneType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="name" type="{http://uniprot.org/uniprot}geneNameType" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the name property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the name property.
++ * This is why there is not a <CODE>set</CODE> method for the name property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link GeneNameType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database.
*
-- * <p>Java class for importedFromType complex type.
++ * <p>Java class for importedFromType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="importedFromType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-- * </sequence>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="importedFromType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for interactantType complex type.
++ * <p>Java class for interactantType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="interactantType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <group ref="{http://uniprot.org/uniprot}interactantGroup" minOccurs="0"/>
-- * <attribute name="intactId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="interactantType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}interactantGroup" minOccurs="0"/&gt;
++ * &lt;attribute name="intactId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes isoforms in 'alternative products' annotations.
*
-- * <p>Java class for isoformType complex type.
++ * <p>Java class for isoformType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="isoformType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="id" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-- * <element name="name" maxOccurs="unbounded">
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </element>
-- * <element name="sequence">
-- * <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>
-- * </element>
-- * <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- * </sequence>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="isoformType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="id" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
++ * &lt;element name="name" maxOccurs="unbounded"&gt;
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="sequence"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="not described"/&gt;
++ * &lt;enumeration value="described"/&gt;
++ * &lt;enumeration value="displayed"/&gt;
++ * &lt;enumeration value="external"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the id property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the id property.
++ * This is why there is not a <CODE>set</CODE> method for the id property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getId().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the name property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the name property.
++ * This is why there is not a <CODE>set</CODE> method for the name property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link IsoformType.Name }
*
/**
* Gets the value of the text property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the text property.
++ * This is why there is not a <CODE>set</CODE> method for the text property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getText().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="not described"/&gt;
++ * &lt;enumeration value="described"/&gt;
++ * &lt;enumeration value="displayed"/&gt;
++ * &lt;enumeration value="external"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for keywordType complex type.
++ * <p>Java class for keywordType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="keywordType">
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="keywordType"&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry.
*
-- * <p>Java class for locationType complex type.
++ * <p>Java class for locationType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="locationType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <choice>
-- * <sequence>
-- * <element name="begin" type="{http://uniprot.org/uniprot}positionType"/>
-- * <element name="end" type="{http://uniprot.org/uniprot}positionType"/>
-- * </sequence>
-- * <element name="position" type="{http://uniprot.org/uniprot}positionType"/>
-- * </choice>
-- * <attribute name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="locationType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;choice&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="begin" type="{http://uniprot.org/uniprot}positionType"/&gt;
++ * &lt;element name="end" type="{http://uniprot.org/uniprot}positionType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;element name="position" type="{http://uniprot.org/uniprot}positionType"/&gt;
++ * &lt;/choice&gt;
++ * &lt;attribute name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes a molecule by name or unique identifier.
*
-- * <p>Java class for moleculeType complex type.
++ * <p>Java class for moleculeType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="moleculeType">
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="moleculeType"&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for nameListType complex type.
++ * <p>Java class for nameListType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="nameListType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <choice maxOccurs="unbounded">
-- * <element name="consortium" type="{http://uniprot.org/uniprot}consortiumType"/>
-- * <element name="person" type="{http://uniprot.org/uniprot}personType"/>
-- * </choice>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="nameListType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;choice maxOccurs="unbounded"&gt;
++ * &lt;element name="consortium" type="{http://uniprot.org/uniprot}consortiumType"/&gt;
++ * &lt;element name="person" type="{http://uniprot.org/uniprot}personType"/&gt;
++ * &lt;/choice&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the consortiumOrPerson property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property.
++ * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getConsortiumOrPerson().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ConsortiumType }
* {@link PersonType }
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* This object contains factory methods for each
* Java content interface and Java element interface
* generated in the jalview.xml.binding.uniprot package.
