X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=5af94e42b7a11bdd4b3ab2d7fc4786bc64ffa17b;hb=f7791271668cdcf6e87b638f0e6475ccdea6a3f9;hp=58045cb43c4a667b4fc624ad5bda1d2884b458c8;hpb=4b53c6f969986c258e6cfbe20781c497caf33618;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 58045cb..5af94e4 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -20,21 +20,6 @@
  */
 package jalview.jbgui;
 
-import jalview.bin.Cache;
-import jalview.fts.core.FTSDataColumnPreferences;
-import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.gui.Desktop;
-import jalview.gui.JalviewBooleanRadioButtons;
-import jalview.gui.JvOptionPane;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.BackupFilenameParts;
-import jalview.io.BackupFiles;
-import jalview.io.BackupFilesPresetEntry;
-import jalview.io.IntKeyStringValueEntry;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -66,6 +51,7 @@ import javax.swing.JComboBox;
 import javax.swing.JFileChooser;
 import javax.swing.JLabel;
 import javax.swing.JPanel;
+import javax.swing.JPasswordField;
 import javax.swing.JRadioButton;
 import javax.swing.JScrollPane;
 import javax.swing.JSpinner;
@@ -83,9 +69,27 @@ import javax.swing.border.EtchedBorder;
 import javax.swing.border.TitledBorder;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
 import javax.swing.table.TableCellEditor;
 import javax.swing.table.TableCellRenderer;
 
+import jalview.bin.Cache;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.Desktop;
+import jalview.gui.JalviewBooleanRadioButtons;
+import jalview.gui.JvOptionPane;
+import jalview.gui.JvSwingUtils;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFilenameParts;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
+import jalview.io.IntKeyStringValueEntry;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+
 /**
  * Base class for the Preferences panel.
  * 
@@ -179,9 +183,9 @@ public class GPreferences extends JPanel
 
   protected JComboBox<String> structViewer = new JComboBox<>();
 
-  protected JLabel chimeraPathLabel;
+  protected JLabel structureViewerPathLabel;
 
-  protected JTextField chimeraPath = new JTextField();
+  protected JTextField structureViewerPath = new JTextField();
 
   protected ButtonGroup mappingMethod = new ButtonGroup();
 
@@ -216,6 +220,8 @@ public class GPreferences extends JPanel
   /*
    * Connections tab components
    */
+  protected JPanel connectTab;
+
   protected JTable linkUrlTable = new JTable();
 
   protected JButton editLink = new JButton();
@@ -228,17 +234,49 @@ public class GPreferences extends JPanel
 
   protected JButton userOnly = new JButton();
 
+  protected JLabel httpLabel = new JLabel();
+
+  protected JLabel httpsLabel = new JLabel();
+
   protected JLabel portLabel = new JLabel();
 
   protected JLabel serverLabel = new JLabel();
 
-  protected JTextField proxyServerTB = new JTextField();
+  protected JLabel portLabel2 = new JLabel();
 
-  protected JTextField proxyPortTB = new JTextField();
+  protected JLabel serverLabel2 = new JLabel();
+
+  protected JLabel proxyAuthUsernameLabel = new JLabel();
+
+  protected JLabel proxyAuthPasswordLabel = new JLabel();
+
+  protected JLabel passwordNotStoredLabel = new JLabel();
+
+  protected JTextField proxyServerHttpTB = new JTextField();
+
+  protected JTextField proxyPortHttpTB = new JTextField();
+
+  protected JTextField proxyServerHttpsTB = new JTextField();
+
+  protected JTextField proxyPortHttpsTB = new JTextField();
+
+  protected JCheckBox proxyAuth = new JCheckBox();
+
+  protected JTextField proxyAuthUsernameTB = new JTextField();
+
+  protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
 
   protected JTextField defaultBrowser = new JTextField();
 
-  protected JCheckBox useProxy = new JCheckBox();
+  protected ButtonGroup proxyType = new ButtonGroup();
+
+  protected JRadioButton noProxy = new JRadioButton();
+
+  protected JRadioButton systemProxy = new JRadioButton();
+
+  protected JRadioButton customProxy = new JRadioButton();
+
+  protected JButton applyProxyButton = new JButton();
 
   protected JCheckBox usagestats = new JCheckBox();
 
@@ -251,6 +289,10 @@ public class GPreferences extends JPanel
    */
   protected JComboBox<Object> epsRendering = new JComboBox<>();
 
+  protected JComboBox<Object> htmlRendering = new JComboBox<>();
+
+  protected JComboBox<Object> svgRendering = new JComboBox<>();
+
   protected JLabel userIdWidthlabel = new JLabel();
 
   protected JCheckBox autoIdWidth = new JCheckBox();
@@ -335,6 +377,10 @@ public class GPreferences extends JPanel
 
   protected JTextArea backupfilesExampleLabel = new JTextArea();
 
