JAL-3103 Put jalview.jar first in getdown for .properties files. Remove now-not-neede...
[jalview.git] / src / jalview / gui / Preferences.java
index 6fa63fe..17f6af6 100755 (executable)
@@ -31,9 +31,10 @@ import java.awt.event.MouseEvent;
 import java.io.File;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.CompletableFuture;
 
 import javax.help.HelpSetException;
-import javax.swing.JColorChooser;
+import javax.swing.JComboBox;
 import javax.swing.JFileChooser;
 import javax.swing.JInternalFrame;
 import javax.swing.JPanel;
@@ -50,9 +51,12 @@ import javax.swing.table.TableColumn;
 import javax.swing.table.TableModel;
 import javax.swing.table.TableRowSorter;
 
+import edu.stanford.ejalbert.launching.IBrowserLaunching;
 import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
 import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.MemorySetting;
 import jalview.ext.pymol.PymolManager;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
@@ -70,6 +74,7 @@ import jalview.urls.UrlLinkTableModel;
 import jalview.urls.api.UrlProviderFactoryI;
 import jalview.urls.api.UrlProviderI;
 import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.BrowserLauncher;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
 import jalview.util.UrlConstants;
@@ -81,6 +86,10 @@ import jalview.ws.sifts.SiftsSettings;
  * @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";
@@ -127,6 +136,10 @@ public class Preferences extends GPreferences
 
   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 $SEQUENCE_ID=/.possible | chars ./=$
@@ -186,19 +199,72 @@ public class Preferences extends GPreferences
   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();
     frame.setContentPane(this);
-    wsPrefs = new WsPreferences();
-    wsTab.add(wsPrefs, BorderLayout.CENTER);
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      wsPrefs = new WsPreferences();
+      wsTab.add(wsPrefs, BorderLayout.CENTER);
+    }
     int width = 500, height = 450;
-    new jalview.util.Platform();
-    if (Platform.isAMac())
+    if (Platform.isAMacAndNotJS())
     {
       width = 570;
       height = 480;
@@ -293,8 +359,8 @@ public class Preferences extends GPreferences
     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
@@ -321,12 +387,10 @@ public class Preferences extends GPreferences
     /*
      * Set overview panel defaults
      */
-    gapColour.setBackground(
-            Cache.getDefaultColour(GAP_COLOUR,
-                    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
-    hiddenColour.setBackground(
-            Cache.getDefaultColour(HIDDEN_COLOUR,
-                    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+    gapColour.setBackground(Cache.getDefaultColour(GAP_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+    hiddenColour.setBackground(Cache.getDefaultColour(HIDDEN_COLOUR,
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
     useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
@@ -336,20 +400,19 @@ public class Preferences extends GPreferences
     /*
      * 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);
 
     /*
      * set choice of structure viewer, and path if saved as a preference;
      * default to Jmol (first choice) if an unexpected value is found
      */
-    String viewerType = Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name());
+    String viewerType = Cache.getDefault(STRUCTURE_DISPLAY,
+            ViewerType.JMOL.name());
     structViewer.setSelectedItem(viewerType);
     String viewerPath = "";
     ViewerType type = null;
@@ -372,7 +435,7 @@ public class Preferences extends GPreferences
       }
     } catch (IllegalArgumentException e)
     {
-      Cache.log.error("Unknown structure viewer type: " + viewerType
+      Console.error("Unknown structure viewer type: " + viewerType
               + ", defaulting to Jmol");
       type = ViewerType.JMOL;
     }
@@ -385,10 +448,28 @@ public class Preferences extends GPreferences
       {
         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)
+          {
+            Console.error("Failed to set path - unknown viewer type", x);
+          }
         }
       }
     });
@@ -425,7 +506,8 @@ public class Preferences extends GPreferences
             new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
 
     sorter.setSortKeys(sortKeys);
-    sorter.sort();
+    // BH 2018 setSortKeys will do the sort
+    // sorter.sort();
 
     // set up filtering
     ActionListener onReset;
@@ -442,7 +524,7 @@ public class Preferences extends GPreferences
     doReset.addActionListener(onReset);
 
     // filter to display only custom urls
-    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
+    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
     {
       @Override
       public boolean include(
@@ -528,12 +610,42 @@ public class Preferences extends GPreferences
       }
     }
 
