X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=7a4dbc01d29256833aee1b57c971dba56ca8c34a;hb=892a62261b740199fbc664c012107ae4392b7521;hp=35641f81d7f1815baf67fe5666201591a339654a;hpb=26b115b0a77d521da92a06572d9b7819c2d0d49a;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 35641f8..7a4dbc0 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -20,27 +20,6 @@
  */
 package jalview.gui;
 
-import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
-import jalview.bin.Cache;
-import jalview.gui.Help.HelpId;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.FileFormatI;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GPreferences;
-import jalview.jbgui.GSequenceLink;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemes;
-import jalview.schemes.ResidueColourScheme;
-import jalview.urls.UrlLinkTableModel;
-import jalview.urls.api.UrlProviderFactoryI;
-import jalview.urls.api.UrlProviderI;
-import jalview.urls.desktop.DesktopUrlProviderFactory;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.util.UrlConstants;
-import jalview.ws.sifts.SiftsSettings;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -52,6 +31,7 @@ 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.JComboBox;
@@ -71,7 +51,34 @@ 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;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.FileFormatI;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+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;
+import jalview.ws.sifts.SiftsSettings;
 
 /**
  * DOCUMENT ME!
@@ -79,6 +86,10 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  * @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";
@@ -103,6 +114,10 @@ public class Preferences extends GPreferences
 
   public static final String CHIMERA_PATH = "CHIMERA_PATH";
 
+  public static final String CHIMERAX_PATH = "CHIMERAX_PATH";
+
+  public static final String PYMOL_PATH = "PYMOL_PATH";
+
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
 
   public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
@@ -121,6 +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 $SEQUENCE_ID=/.possible | chars ./=$
@@ -180,15 +199,66 @@ 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);
     if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
     {
       wsPrefs = new WsPreferences();
       wsTab.add(wsPrefs, BorderLayout.CENTER);
@@ -253,7 +323,7 @@ public class Preferences extends GPreferences
     fontStyleCB.setSelectedItem(
             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
-    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
     scaleProteinToCdna
             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 
@@ -289,8 +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
@@ -317,38 +387,90 @@ 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());
     showHiddenAtStart
-            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 
     /*
-     * Set Structure tab defaults.
+     * 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);
-    structViewer.setSelectedItem(
-            Cache.getDefault(STRUCTURE_DISPLAY, ViewerType.JMOL.name()));
-    chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
-    chimeraPath.addActionListener(new ActionListener()
+
+    /*
+     * 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());
+    structViewer.setSelectedItem(viewerType);
+    String viewerPath = "";
+    ViewerType type = null;
+    try
+    {
+      type = ViewerType.valueOf(viewerType);
+      switch (type)
+      {
+      case JMOL:
+        break;
+      case CHIMERA:
+        viewerPath = Cache.getDefault(CHIMERA_PATH, "");
+        break;
+      case CHIMERAX:
+        viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
+        break;
+      case PYMOL:
+        viewerPath = Cache.getDefault(PYMOL_PATH, "");
+        break;
+      }
+    } catch (IllegalArgumentException e)
+    {
+      Console.error("Unknown structure viewer type: " + viewerType
+              + ", defaulting to Jmol");
+      type = ViewerType.JMOL;
+    }
+    structureViewerPath.setText(viewerPath);
+
+    structureViewerPath.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        validateChimeraPath();
+        if (validateViewerPath())
+        {
+          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);
+          }
+        }
       }
     });
 
@@ -488,10 +610,36 @@ 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", ""));
+    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);
 
     defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
 
@@ -535,6 +683,16 @@ public class Preferences extends GPreferences
 
     annotations_actionPerformed(null); // update the display of the annotation
                                        // settings
+
+    /*
+     * Set Backups tab defaults
+     */
+    loadLastSavedBackupsOptions();
+
+    /*
+     * Set Startup tab defaults
+     */
+
   }
 
   /**
@@ -550,7 +708,7 @@ public class Preferences extends GPreferences
     comboBox.addItem(promptEachTimeOpt);
     comboBox.addItem(lineArtOpt);
     comboBox.addItem(textOpt);
-    
+
     /*
      * JalviewJS doesn't support Lineart so force it to Text
      */
@@ -584,6 +742,11 @@ public class Preferences extends GPreferences
       return;
     }
 
+    /* 
+     * Set proxy settings first (to be before web services refresh)
+     */
+    saveProxySettings();
+
     /*
      * Save Visual settings
      */
@@ -690,13 +853,23 @@ 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()));
-    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY,
-            structViewer.getSelectedItem().toString());
-    Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+    String viewer = structViewer.getSelectedItem().toString();
+    String viewerPath = structureViewerPath.getText();
+    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, viewer);
+    if (viewer.equals(ViewerType.CHIMERA.name()))
+    {
+      Cache.setOrRemove(CHIMERA_PATH, viewerPath);
+    }
+    else if (viewer.equals(ViewerType.CHIMERAX.name()))
+    {
+      Cache.setOrRemove(CHIMERAX_PATH, viewerPath);
+    }
+    else if (viewer.equals(ViewerType.PYMOL.name()))
+    {
+      Cache.setOrRemove(PYMOL_PATH, viewerPath);
+    }
     Cache.applicationProperties.setProperty("MAP_WITH_SIFTS",
             Boolean.toString(siftsMapping.isSelected()));
     SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
@@ -714,9 +887,19 @@ public class Preferences extends GPreferences
     /*
      * 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", defaultBrowser.getText());
+    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);
@@ -744,23 +927,6 @@ 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())
@@ -823,6 +989,45 @@ public class Preferences extends GPreferences
     {
       wsPrefs.updateAndRefreshWsMenuConfig(false);
     }
+
+    /*
+     * Save Backups settings
+     */
+    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+            Boolean.toString(enableBackupFiles.isSelected()));
+    int preset = getComboIntStringKey(backupfilesPresetsCombo);
+    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());
+    }
+
+    BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .get(preset);
+    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
@@ -833,6 +1038,30 @@ 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.
@@ -852,7 +1081,7 @@ public class Preferences extends GPreferences
   @Override
   protected boolean validateStructure()
   {
-    return validateChimeraPath();
+    return validateViewerPath();
 