+  private final JTabbedPane tabbedPane = new JTabbedPane();
+
+  private JLabel messageLabel = new JLabel("", JLabel.CENTER);
+
   /**
    * Creates a new GPreferences object.
    */
@@ -356,8 +402,12 @@ public class GPreferences extends JPanel
    */
   private void jbInit() throws Exception
   {
-    final JTabbedPane tabbedPane = new JTabbedPane();
+    // final JTabbedPane tabbedPane = new JTabbedPane();
     this.setLayout(new BorderLayout());
+
+    // message label at top
+    this.add(messageLabel, BorderLayout.NORTH);
+
     JPanel okCancelPanel = initOkCancelPanel();
     this.add(tabbedPane, BorderLayout.CENTER);
     this.add(okCancelPanel, BorderLayout.SOUTH);
@@ -377,8 +427,11 @@ public class GPreferences extends JPanel
     tabbedPane.add(initConnectionsTab(),
             MessageManager.getString("label.connections"));
 
-    tabbedPane.add(initBackupsTab(),
-            MessageManager.getString("label.backups"));
+    if (!Platform.isJS())
+    {
+      tabbedPane.add(initBackupsTab(),
+              MessageManager.getString("label.backups"));
+    }
 
     tabbedPane.add(initLinksTab(),
             MessageManager.getString("label.urllinks"));
@@ -392,12 +445,16 @@ public class GPreferences extends JPanel
     /*
      * See WsPreferences for the real work of configuring this tab.
      */
-    wsTab.setLayout(new BorderLayout());
-    tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+    if (!Platform.isJS())
+    {
+      wsTab.setLayout(new BorderLayout());
+      tabbedPane.add(wsTab, MessageManager.getString("label.web_services"));
+    }
 
     /*
      * Handler to validate a tab before leaving it - currently only for
      * Structure.
+     * Adding a clearMessage() so messages are cleared when changing tabs.
      */
     tabbedPane.addChangeListener(new ChangeListener()
     {
@@ -416,11 +473,57 @@ public class GPreferences extends JPanel
           }
         }
         lastTab = tabbedPane.getSelectedComponent();
+
+        clearMessage();
       }
 
     });
   }
 
+  public void setMessage(String message)
+  {
+    if (message != null)
+    {
+      messageLabel.setText(message);
+      messageLabel.setFont(LABEL_FONT_BOLD);
+      messageLabel.setForeground(Color.RED.darker());
+      messageLabel.revalidate();
+      messageLabel.repaint();
+    }
+    // note message not cleared if message is null. call clearMessage()
+    // directly.
+    this.revalidate();
+    this.repaint();
+  }
+
+  public void clearMessage()
+  {
+    // only repaint if message exists
+    if (messageLabel.getText() != null
+            && messageLabel.getText().length() > 0)
+    {
+      messageLabel.setText("");
+      messageLabel.revalidate();
+      messageLabel.repaint();
+      this.revalidate();
+      this.repaint();
+    }
+  }
+
+  public final static int CONNECTIONS_TAB = 5;
+
+  public void selectTab(int selectTab)
+  {
+    // select a given tab - currently only for Connections
+    switch (selectTab)
+    {
+    case CONNECTIONS_TAB:
+      tabbedPane.setSelectedComponent(connectTab);
+      break;
+    default:
+    }
+  }
+
   /**
    * Initialises the Editing tabbed panel.
    * 
@@ -451,7 +554,7 @@ public class GPreferences extends JPanel
   }
 