-    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", ""));
-
-    defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
+    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:
+      Console.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);
+
+    String browserPref = Cache.getDefault("DEFAULT_BROWSER", "");
+    if (browserPref != null)
+    {
+      defaultBrowser.getModel().setSelectedItem(browserPref);
+    }
 
     usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
     // note antisense here: default is true
@@ -544,23 +656,9 @@ public class Preferences extends GPreferences
     /*
      * Set Output tab defaults
      */
-    epsRendering.addItem(promptEachTimeOpt);
-    epsRendering.addItem(lineArtOpt);
-    epsRendering.addItem(textOpt);
-    String defaultEPS = Cache.getDefault("EPS_RENDERING",
-            "Prompt each time");
-    if (defaultEPS.equalsIgnoreCase("Text"))
-    {
-      epsRendering.setSelectedItem(textOpt);
-    }
-    else if (defaultEPS.equalsIgnoreCase("Lineart"))
-    {
-      epsRendering.setSelectedItem(lineArtOpt);
-    }
-    else
-    {
-      epsRendering.setSelectedItem(promptEachTimeOpt);
-    }
+    setupOutputCombo(epsRendering, "EPS_RENDERING");
+    setupOutputCombo(htmlRendering, "HTML_RENDERING");
+    setupOutputCombo(svgRendering, "SVG_RENDERING");
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
@@ -589,12 +687,49 @@ public class Preferences extends GPreferences
 
     annotations_actionPerformed(null); // update the display of the annotation
                                        // settings
-    
-    
+
     /*
      * Set Backups tab defaults
      */
     loadLastSavedBackupsOptions();
+
+    /*
+     * Set Startup tab defaults
+     */
+
+  }
+
+  /**
+   * A helper method that sets the items and initial selection in a character
+   * rendering option list (Prompt each time/Lineart/Text)
+   * 
+   * @param comboBox
+   * @param propertyKey
+   */
+  protected void setupOutputCombo(JComboBox<Object> comboBox,
+          String propertyKey)
+  {
+    comboBox.addItem(promptEachTimeOpt);
+    comboBox.addItem(lineArtOpt);
+    comboBox.addItem(textOpt);
+
+    /*
+     * JalviewJS doesn't support Lineart so force it to Text
+     */
+    String defaultOption = Platform.isJS() ? "Text"
+            : Cache.getDefault(propertyKey, "Prompt each time");
+    if (defaultOption.equalsIgnoreCase("Text"))
+    {
+      comboBox.setSelectedItem(textOpt);
+    }
+    else if (defaultOption.equalsIgnoreCase("Lineart"))
+    {
+      comboBox.setSelectedItem(lineArtOpt);
+    }
+    else
+    {
+      comboBox.setSelectedItem(promptEachTimeOpt);
+    }
   }
 
   /**
@@ -611,6 +746,11 @@ public class Preferences extends GPreferences
       return;
     }
 
+    /* 
+     * Set proxy settings first (to be before web services refresh)
+     */
+    saveProxySettings();
+
     /*
      * Save Visual settings
      */
@@ -717,14 +857,11 @@ public class Preferences extends GPreferences
             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();
     String viewerPath = structureViewerPath.getText();
-    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
-            viewer);
+    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
     if (viewer.equals(ViewerType.CHIMERA.name()))
     {
       Cache.setOrRemove(CHIMERA_PATH, viewerPath);
@@ -746,13 +883,28 @@ public class Preferences extends GPreferences
      */
     Cache.applicationProperties.setProperty("EPS_RENDERING",
             ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+    Cache.applicationProperties.setProperty("HTML_RENDERING",
+            ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
+    Cache.applicationProperties.setProperty("SVG_RENDERING",
+            ((OptionsParam) svgRendering.getSelectedItem()).getCode());
 
     /*
      * Save Connections settings
      */
-    Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+    // Proxy settings set first (to catch web services)
 
-    jalview.util.BrowserLauncher.resetBrowser();
+    Cache.setOrRemove("DEFAULT_BROWSER",
+            (String) defaultBrowser.getSelectedItem());
+    if (Cache.getProperty("DEFAULT_BROWSER") != null)
+    {
+      System.setProperty(IBrowserLaunching.BROWSER_SYSTEM_PROPERTY,
+              Cache.getProperty("DEFAULT_BROWSER"));
+    }
+    else
+    {
+      System.clearProperty(IBrowserLaunching.BROWSER_SYSTEM_PROPERTY);
+    }
+    BrowserLauncher.resetBrowser();
 
     // save user-defined and selected links
     String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
@@ -780,23 +932,6 @@ public class Preferences extends GPreferences
     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())
@@ -855,7 +990,10 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
-    wsPrefs.updateAndRefreshWsMenuConfig(false);
+    if (!Platform.isJS())
+    {
+      wsPrefs.updateAndRefreshWsMenuConfig(false);
+    }
 
     /*
      * Save Backups settings
@@ -863,16 +1001,16 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
             Boolean.toString(enableBackupFiles.isSelected()));
     int preset = getComboIntStringKey(backupfilesPresetsCombo);
-    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET",
+            Integer.toString(preset));
 
     if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
     {
       BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
       BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
               BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
-      Cache.applicationProperties
-              .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
-                      customBFPE.toString());
+      Cache.applicationProperties.setProperty(
+              BackupFilesPresetEntry.CUSTOMCONFIG, customBFPE.toString());
     }
 
     BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
@@ -880,6 +1018,21 @@ public class Preferences extends GPreferences
     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
@@ -890,6 +1043,30 @@ public class Preferences extends GPreferences
     }
   }
 