   }
 
@@ -972,7 +1201,7 @@ 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;
     }
 
@@ -1024,7 +1253,7 @@ 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
@@ -1040,8 +1269,11 @@ public class Preferences extends GPreferences
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     // TODO: JAL-3048 not needed for j2s
-    /*
-     * @j2sNative
+    if (!Platform.isJS()) // BH 2019
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
      */
     {
       JFileChooser chooser = new JFileChooser(".");
@@ -1098,8 +1330,7 @@ public class Preferences extends GPreferences
     if (!useLegacyGap.isSelected())
     {
       JalviewColourChooser.showColourChooser(this,
-              MessageManager.getString("label.select_gap_colour"),
-              gap);
+              MessageManager.getString("label.select_gap_colour"), gap);
     }
   }
 
@@ -1107,8 +1338,7 @@ public class Preferences extends GPreferences
   public void hiddenColour_actionPerformed(JPanel hidden)
   {
     JalviewColourChooser.showColourChooser(this,
-            MessageManager.getString("label.select_hidden_colour"),
-            hidden);
+            MessageManager.getString("label.select_hidden_colour"), hidden);
   }
 
   @Override
@@ -1134,7 +1364,7 @@ public class Preferences extends GPreferences
   {
     useLegacyGap.setSelected(false);
     useLegacyGaps_actionPerformed(null);
-    showHiddenAtStart.setSelected(true);
+    showHiddenAtStart.setSelected(false);
     hiddenColour.setBackground(
             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
   }
@@ -1173,19 +1403,20 @@ public class Preferences extends GPreferences
   }
 
   /**
-   * Returns true if chimera path is to a valid executable, else show an error
-   * dialog.
+   * 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 validateChimeraPath()
+  private boolean validateViewerPath()
   {
-    if (chimeraPath.getText().trim().length() > 0)
+    if (structureViewerPath.getText().trim().length() > 0)
     {
-      File f = new File(chimeraPath.getText());
+      File f = new File(structureViewerPath.getText());
       if (!f.canExecute())
       {
         JvOptionPane.showInternalMessageDialog(Desktop.desktop,
-                MessageManager.getString("label.invalid_chimera_path"),
-                MessageManager.getString("label.invalid_name"),
+                MessageManager.getString("label.invalid_viewer_path"),
+                MessageManager.getString("label.invalid_viewer_path"),
                 JvOptionPane.ERROR_MESSAGE);
         return false;
       }
@@ -1194,23 +1425,57 @@ public class Preferences extends GPreferences
   }
 
   /**
-   * If Chimera 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)
   {
-    if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+    if (selectedItem.equals(ViewerType.JMOL.name()))
     {
+      structureViewerPath.setEnabled(false);
+      structureViewerPathLabel.setEnabled(false);
       return;
     }
     boolean found = false;
+    structureViewerPath.setEnabled(true);
+    structureViewerPathLabel.setEnabled(true);
+    structureViewerPathLabel.setText(MessageManager
+            .formatMessage("label.viewer_path", selectedItem));
 
     /*
-     * Try user-specified and standard paths for Chimera executable.
+     * Try user-specified and standard paths for structure viewer executable
      */
-    List<String> paths = StructureManager.getChimeraPaths();
-    paths.add(0, chimeraPath.getText());
+    String viewerPath = "";
+    List<String> paths = null;
+    try
+    {
+      ViewerType viewerType = ViewerType.valueOf(selectedItem);
+      switch (viewerType)
+      {
+      case JMOL:
+        // dealt with above
+        break;
+      case CHIMERA:
+        viewerPath = Cache.getDefault(CHIMERA_PATH, "");
+        paths = StructureManager.getChimeraPaths(false);
+        break;
+      case CHIMERAX:
+        viewerPath = Cache.getDefault(CHIMERAX_PATH, "");
+        paths = StructureManager.getChimeraPaths(true);
+        break;
+      case PYMOL:
+        viewerPath = Cache.getDefault(PYMOL_PATH, "");
+        paths = PymolManager.getPymolPaths();
+        break;
+      }
+    } catch (IllegalArgumentException e)
+    {
+      // only valid entries should be in the drop-down
+    }
+    structureViewerPath.setText(viewerPath);
+
+    paths.add(0, structureViewerPath.getText());
     for (String path : paths)
     {
       if (new File(path.trim()).canExecute())
@@ -1219,16 +1484,19 @@ public class Preferences extends GPreferences
         break;
       }
     }
+
     if (!found)
     {
       String[] options = { "OK", "Help" };
       int showHelp = JvOptionPane.showInternalOptionDialog(Desktop.desktop,
               JvSwingUtils.wrapTooltip(true,
-                      MessageManager.getString("label.chimera_missing")),
+                      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);
@@ -1237,6 +1505,24 @@ 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)
+          {
+          }
+        });
+      }
     }
   }