   /**
-   * Initialises the Output tabbed panel.
+   * Initialises the Output tab
    * 
    * @return
    */
@@ -459,18 +562,35 @@ public class GPreferences extends JPanel
   {
     JPanel outputTab = new JPanel();
     outputTab.setLayout(null);
-    JLabel epsLabel = new JLabel();
+
+    JLabel epsLabel = new JLabel(
+            MessageManager.formatMessage("label.rendering_style", "EPS"));
     epsLabel.setFont(LABEL_FONT);
     epsLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    epsLabel.setText(MessageManager.getString("label.eps_rendering_style"));
-    epsLabel.setBounds(new Rectangle(9, 31, 140, 24));
+    epsLabel.setBounds(new Rectangle(9, 31, 160, 24));
     epsRendering.setFont(LABEL_FONT);
-    epsRendering.setBounds(new Rectangle(154, 34, 187, 21));
+    epsRendering.setBounds(new Rectangle(174, 34, 187, 21));
+    JLabel htmlLabel = new JLabel(
+            MessageManager.formatMessage("label.rendering_style", "HTML"));
+    htmlLabel.setFont(LABEL_FONT);
+    htmlLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    htmlLabel.setBounds(new Rectangle(9, 55, 160, 24));
+    htmlRendering.setFont(LABEL_FONT);
+    htmlRendering.setBounds(new Rectangle(174, 58, 187, 21));
+    JLabel svgLabel = new JLabel(
+            MessageManager.formatMessage("label.rendering_style", "SVG"));
+    svgLabel.setFont(LABEL_FONT);
+    svgLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    svgLabel.setBounds(new Rectangle(9, 79, 160, 24));
+    svgRendering.setFont(LABEL_FONT);
+    svgRendering.setBounds(new Rectangle(174, 82, 187, 21));
+
     JLabel jLabel1 = new JLabel();
     jLabel1.setFont(LABEL_FONT);
     jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
     jLabel1.setText(MessageManager.getString("label.append_start_end"));
     jLabel1.setFont(LABEL_FONT);
+
     fastajv.setFont(LABEL_FONT);
     fastajv.setHorizontalAlignment(SwingConstants.LEFT);
     clustaljv.setText(MessageManager.getString("label.clustal") + "     ");
@@ -487,7 +607,7 @@ public class GPreferences extends JPanel
     TitledBorder titledBorder2 = new TitledBorder(
             MessageManager.getString("label.file_output"));
     jPanel11.setBorder(titledBorder2);
-    jPanel11.setBounds(new Rectangle(30, 72, 196, 182));
+    jPanel11.setBounds(new Rectangle(30, 120, 196, 182));
     GridLayout gridLayout3 = new GridLayout();
     jPanel11.setLayout(gridLayout3);
     gridLayout3.setRows(8);
@@ -506,7 +626,7 @@ public class GPreferences extends JPanel
             MessageManager.getString("label.automatically_set_id_width"));
     autoIdWidth.setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
             .getString("label.adjusts_width_generated_eps_png")));
-    autoIdWidth.setBounds(new Rectangle(228, 96, 188, 23));
+    autoIdWidth.setBounds(new Rectangle(228, 144, 320, 23));
     autoIdWidth.addActionListener(new ActionListener()
     {
 
@@ -524,10 +644,10 @@ public class GPreferences extends JPanel
     userIdWidthlabel.setToolTipText(
             JvSwingUtils.wrapTooltip(true, MessageManager.getString(
                     "label.manually_specify_width_left_column")));
-    userIdWidthlabel.setBounds(new Rectangle(236, 120, 168, 23));
+    userIdWidthlabel.setBounds(new Rectangle(236, 168, 320, 23));
     userIdWidth.setFont(JvSwingUtils.getTextAreaFont());
     userIdWidth.setText("");
-    userIdWidth.setBounds(new Rectangle(232, 144, 84, 23));
+    userIdWidth.setBounds(new Rectangle(232, 192, 84, 23));
     userIdWidth.addActionListener(new ActionListener()
     {
 
@@ -540,10 +660,10 @@ public class GPreferences extends JPanel
     modellerOutput.setFont(LABEL_FONT);
     modellerOutput
             .setText(MessageManager.getString("label.use_modeller_output"));
-    modellerOutput.setBounds(new Rectangle(228, 226, 168, 23));
+    modellerOutput.setBounds(new Rectangle(228, 274, 320, 23));
     embbedBioJSON.setFont(LABEL_FONT);
     embbedBioJSON.setText(MessageManager.getString("label.embbed_biojson"));
-    embbedBioJSON.setBounds(new Rectangle(228, 200, 250, 23));
+    embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
 
     jPanel11.add(jLabel1);
     jPanel11.add(blcjv);
@@ -557,9 +677,19 @@ public class GPreferences extends JPanel
     outputTab.add(userIdWidth);
     outputTab.add(userIdWidthlabel);
     outputTab.add(modellerOutput);
-    outputTab.add(embbedBioJSON);
-    outputTab.add(epsLabel);
-    outputTab.add(epsRendering);
+    if (!Platform.isJS())
+    {
+      /*
+       * JalviewJS doesn't support Lineart option or SVG output
+       */
+      outputTab.add(embbedBioJSON);
+      outputTab.add(epsLabel);
+      outputTab.add(epsRendering);
+      outputTab.add(htmlLabel);
+      outputTab.add(htmlRendering);
+      outputTab.add(svgLabel);
+      outputTab.add(svgRendering);
+    }
     outputTab.add(jPanel11);
     return outputTab;
   }
@@ -571,7 +701,7 @@ public class GPreferences extends JPanel
    */
   private JPanel initConnectionsTab()
   {
-    JPanel connectTab = new JPanel();
+    connectTab = new JPanel();
     connectTab.setLayout(new GridBagLayout());
 
     // Label for browser text box
@@ -842,63 +972,366 @@ public class GPreferences extends JPanel
   private JPanel initConnTabProxyPanel()
   {
     // Label for server text box
-    serverLabel.setText(MessageManager.getString("label.address"));
+    serverLabel.setText(MessageManager.getString("label.host") + ": ");
     serverLabel.setHorizontalAlignment(SwingConstants.RIGHT);
     serverLabel.setFont(LABEL_FONT);
+    serverLabel2.setText(MessageManager.getString("label.host") + ": ");
+    serverLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+    serverLabel2.setFont(LABEL_FONT);
 