+  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.
@@ -919,6 +1096,7 @@ public class Preferences extends GPreferences
   @Override
   public void startupFileTextfield_mouseClicked()
   {
+    // TODO: JAL-3048 not needed for Jalview-JS
     String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
     JalviewFileChooser chooser = JalviewFileChooser
             .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
@@ -952,8 +1130,11 @@ public class Preferences extends GPreferences
   {
     try
     {
-      wsPrefs.updateWsMenuConfig(true);
-      wsPrefs.refreshWs_actionPerformed(e);
+      if (!Platform.isJS())
+      {
+        wsPrefs.updateWsMenuConfig(true);
+        wsPrefs.refreshWs_actionPerformed(e);
+      }
       frame.setClosed(true);
     } catch (Exception ex)
     {
@@ -1025,7 +1206,7 @@ public class Preferences extends GPreferences
     if (index == -1)
     {
       // button no longer enabled if row is not selected
-      Cache.log.debug("Edit with no row selected in linkUrlTable");
+      Console.debug("Edit with no row selected in linkUrlTable");
       return;
     }
 
@@ -1077,7 +1258,7 @@ public class Preferences extends GPreferences
     if (index == -1)
     {
       // button no longer enabled if row is not selected
-      Cache.log.debug("Delete with no row selected in linkUrlTable");
+      Console.debug("Delete with no row selected in linkUrlTable");
       return;
     }
     else
@@ -1092,17 +1273,26 @@ public class Preferences extends GPreferences
   @Override
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
-    JFileChooser chooser = new JFileChooser(".");
-    chooser.setDialogTitle(
-            MessageManager.getString("label.select_default_browser"));
+    // TODO: JAL-3048 not needed for j2s
+    if (!Platform.isJS()) // BH 2019
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      JFileChooser chooser = new JFileChooser(".");
+      chooser.setDialogTitle(
+              MessageManager.getString("label.select_default_browser"));
 
-    int value = chooser.showOpenDialog(this);
+      int value = chooser.showOpenDialog(this);
 
-    if (value == JFileChooser.APPROVE_OPTION)
-    {
-      defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+      if (value == JFileChooser.APPROVE_OPTION)
+      {
+        defaultBrowser.getModel().setSelectedItem(
+                chooser.getSelectedFile().getAbsolutePath());
+      }
     }
-
   }
 
   /*
@@ -1127,27 +1317,17 @@ public class Preferences extends GPreferences
   @Override
   public void minColour_actionPerformed(JPanel panel)
   {
-    Color col = JColorChooser.showDialog(this,
+    JalviewColourChooser.showColourChooser(this,
             MessageManager.getString("label.select_colour_minimum_value"),
-            minColour.getBackground());
-    if (col != null)
-    {
-      panel.setBackground(col);
-    }
-    panel.repaint();
+            panel);
   }
 
   @Override
   public void maxColour_actionPerformed(JPanel panel)
   {
-    Color col = JColorChooser.showDialog(this,
+    JalviewColourChooser.showColourChooser(this,
             MessageManager.getString("label.select_colour_maximum_value"),
-            maxColour.getBackground());
-    if (col != null)
-    {
-      panel.setBackground(col);
-    }
-    panel.repaint();
+            panel);
   }
 
   @Override
@@ -1155,28 +1335,16 @@ public class Preferences extends GPreferences
   {
     if (!useLegacyGap.isSelected())
     {
-      Color col = JColorChooser.showDialog(this,
-              MessageManager.getString("label.select_gap_colour"),
-              gapColour.getBackground());
-      if (col != null)
-      {
-        gap.setBackground(col);
-      }
-      gap.repaint();
+      JalviewColourChooser.showColourChooser(this,
+              MessageManager.getString("label.select_gap_colour"), gap);
     }
   }
 
   @Override
   public void hiddenColour_actionPerformed(JPanel hidden)
   {
-    Color col = JColorChooser.showDialog(this,
-            MessageManager.getString("label.select_hidden_colour"),
-            hiddenColour.getBackground());
-    if (col != null)
-    {
-      hidden.setBackground(col);
-    }
-    hidden.repaint();
+    JalviewColourChooser.showColourChooser(this,
+            MessageManager.getString("label.select_hidden_colour"), hidden);
   }
 
   @Override
@@ -1224,12 +1392,12 @@ public class Preferences extends GPreferences
       }
     } catch (NumberFormatException x)
     {
+      userIdWidth.setText("");
       JvOptionPane.showInternalMessageDialog(Desktop.desktop,
               MessageManager
                       .getString("warn.user_defined_width_requirements"),
               MessageManager.getString("label.invalid_id_column_width"),
               JvOptionPane.WARNING_MESSAGE);
-      userIdWidth.setText("");
     }
   }
 
@@ -1331,8 +1499,10 @@ public class Preferences extends GPreferences
                       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);
@@ -1341,6 +1511,24 @@ public class Preferences extends GPreferences
           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)
+          {
+          }
+        });
+      }
     }
   }