-- * <p>An ObjectFactory allows you to programatically
++ * <p>An ObjectFactory allows you to programatically
* construct new instances of the Java representation
* for XML content. The Java representation of XML
* content can consist of schema derived interfaces
}
/**
-- * Create an instance of {@link SourceDataType }
++ * Create an instance of {@link IsoformType }
*
*/
-- public SourceDataType createSourceDataType() {
-- return new SourceDataType();
++ public IsoformType createIsoformType() {
++ return new IsoformType();
}
/**
-- * Create an instance of {@link IsoformType }
++ * Create an instance of {@link SourceDataType }
*
*/
-- public IsoformType createIsoformType() {
-- return new IsoformType();
++ public SourceDataType createSourceDataType() {
++ return new SourceDataType();
}
/**
}
/**
++ * Create an instance of {@link Uniprot }
++ *
++ */
++ public Uniprot createUniprot() {
++ return new Uniprot();
++ }
++
++ /**
* Create an instance of {@link Entry }
*
*/
}
/**
-- * Create an instance of {@link Uniprot }
++ * Create an instance of {@link GeneNameType }
*
*/
-- public Uniprot createUniprot() {
-- return new Uniprot();
++ public GeneNameType createGeneNameType() {
++ return new GeneNameType();
++ }
++
++ /**
++ * Create an instance of {@link OrganismNameType }
++ *
++ */
++ public OrganismNameType createOrganismNameType() {
++ return new OrganismNameType();
}
/**
}
/**
-- * Create an instance of {@link PositionType }
++ * Create an instance of {@link CitationType }
*
*/
-- public PositionType createPositionType() {
-- return new PositionType();
++ public CitationType createCitationType() {
++ return new CitationType();
}
/**
}
/**
-- * Create an instance of {@link GeneNameType }
-- *
-- */
-- public GeneNameType createGeneNameType() {
-- return new GeneNameType();
-- }
--
-- /**
-- * Create an instance of {@link LocationType }
++ * Create an instance of {@link PersonType }
*
*/
-- public LocationType createLocationType() {
-- return new LocationType();
++ public PersonType createPersonType() {
++ return new PersonType();
}
/**
-- * Create an instance of {@link CitationType }
++ * Create an instance of {@link NameListType }
*
*/
-- public CitationType createCitationType() {
-- return new CitationType();
++ public NameListType createNameListType() {
++ return new NameListType();
}
/**
-- * Create an instance of {@link PropertyType }
++ * Create an instance of {@link ReactionType }
*
*/
-- public PropertyType createPropertyType() {
-- return new PropertyType();
++ public ReactionType createReactionType() {
++ return new ReactionType();
}
/**
}
/**
-- * Create an instance of {@link EvidencedStringType }
++ * Create an instance of {@link SubcellularLocationType }
*
*/
-- public EvidencedStringType createEvidencedStringType() {
-- return new EvidencedStringType();
++ public SubcellularLocationType createSubcellularLocationType() {
++ return new SubcellularLocationType();
}
/**
-- * Create an instance of {@link PersonType }
++ * Create an instance of {@link EventType }
*
*/
-- public PersonType createPersonType() {
-- return new PersonType();
++ public EventType createEventType() {
++ return new EventType();
}
/**
-- * Create an instance of {@link ImportedFromType }
++ * Create an instance of {@link InteractantType }
*
*/
-- public ImportedFromType createImportedFromType() {
-- return new ImportedFromType();
++ public InteractantType createInteractantType() {
++ return new InteractantType();
}
/**
-- * Create an instance of {@link EventType }
++ * Create an instance of {@link PropertyType }
*
*/
-- public EventType createEventType() {
-- return new EventType();
++ public PropertyType createPropertyType() {
++ return new PropertyType();
}
/**
-- * Create an instance of {@link InteractantType }
++ * Create an instance of {@link LocationType }
*
*/
-- public InteractantType createInteractantType() {
-- return new InteractantType();
++ public LocationType createLocationType() {
++ return new LocationType();
}
/**
-- * Create an instance of {@link NameListType }
++ * Create an instance of {@link PositionType }
*
*/
-- public NameListType createNameListType() {
-- return new NameListType();
++ public PositionType createPositionType() {
++ return new PositionType();
}
/**
-- * Create an instance of {@link ReactionType }
++ * Create an instance of {@link MoleculeType }
*
*/
-- public ReactionType createReactionType() {
-- return new ReactionType();
++ public MoleculeType createMoleculeType() {
++ return new MoleculeType();
}
/**
}
/**
-- * Create an instance of {@link MoleculeType }
++ * Create an instance of {@link ImportedFromType }
*
*/
-- public MoleculeType createMoleculeType() {
-- return new MoleculeType();
++ public ImportedFromType createImportedFromType() {
++ return new ImportedFromType();
}
/**
-- * Create an instance of {@link OrganismNameType }
++ * Create an instance of {@link EvidencedStringType }
*
*/
-- public OrganismNameType createOrganismNameType() {
-- return new OrganismNameType();
++ public EvidencedStringType createEvidencedStringType() {
++ return new EvidencedStringType();
}
/**
-- * Create an instance of {@link SubcellularLocationType }
++ * Create an instance of {@link IsoformType.Name }
*
*/
-- public SubcellularLocationType createSubcellularLocationType() {
-- return new SubcellularLocationType();
++ 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 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 }
*
*/
}
/**
-- * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}}
++ * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}
*
++ * @param value
++ * Java instance representing xml element's value.