     // Proxy server and port text boxes
-    proxyServerTB.setFont(LABEL_FONT);
-    proxyPortTB.setFont(LABEL_FONT);
+    proxyServerHttpTB.setFont(LABEL_FONT);
+    proxyServerHttpTB.setColumns(40);
+    proxyPortHttpTB.setFont(LABEL_FONT);
+    proxyPortHttpTB.setColumns(4);
+    proxyServerHttpsTB.setFont(LABEL_FONT);
+    proxyServerHttpsTB.setColumns(40);
+    proxyPortHttpsTB.setFont(LABEL_FONT);
+    proxyPortHttpsTB.setColumns(4);
+    proxyAuthUsernameTB.setFont(LABEL_FONT);
+    proxyAuthUsernameTB.setColumns(30);
+
+    // check for any change to enable applyProxyButton
+    DocumentListener d = new DocumentListener()
+    {
+      @Override
+      public void changedUpdate(DocumentEvent e)
+      {
+        applyProxyButtonEnabled(true);
+      }
+
+      @Override
+      public void insertUpdate(DocumentEvent e)
+      {
+        applyProxyButtonEnabled(true);
+      }
+
+      @Override
+      public void removeUpdate(DocumentEvent e)
+      {
+        applyProxyButtonEnabled(true);
+      }
+    };
+    proxyServerHttpTB.getDocument().addDocumentListener(d);
+    proxyPortHttpTB.getDocument().addDocumentListener(d);
+    proxyServerHttpsTB.getDocument().addDocumentListener(d);
+    proxyPortHttpsTB.getDocument().addDocumentListener(d);
+    proxyAuthUsernameTB.getDocument().addDocumentListener(d);
+    proxyAuthPasswordPB.setFont(LABEL_FONT);
+    proxyAuthPasswordPB.setColumns(30);
+    proxyAuthPasswordPB.getDocument()
+            .addDocumentListener(new DocumentListener()
+            {
+              @Override
+              public void changedUpdate(DocumentEvent e)
+              {
+                proxyAuthPasswordCheckHighlight(true);
+                applyProxyButtonEnabled(true);
+              }
+
+              @Override
+              public void insertUpdate(DocumentEvent e)
+              {
+                proxyAuthPasswordCheckHighlight(true);
+                applyProxyButtonEnabled(true);
+              }
+
+              @Override
+              public void removeUpdate(DocumentEvent e)
+              {
+                proxyAuthPasswordCheckHighlight(true);
+                applyProxyButtonEnabled(true);
+              }
+
+            });
 
     // Label for Port text box
     portLabel.setFont(LABEL_FONT);
     portLabel.setHorizontalAlignment(SwingConstants.RIGHT);
-    portLabel.setText(MessageManager.getString("label.port"));
-
-    // Use proxy server checkbox
-    useProxy.setFont(LABEL_FONT);
-    useProxy.setHorizontalAlignment(SwingConstants.RIGHT);
-    useProxy.setHorizontalTextPosition(SwingConstants.LEADING);
-    useProxy.setText(MessageManager.getString("label.use_proxy_server"));
-    useProxy.addActionListener(new ActionListener()
+    portLabel.setText(MessageManager.getString("label.port") + ": ");
+    portLabel2.setFont(LABEL_FONT);
+    portLabel2.setHorizontalAlignment(SwingConstants.RIGHT);
+    portLabel2.setText(MessageManager.getString("label.port") + ": ");
+
+    httpLabel.setText("HTTP");
+    httpLabel.setFont(LABEL_FONT_BOLD);
+    httpLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    httpsLabel.setText("HTTPS");
+    httpsLabel.setFont(LABEL_FONT_BOLD);
+    httpsLabel.setHorizontalAlignment(SwingConstants.LEFT);
+
+    proxyAuthUsernameLabel
+            .setText(MessageManager.getString("label.username") + ": ");
+    proxyAuthUsernameLabel.setFont(LABEL_FONT);
+    proxyAuthUsernameLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    proxyAuthPasswordLabel
+            .setText(MessageManager.getString("label.password") + ": ");
+    proxyAuthPasswordLabel.setFont(LABEL_FONT);
+    proxyAuthPasswordLabel.setHorizontalAlignment(SwingConstants.RIGHT);
+    passwordNotStoredLabel.setText(
+            "(" + MessageManager.getString("label.not_stored") + ")");
+    passwordNotStoredLabel.setFont(LABEL_FONT_ITALIC);
+    passwordNotStoredLabel.setHorizontalAlignment(SwingConstants.LEFT);
+
+    // Proxy type radio buttons
+    noProxy.setFont(LABEL_FONT);
+    noProxy.setHorizontalAlignment(SwingConstants.LEFT);
+    noProxy.setText(MessageManager.getString("label.no_proxy"));
+    systemProxy.setFont(LABEL_FONT);
+    systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
+    systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
+            displayUserHostPort(Cache.startupProxyProperties[4],
+                    Cache.startupProxyProperties[0],
+                    Cache.startupProxyProperties[1]),
+            displayUserHostPort(Cache.startupProxyProperties[6],
+                    Cache.startupProxyProperties[2],
+                    Cache.startupProxyProperties[3])));
+    customProxy.setFont(LABEL_FONT);
+    customProxy.setHorizontalAlignment(SwingConstants.LEFT);
+    customProxy.setText(
+            MessageManager.getString("label.use_proxy_server") + ":");
+    ActionListener al = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        proxyType_actionPerformed();
+      }
+    };
+    noProxy.addActionListener(al);
+    systemProxy.addActionListener(al);
+    customProxy.addActionListener(al);
+    proxyType.add(noProxy);
+    proxyType.add(systemProxy);
+    proxyType.add(customProxy);
+
+    proxyAuth.setFont(LABEL_FONT);
+    proxyAuth.setHorizontalAlignment(SwingConstants.LEFT);
+    proxyAuth.setText(MessageManager.getString("label.auth_required"));
+    proxyAuth.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        useProxy_actionPerformed();
+        proxyAuth_actionPerformed();
       }
     });
 
+    setCustomProxyEnabled();
+
     // Make proxy server panel
     JPanel proxyPanel = new JPanel();
     TitledBorder titledBorder1 = new TitledBorder(
-            MessageManager.getString("label.proxy_server"));
+            MessageManager.getString("label.proxy_servers"));
     proxyPanel.setBorder(titledBorder1);
     proxyPanel.setLayout(new GridBagLayout());
-    proxyPanel.add(serverLabel,
-            new GridBagConstraints(0, 1, 1, 1, 0.0, 0.0,
-                    GridBagConstraints.WEST, GridBagConstraints.NONE,
-                    new Insets(0, 2, 2, 0), 5, 0));
-    proxyPanel.add(portLabel,
-            new GridBagConstraints(2, 1, 1, 1, 0.0, 0.0,
-                    GridBagConstraints.WEST, GridBagConstraints.NONE,
-                    new Insets(0, 0, 2, 0), 11, 0));
-    proxyPanel.add(useProxy,
-            new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0,
-                    GridBagConstraints.WEST, GridBagConstraints.NONE,
-                    new Insets(0, 2, 5, 185), 2, -4));
-    proxyPanel.add(proxyPortTB,
-            new GridBagConstraints(3, 1, 1, 1, 1.0, 0.0,
-                    GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-                    new Insets(0, 2, 2, 2), 54, 1));
-    proxyPanel.add(proxyServerTB,
-            new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0,
-                    GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
-                    new Insets(0, 2, 2, 0), 263, 1));
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.fill = GridBagConstraints.HORIZONTAL;
+    gbc.weightx = 1.0;
+
+    GridBagConstraints c = new GridBagConstraints();
+    // Proxy type radio buttons (3)
+    JPanel ptPanel = new JPanel();
+    ptPanel.setLayout(new GridBagLayout());
+    c.weightx = 1.0;
+    c.gridy = 0;
+    c.gridx = 0;
+    c.gridwidth = 1;
+    c.fill = GridBagConstraints.HORIZONTAL;
+    ptPanel.add(noProxy, c);
+    c.gridy++;
+    ptPanel.add(systemProxy, c);
+    c.gridy++;
+    ptPanel.add(customProxy, c);
+
+    gbc.gridy = 0;
+    proxyPanel.add(ptPanel, gbc);
+
+    // host and port text boxes
+    JPanel hpPanel = new JPanel();
+    hpPanel.setLayout(new GridBagLayout());
+    // HTTP host port row
+    c.gridy = 0;
+    c.gridx = 0;
+
+    c.weightx = 0.1;
+    c.anchor = GridBagConstraints.LINE_START;
+    hpPanel.add(httpLabel, c);
+
+    c.gridx++;
+    c.weightx = 0.1;
+    c.anchor = GridBagConstraints.LINE_END;
+    hpPanel.add(serverLabel, c);
+
+    c.gridx++;
+    c.weightx = 1.0;
+    c.anchor = GridBagConstraints.LINE_START;
+    hpPanel.add(proxyServerHttpTB, c);
+
+    c.gridx++;
+    c.weightx = 0.1;
+    c.anchor = GridBagConstraints.LINE_END;
+    hpPanel.add(portLabel, c);
+
+    c.gridx++;
+    c.weightx = 0.2;
+    c.anchor = GridBagConstraints.LINE_START;
+    hpPanel.add(proxyPortHttpTB, c);
+
+    // HTTPS host port row
+    c.gridy++;
+    c.gridx = 0;
+    c.gridwidth = 1;
+
+    c.anchor = GridBagConstraints.LINE_START;
+    hpPanel.add(httpsLabel, c);
+
+    c.gridx++;
+    c.anchor = GridBagConstraints.LINE_END;
+    hpPanel.add(serverLabel2, c);
+
+    c.gridx++;
+    c.anchor = GridBagConstraints.LINE_START;
+    hpPanel.add(proxyServerHttpsTB, c);
+
+    c.gridx++;
+    c.anchor = GridBagConstraints.LINE_END;
+    hpPanel.add(portLabel2, c);
+
+    c.gridx++;
+    c.anchor = GridBagConstraints.LINE_START;
+    hpPanel.add(proxyPortHttpsTB, c);
+
+    gbc.gridy++;
+    proxyPanel.add(hpPanel, gbc);
+
+    if (!Platform.isJS())
+    /**
+     * java.net.Authenticator is not implemented in SwingJS. Not displaying the
+     * Authentication options in Preferences.
+     * 
+     * @j2sIgnore
+     * 
+     */
+    {
+      // Require authentication checkbox
+      gbc.gridy++;
+      proxyPanel.add(proxyAuth, gbc);
+
+      // username and password
+      JPanel upPanel = new JPanel();
+      upPanel.setLayout(new GridBagLayout());
+      // username row
+      c.gridy = 0;
+      c.gridx = 0;
+      c.gridwidth = 1;
+      c.weightx = 0.4;
+      c.anchor = GridBagConstraints.LINE_END;
+      upPanel.add(proxyAuthUsernameLabel, c);
+
+      c.gridx++;
+      c.weightx = 1.0;
+      c.anchor = GridBagConstraints.LINE_START;
+      upPanel.add(proxyAuthUsernameTB, c);
+
+      // password row
+      c.gridy++;
+      c.gridx = 0;
+      c.weightx = 0.4;
+      c.anchor = GridBagConstraints.LINE_END;
+      upPanel.add(proxyAuthPasswordLabel, c);
+
+      c.gridx++;
+      c.weightx = 1.0;
+      c.anchor = GridBagConstraints.LINE_START;
+      upPanel.add(proxyAuthPasswordPB, c);
+
+      c.gridx++;
+      c.weightx = 0.4;
+      c.anchor = GridBagConstraints.LINE_START;
+      upPanel.add(passwordNotStoredLabel, c);
+
+      gbc.gridy++;
+      proxyPanel.add(upPanel, gbc);
+
+    } // end j2sIgnore
+
+    applyProxyButton.setText(MessageManager.getString("action.apply"));
+    applyProxyButton.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        saveProxySettings();
+        applyProxyButton.setEnabled(false);
+      }
+    });
+    gbc.gridy++;
+    gbc.fill = GridBagConstraints.NONE;
+    gbc.anchor = GridBagConstraints.LINE_END;
+    proxyPanel.add(applyProxyButton, gbc);
 