++ * @return
++ * the new instance of {@link JAXBElement }{@code <}{@link String }{@code >}
*/
@XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright")
public JAXBElement<String> createCopyright(String value) {
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes different types of source organism names.
*
-- * <p>Java class for organismNameType complex type.
++ * <p>Java class for organismNameType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="organismNameType">
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="type" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="common"/>
-- * <enumeration value="full"/>
-- * <enumeration value="scientific"/>
-- * <enumeration value="synonym"/>
-- * <enumeration value="abbreviation"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="organismNameType"&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="common"/&gt;
++ * &lt;enumeration value="full"/&gt;
++ * &lt;enumeration value="scientific"/&gt;
++ * &lt;enumeration value="synonym"/&gt;
++ * &lt;enumeration value="abbreviation"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes the source organism.
*
-- * <p>Java class for organismType complex type.
++ * <p>Java class for organismType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="organismType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="name" type="{http://uniprot.org/uniprot}organismNameType" maxOccurs="unbounded"/>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/>
-- * <element name="lineage" minOccurs="0">
-- * <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>
-- * </element>
-- * </sequence>
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="organismType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="name" type="{http://uniprot.org/uniprot}organismNameType" maxOccurs="unbounded"/&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/&gt;
++ * &lt;element name="lineage" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the name property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the name property.
++ * This is why there is not a <CODE>set</CODE> method for the name property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link OrganismNameType }
*
/**
* Gets the value of the dbReference property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
++ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getDbReference().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link DbReferenceType }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the taxon property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the taxon property.
++ * This is why there is not a <CODE>set</CODE> method for the taxon property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getTaxon().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for personType complex type.
++ * <p>Java class for personType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="personType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="personType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes a physiological reaction.
*
-- * <p>Java class for physiologicalReactionType complex type.
++ * <p>Java class for physiologicalReactionType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="physiologicalReactionType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-- * </sequence>
-- * <attribute name="direction" use="required">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="left-to-right"/>
-- * <enumeration value="right-to-left"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="physiologicalReactionType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="direction" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="left-to-right"/&gt;
++ * &lt;enumeration value="right-to-left"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for positionType complex type.
++ * <p>Java class for positionType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="positionType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <attribute name="position" type="{http://www.w3.org/2001/XMLSchema}unsignedLong" />
-- * <attribute name="status" default="certain">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="certain"/>
-- * <enumeration value="uncertain"/>
-- * <enumeration value="less than"/>
-- * <enumeration value="greater than"/>
-- * <enumeration value="unknown"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="positionType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="position" type="{http://www.w3.org/2001/XMLSchema}unsignedLong" /&gt;
++ * &lt;attribute name="status" default="certain"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="certain"/&gt;
++ * &lt;enumeration value="uncertain"/&gt;
++ * &lt;enumeration value="less than"/&gt;
++ * &lt;enumeration value="greater than"/&gt;
++ * &lt;enumeration value="unknown"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for propertyType complex type.
++ * <p>Java class for propertyType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="propertyType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <attribute name="type" 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>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="propertyType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes the evidence for the protein's existence.
* Equivalent to the flat file PE-line.
*
-- * <p>Java class for proteinExistenceType complex type.
++ * <p>Java class for proteinExistenceType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="proteinExistenceType">
-- * <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="evidence at protein level"/>
-- * <enumeration value="evidence at transcript level"/>
-- * <enumeration value="inferred from homology"/>
-- * <enumeration value="predicted"/>
-- * <enumeration value="uncertain"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="proteinExistenceType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;attribute name="type" use="required"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="evidence at protein level"/&gt;
++ * &lt;enumeration value="evidence at transcript level"/&gt;
++ * &lt;enumeration value="inferred from homology"/&gt;
++ * &lt;enumeration value="predicted"/&gt;
++ * &lt;enumeration value="uncertain"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes the names for the protein and parts thereof.
* Equivalent to the flat file DE-line.
*
-- * <p>Java class for proteinType complex type.