     return proxyPanel;
   }
 
+  public void proxyAuthPasswordCheckHighlight(boolean enabled)
+  {
+    proxyAuthPasswordCheckHighlight(enabled, false);
+  }
+
+  public void proxyAuthPasswordCheckHighlight(boolean enabled,
+          boolean grabFocus)
+  {
+    if (enabled && proxyType.isSelected(customProxy.getModel())
+            && proxyAuth.isSelected()
+            && !proxyAuthUsernameTB.getText().isEmpty()
+            && proxyAuthPasswordPB.getDocument().getLength() == 0)
+    {
+      if (grabFocus)
+        proxyAuthPasswordPB.grabFocus();
+      proxyAuthPasswordPB.setBackground(Color.PINK);
+    }
+    else
+    {
+      proxyAuthPasswordPB.setBackground(Color.WHITE);
+    }
+  }
+
+  public void applyProxyButtonEnabled(boolean enabled)
+  {
+    applyProxyButton.setEnabled(enabled);
+  }
+
+  public void saveProxySettings()
+  {
+    // overridden in Preferences
+  }
+
+  private String displayUserHostPort(String user, String host, String port)
+  {
+    boolean hostBlank = (host == null || host.isEmpty());
+    boolean portBlank = (port == null || port.isEmpty());
+    if (hostBlank && portBlank)
+    {
+      return MessageManager.getString("label.none");
+    }
+
+    StringBuilder sb = new StringBuilder();
+    if (user != null)
+    {
+      sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
+              : user);
+      sb.append("@");
+    }
+    sb.append(hostBlank ? "" : host);
+    if (!portBlank)
+    {
+      sb.append(":");
+      sb.append(port);
+    }
+    return sb.toString();
+  }
+
   /**
    * Initialises the checkboxes in the Connections tab
    */
@@ -1248,11 +1681,16 @@ public class GPreferences extends JPanel
     viewerLabel.setBounds(new Rectangle(10, ypos, 220, height));
     structureTab.add(viewerLabel);
 