++ * <p>Java class for proteinType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="proteinType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- * <element name="domain" maxOccurs="unbounded" minOccurs="0">
-- * <complexType>
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </element>
-- * <element name="component" maxOccurs="unbounded" minOccurs="0">
-- * <complexType>
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </element>
-- * </sequence>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="proteinType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt;
++ * &lt;element name="domain" maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="component" maxOccurs="unbounded" minOccurs="0"&gt;
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the alternativeName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
++ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getAlternativeName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.AlternativeName }
*
/**
* Gets the value of the submittedName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the submittedName property.
++ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getSubmittedName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.SubmittedName }
*
/**
* Gets the value of the cdAntigenName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
++ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getCdAntigenName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the innName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the innName property.
++ * This is why there is not a <CODE>set</CODE> method for the innName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getInnName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the domain property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the domain property.
++ * This is why there is not a <CODE>set</CODE> method for the domain property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getDomain().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.Domain }
*
/**
* Gets the value of the component property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the component property.
++ * This is why there is not a <CODE>set</CODE> method for the component property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getComponent().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.Component }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/&gt;
++ * &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the shortName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the shortName property.
++ * This is why there is not a <CODE>set</CODE> method for the shortName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getShortName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the ecNumber property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
++ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEcNumber().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the alternativeName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
++ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getAlternativeName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.AlternativeName }
*
/**
* Gets the value of the submittedName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the submittedName property.
++ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getSubmittedName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.SubmittedName }
*
/**
* Gets the value of the cdAntigenName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
++ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getCdAntigenName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the innName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the innName property.
++ * This is why there is not a <CODE>set</CODE> method for the innName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getInnName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the alternativeName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
++ * This is why there is not a <CODE>set</CODE> method for the alternativeName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getAlternativeName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.AlternativeName }
*
/**
* Gets the value of the submittedName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the submittedName property.
++ * This is why there is not a <CODE>set</CODE> method for the submittedName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getSubmittedName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link ProteinType.SubmittedName }
*
/**
* Gets the value of the cdAntigenName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
++ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getCdAntigenName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the innName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the innName property.
++ * This is why there is not a <CODE>set</CODE> method for the innName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getInnName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/&gt;
++ * &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the shortName property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the shortName property.
++ * This is why there is not a <CODE>set</CODE> method for the shortName property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getShortName().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the ecNumber property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
++ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEcNumber().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <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>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/&gt;
++ * &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the ecNumber property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
++ * This is why there is not a <CODE>set</CODE> method for the ecNumber property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEcNumber().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes a chemical reaction.
*
-- * <p>Java class for reactionType complex type.
++ * <p>Java class for reactionType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="reactionType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="text" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/>
-- * </sequence>
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="reactionType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="text" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the dbReference property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the dbReference property.
++ * This is why there is not a <CODE>set</CODE> method for the dbReference property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getDbReference().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link DbReferenceType }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes a citation and a summary of its content.
* Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines.
*
-- * <p>Java class for referenceType complex type.
++ * <p>Java class for referenceType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="referenceType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="citation" type="{http://uniprot.org/uniprot}citationType"/>
-- * <group ref="{http://uniprot.org/uniprot}sptrCitationGroup"/>
-- * </sequence>
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="referenceType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="citation" type="{http://uniprot.org/uniprot}citationType"/&gt;
++ * &lt;group ref="{http://uniprot.org/uniprot}sptrCitationGroup"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the scope property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the scope property.
++ * This is why there is not a <CODE>set</CODE> method for the scope property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getScope().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for sequenceType complex type.
++ * <p>Java class for sequenceType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="sequenceType">
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- * <attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- * <attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- * <attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
-- * <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- * <attribute name="precursor" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-- * <attribute name="fragment">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="single"/>
-- * <enumeration value="multiple"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="sequenceType"&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
++ * &lt;attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" /&gt;
++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
++ * &lt;attribute name="precursor" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
++ * &lt;attribute name="fragment"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="single"/&gt;
++ * &lt;enumeration value="multiple"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
* Describes the source of the sequence according to the citation.
* Equivalent to the flat file RC-line.
*
-- * <p>Java class for sourceDataType complex type.
++ * <p>Java class for sourceDataType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="sourceDataType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <choice maxOccurs="unbounded">
-- * <element name="strain">
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </element>
-- * <element name="plasmid">
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </element>
-- * <element name="transposon">
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </element>
-- * <element name="tissue">
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </element>
-- * </choice>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="sourceDataType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;choice maxOccurs="unbounded"&gt;
++ * &lt;element name="strain"&gt;
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="plasmid"&gt;
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="transposon"&gt;
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;element name="tissue"&gt;
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * &lt;/element&gt;
++ * &lt;/choice&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the strainOrPlasmidOrTransposon property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon property.
++ * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getStrainOrPlasmidOrTransposon().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link SourceDataType.Strain }
* {@link SourceDataType.Plasmid }
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the evidence property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the evidence property.
++ * This is why there is not a <CODE>set</CODE> method for the evidence property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEvidence().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry).
*
-- * <p>Java class for sourceType complex type.
++ * <p>Java class for sourceType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="sourceType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" minOccurs="0"/>
-- * </sequence>
-- * <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="sourceType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Indicates whether the name of a plasmid is known or unknown.
*
-- * <p>Java class for statusType complex type.
++ * <p>Java class for statusType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="statusType">
-- * <simpleContent>
-- * <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- * <attribute name="status" default="known">
-- * <simpleType>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- * <enumeration value="known"/>
-- * <enumeration value="unknown"/>
-- * </restriction>
-- * </simpleType>
-- * </attribute>
-- * </extension>
-- * </simpleContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="statusType"&gt;
++ * &lt;simpleContent&gt;
++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
++ * &lt;attribute name="status" default="known"&gt;
++ * &lt;simpleType&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt;
++ * &lt;enumeration value="known"/&gt;
++ * &lt;enumeration value="unknown"/&gt;
++ * &lt;/restriction&gt;
++ * &lt;/simpleType&gt;
++ * &lt;/attribute&gt;
++ * &lt;/extension&gt;
++ * &lt;/simpleContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
* Describes the subcellular location and optionally the topology and orientation of a molecule.
*
-- * <p>Java class for subcellularLocationType complex type.
++ * <p>Java class for subcellularLocationType complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType name="subcellularLocationType">
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element name="location" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-- * <element name="topology" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- * <element name="orientation" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- * </sequence>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType name="subcellularLocationType"&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element name="location" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt;
++ * &lt;element name="topology" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;element name="orientation" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the location property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the location property.
++ * This is why there is not a <CODE>set</CODE> method for the location property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getLocation().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the topology property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the topology property.
++ * This is why there is not a <CODE>set</CODE> method for the topology property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getTopology().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
/**
* Gets the value of the orientation property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the orientation property.
++ * This is why there is not a <CODE>set</CODE> method for the orientation property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getOrientation().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link EvidencedStringType }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
/**
-- * <p>Java class for anonymous complex type.
++ * <p>Java class for anonymous complex type.
*
-- * <p>The following schema fragment specifies the expected content contained within this class.
++ * <p>The following schema fragment specifies the expected content contained within this class.
*
-- * <pre>
-- * <complexType>
-- * <complexContent>
-- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- * <sequence>
-- * <element ref="{http://uniprot.org/uniprot}entry" maxOccurs="unbounded"/>
-- * <element ref="{http://uniprot.org/uniprot}copyright" minOccurs="0"/>
-- * </sequence>
-- * </restriction>
-- * </complexContent>
-- * </complexType>
-- * </pre>
++ * <pre>
++ * &lt;complexType&gt;
++ * &lt;complexContent&gt;
++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
++ * &lt;sequence&gt;
++ * &lt;element ref="{http://uniprot.org/uniprot}entry" maxOccurs="unbounded"/&gt;
++ * &lt;element ref="{http://uniprot.org/uniprot}copyright" minOccurs="0"/&gt;
++ * &lt;/sequence&gt;
++ * &lt;/restriction&gt;
++ * &lt;/complexContent&gt;
++ * &lt;/complexType&gt;
++ * </pre>
*
*
*/
/**
* Gets the value of the entry property.
*
-- * <p>
++ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
-- * This is why there is not a <CODE>set</CODE> method for the entry property.
++ * This is why there is not a <CODE>set</CODE> method for the entry property.
*
-- * <p>
++ * <p>
* For example, to add a new item, do as follows:
-- * <pre>
++ * <pre>
* getEntry().add(newItem);
-- * </pre>
++ * </pre>
*
*
-- * <p>
++ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Entry }
*
//
--// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
--// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
++// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
--// Generated on: 2019.04.05 at 08:01:44 AM BST
++// Generated on: 2022.02.07 at 04:44:21 PM GMT
//
@javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
git://source.jalview.org / jalview.git / commitdiff