+    /*
+     * add all external viewers as options here - check 
+     * when selected whether the program is installed
+     */
     structViewer.setFont(LABEL_FONT);
     structViewer.setBounds(new Rectangle(190, ypos, 120, height));
     structViewer.addItem(ViewerType.JMOL.name());
     structViewer.addItem(ViewerType.CHIMERA.name());
     structViewer.addItem(ViewerType.CHIMERAX.name());
+    structViewer.addItem(ViewerType.PYMOL.name());
     structViewer.addActionListener(new ActionListener()
     {
       @Override
@@ -1265,38 +1703,40 @@ public class GPreferences extends JPanel
     structureTab.add(structViewer);
 
     ypos += lineSpacing;
-    chimeraPathLabel = new JLabel();
-    chimeraPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11));
-    chimeraPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
-    chimeraPathLabel.setText(MessageManager
-            .formatMessage("label.chimera_path", "Chimera(X)"));
-    chimeraPathLabel.setBounds(new Rectangle(10, ypos, 170, height));
-    chimeraPathLabel.setEnabled(false);
-    structureTab.add(chimeraPathLabel);
-
-    chimeraPath.setFont(LABEL_FONT);
-    chimeraPath.setText("");
-    chimeraPath.setEnabled(false);
+    structureViewerPathLabel = new JLabel();
+    structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0,
+                                                 // 11));
+    structureViewerPathLabel.setHorizontalAlignment(SwingConstants.LEFT);
+    structureViewerPathLabel.setText(MessageManager
+            .formatMessage("label.viewer_path", "Chimera(X)"));
+    structureViewerPathLabel
+            .setBounds(new Rectangle(10, ypos, 170, height));
+    structureViewerPathLabel.setEnabled(false);
+    structureTab.add(structureViewerPathLabel);
+
+    structureViewerPath.setFont(LABEL_FONT);
+    structureViewerPath.setText("");
+    structureViewerPath.setEnabled(false);
     final String tooltip = JvSwingUtils.wrapTooltip(true,
-            MessageManager.getString("label.chimera_path_tip"));
-    chimeraPath.setToolTipText(tooltip);
-    chimeraPath.setBounds(new Rectangle(190, ypos, 290, height));
-    chimeraPath.addMouseListener(new MouseAdapter()
+            MessageManager.getString("label.viewer_path_tip"));
+    structureViewerPath.setToolTipText(tooltip);
+    structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
+    structureViewerPath.addMouseListener(new MouseAdapter()
     {
       @Override
       public void mouseClicked(MouseEvent e)
       {
-        if (chimeraPath.isEnabled() && e.getClickCount() == 2)
+        if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
         {
           String chosen = openFileChooser();
           if (chosen != null)
           {
-            chimeraPath.setText(chosen);
+            structureViewerPath.setText(chosen);
           }
         }
       }
     });
-    structureTab.add(chimeraPath);
+    structureTab.add(structureViewerPath);
 
     ypos += lineSpacing;
     nwMapping.setFont(LABEL_FONT);
@@ -1325,6 +1765,17 @@ public class GPreferences extends JPanel
     docFieldPref.setBounds(new Rectangle(10, ypos, 470, 120));
     structureTab.add(docFieldPref);
 
+    /*
+     * hide Chimera options in JalviewJS
+     */
+    if (Platform.isJS())
+    {
+      structureViewerPathLabel.setVisible(false);
+      structureViewerPath.setVisible(false);
+      viewerLabel.setVisible(false);
+      structViewer.setVisible(false);
+    }
+
     return structureTab;
   }
 
@@ -1701,6 +2152,13 @@ public class GPreferences extends JPanel
     visualTab.add(fontNameCB);
     visualTab.add(fontSizeCB);
     visualTab.add(fontStyleCB);
+
+    if (Platform.isJS())
+    {
+      startupCheckbox.setVisible(false);
+      startupFileTextfield.setVisible(false);
+    }
+
     return visualTab;
   }
 
@@ -1712,8 +2170,8 @@ public class GPreferences extends JPanel
   {
     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
             .getSavedBackupEntry();
-    enableBackupFiles
-            .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+    enableBackupFiles.setSelected(
+            Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
 
     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
             .createBackupFilesPresetEntry(Cache
@@ -1790,7 +2248,6 @@ public class GPreferences extends JPanel
       }
     });
 
-
     // enable checkbox 1 col
     gbc.gridwidth = 1;
     gbc.gridheight = 1;
@@ -1863,8 +2320,8 @@ public class GPreferences extends JPanel
     presetsComboLabel = new JLabel(title + ":");
     presetsPanel.add(presetsComboLabel, gbc);
 
-    List<Object> entries = Arrays
-            .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+    List<Object> entries = Arrays.asList(
+            (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
     List<String> tooltips = Arrays.asList(
             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
@@ -1891,7 +2348,8 @@ public class GPreferences extends JPanel
         {
           if (customiseCheckbox.isSelected())
           {
-            // got here by clicking on customiseCheckbox so don't change the values
+            // got here by clicking on customiseCheckbox so don't change the
+            // values
             backupfilesCustomOptionsSetEnabled();
           }
           else
@@ -1970,13 +2428,11 @@ public class GPreferences extends JPanel
 
   private JPanel initBackupsTabFilenameExamplesPanel()
   {
-    String title = MessageManager
-            .getString("label.scheme_examples");
+    String title = MessageManager.getString("label.scheme_examples");
     TitledBorder tb = new TitledBorder(title);
     exampleFilesPanel.setBorder(tb);
     exampleFilesPanel.setLayout(new GridBagLayout());
 
-
     backupfilesExampleLabel.setEditable(false);
     backupfilesExampleLabel
             .setBackground(exampleFilesPanel.getBackground());
@@ -2037,8 +2493,7 @@ public class GPreferences extends JPanel
   }
 
   protected void setComboIntStringKey(
-          JComboBox<Object> backupfilesPresetsCombo2,
-          int key)
+          JComboBox<Object> backupfilesPresetsCombo2, int key)
   {
     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
     {
@@ -2308,9 +2763,8 @@ public class GPreferences extends JPanel
 
     JPanel jp = new JPanel();
     jp.setLayout(new FlowLayout());
-    oldBackupFilesLabel
-            .setText(MessageManager
-                    .getString("label.autodelete_old_backup_files"));
+    oldBackupFilesLabel.setText(
+            MessageManager.getString("label.autodelete_old_backup_files"));
     oldBackupFilesLabel.setFont(LABEL_FONT);
     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
     jp.add(oldBackupFilesLabel);
@@ -2470,7 +2924,8 @@ public class GPreferences extends JPanel
 
     }
 
-    // add some extra empty lines to pad out the example files box. ugh, please tell
+    // add some extra empty lines to pad out the example files box. ugh, please
+    // tell
     // me how to do this better
     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
     if (remainingLines > 0)
@@ -2512,6 +2967,10 @@ public class GPreferences extends JPanel
     {
       max = def;
     }
+    if (def < min)
+    {
+      def = min;
+    }
     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
     s.setModel(sModel);
 
@@ -2545,8 +3004,7 @@ public class GPreferences extends JPanel
   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
   {
     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
-            && customiseCheckbox.isSelected()
-            && suffixTemplate.getText()
+            && customiseCheckbox.isSelected() && suffixTemplate.getText()
                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
     keepfilesPanel.setEnabled(enabled);
     backupfilesKeepAll.setEnabled(enabled);
@@ -2758,13 +3216,45 @@ public class GPreferences extends JPanel
 
   }
 
-  public void useProxy_actionPerformed()
+  public void setProxyAuthEnabled()
+  {
+    boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
+    proxyAuthUsernameLabel.setEnabled(enabled);
+    proxyAuthPasswordLabel.setEnabled(enabled);
+    passwordNotStoredLabel.setEnabled(enabled);
+    proxyAuthUsernameTB.setEnabled(enabled);
+    proxyAuthPasswordPB.setEnabled(enabled);
+  }
+
+  public void setCustomProxyEnabled()
   {
-    boolean enabled = useProxy.isSelected();
+    boolean enabled = customProxy.isSelected();
     portLabel.setEnabled(enabled);
     serverLabel.setEnabled(enabled);
-    proxyServerTB.setEnabled(enabled);
-    proxyPortTB.setEnabled(enabled);
+    portLabel2.setEnabled(enabled);
+    serverLabel2.setEnabled(enabled);
+    httpLabel.setEnabled(enabled);
+    httpsLabel.setEnabled(enabled);
+    proxyServerHttpTB.setEnabled(enabled);
+    proxyPortHttpTB.setEnabled(enabled);
+    proxyServerHttpsTB.setEnabled(enabled);
+    proxyPortHttpsTB.setEnabled(enabled);
+    proxyAuth.setEnabled(enabled);
+    setProxyAuthEnabled();
+  }
+
+  public void proxyType_actionPerformed()
+  {
+    setCustomProxyEnabled();
+    proxyAuthPasswordCheckHighlight(true);
+    applyProxyButtonEnabled(true);
+  }
+
+  public void proxyAuth_actionPerformed()
+  {
+    setProxyAuthEnabled();
+    proxyAuthPasswordCheckHighlight(true);
+    applyProxyButtonEnabled(true);
   }
 
   /**
@@ -2839,4 +3329,3 @@ public class GPreferences extends JPanel
 
   }
 }
-