X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=19c0a3610a34f625f76690f355c6dfa8ac478471;hb=304e64fb34b32659be1bbfd39fb4e15b2f79586e;hp=c132e49d01a17384a65f19d1d118881a9bdb7ceb;hpb=682ebcd21b2123786463a3f56cc6f7c17f361bae;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index c132e49..19c0a36 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -34,6 +34,7 @@ import jalview.io.BackupFiles;
 import jalview.io.BackupFilesPresetEntry;
 import jalview.io.IntKeyStringValueEntry;
 import jalview.util.MessageManager;
+import jalview.util.Platform;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -53,17 +54,23 @@ import java.awt.event.KeyEvent;
 import java.awt.event.KeyListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
+import java.util.Arrays;
+import java.util.List;
 
+import javax.swing.AbstractButton;
 import javax.swing.AbstractCellEditor;
 import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
 import javax.swing.ButtonGroup;
 import javax.swing.DefaultListCellRenderer;
 import javax.swing.JButton;
 import javax.swing.JCheckBox;
 import javax.swing.JComboBox;
+import javax.swing.JComponent;
 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;
@@ -81,6 +88,8 @@ 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;
 
@@ -158,6 +167,9 @@ public class GPreferences extends JPanel
 
   protected JCheckBox showConsensLogo = new JCheckBox();
 
+  protected JCheckBox showInformationHistogram = new JCheckBox();
+
+  protected JCheckBox showHMMLogo = new JCheckBox();
   protected JCheckBox showDbRefTooltip = new JCheckBox();
 
   protected JCheckBox showNpTooltip = new JCheckBox();
@@ -169,7 +181,6 @@ public class GPreferences extends JPanel
 
   protected JCheckBox structFromPdb = new JCheckBox();
 
-  protected JCheckBox useRnaView = new JCheckBox();
 
   protected JCheckBox addSecondaryStructure = new JCheckBox();
 
@@ -177,7 +188,9 @@ public class GPreferences extends JPanel
 
   protected JComboBox<String> structViewer = new JComboBox<>();
 
-  protected JTextField chimeraPath = new JTextField();
+  protected JLabel structureViewerPathLabel;
+
+  protected JTextField structureViewerPath = new JTextField();
 
   protected ButtonGroup mappingMethod = new ButtonGroup();
 
@@ -212,6 +225,8 @@ public class GPreferences extends JPanel
   /*
    * Connections tab components
    */
+  protected JPanel connectTab;
+
   protected JTable linkUrlTable = new JTable();
 
   protected JButton editLink = new JButton();
@@ -224,17 +239,49 @@ 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 JLabel serverLabel2 = new JLabel();
+
+  protected JLabel proxyAuthUsernameLabel = new JLabel();
+
+  protected JLabel proxyAuthPasswordLabel = new JLabel();
 
-  protected JTextField proxyPortTB = new JTextField();
+  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();
 
@@ -247,6 +294,10 @@ 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();
@@ -281,10 +332,28 @@ public class GPreferences extends JPanel
   protected JCheckBox sortByTree = new JCheckBox();
 
   /*
+   * hmmer tab and components
+   */
+  protected JPanel hmmerTab;
+
+  protected JCheckBox hmmrTrimTermini;
+
+  protected AbstractButton hmmerBackgroundUniprot;
+
+  protected AbstractButton hmmerBackgroundAlignment;
+
+  protected JTextField hmmerSequenceCount;
+
+  protected JTextField hmmerPath;
+
+  protected JTextField cygwinPath;
+
+  /*
    * Web Services tab
    */
   protected JPanel wsTab = new JPanel();
 
+  protected JPanel slivkaTab = new JPanel();
   /*
    * Backups tab components
    * a lot of these are member variables instead of local variables only so that they
@@ -301,7 +370,7 @@ public class GPreferences extends JPanel
 
   protected JButton revertButton = new JButton();
 
-  protected JComboBox<IntKeyStringValueEntry> backupfilesPresetsCombo = new JComboBox<>();
+  protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
 
   private int backupfilesPresetsComboLastSelected = 0;
 
@@ -331,6 +400,9 @@ 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.
    */
@@ -352,8 +424,10 @@ 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);
@@ -373,8 +447,11 @@ 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"));
@@ -385,15 +462,22 @@ public class GPreferences extends JPanel
     tabbedPane.add(initEditingTab(),
             MessageManager.getString("label.editing"));
 
+    tabbedPane.add(initHMMERTab(), MessageManager.getString("label.hmmer"));
     /*
      * 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"));
+      slivkaTab.setLayout(new BorderLayout());
+      tabbedPane.add(slivkaTab, "Slivka 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()
     {
@@ -412,11 +496,62 @@ 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 static enum TabRef
+  {
+    CONNECTIONS_TAB, STRUCTURE_TAB
+  };
+
+  public void selectTab(TabRef selectTab)
+  {
+    // select a given tab - currently only for Connections
+    switch (selectTab)
+    {
+    case CONNECTIONS_TAB:
+      tabbedPane.setSelectedComponent(connectTab);
+      break;
+    case STRUCTURE_TAB:
+      tabbedPane.setSelectedComponent(structureTab);
+      break;
+    default:
+    }
+  }
+
   /**
    * Initialises the Editing tabbed panel.
    * 
@@ -447,6 +582,134 @@ public class GPreferences extends JPanel
   }
 
   /**
+   * Initialises the hmmer tabbed panel
+   * 
+   * @return
+   */
+  private JPanel initHMMERTab()
+  {
+    hmmerTab = new JPanel();
+    hmmerTab.setLayout(new BoxLayout(hmmerTab, BoxLayout.Y_AXIS));
+    hmmerTab.setLayout(new MigLayout("flowy"));
+
+    /*
+     * path to hmmer binaries folder
+     */
+    JPanel installationPanel = new JPanel(new MigLayout("flowy"));
+    // new FlowLayout(FlowLayout.LEFT));
+    JvSwingUtils.createTitledBorder(installationPanel,
+            MessageManager.getString("label.installation"), true);
+    hmmerTab.add(installationPanel);
+    JLabel hmmerLocation = new JLabel(
+            MessageManager.getString("label.hmmer_location"));
+    hmmerLocation.setFont(LABEL_FONT);
+    final int pathFieldLength = 40;
+    hmmerPath = new JTextField(pathFieldLength);
+    hmmerPath.addMouseListener(new MouseAdapter()
+    {
+      @Override
+      public void mouseClicked(MouseEvent e)
+      {
+        if (e.getClickCount() == 2)
+        {
+          String chosen = openFileChooser(true);
+          if (chosen != null)
+          {
+            hmmerPath.setText(chosen);
+            validateHmmerPath();
+          }
+        }
+      }
+    });
+    installationPanel.add(hmmerLocation);
+    installationPanel.add(hmmerPath);
+
+    /*
+     * path to Cygwin binaries folder (for Windows)
+     */
+    if (Platform.isWindowsAndNotJS())
+    {
+      JLabel cygwinLocation = new JLabel(
+              MessageManager.getString("label.cygwin_location"));
+      cygwinLocation.setFont(LABEL_FONT);
+      cygwinPath = new JTextField(pathFieldLength);
+      cygwinPath.addMouseListener(new MouseAdapter()
+      {
+        @Override
+        public void mouseClicked(MouseEvent e)
+        {
+          if (e.getClickCount() == 2)
+          {
+            String chosen = openFileChooser(true);
+            if (chosen != null)
+            {
+              cygwinPath.setText(chosen);
+              validateCygwinPath();
+            }
+          }
+        }
+      });
+      installationPanel.add(cygwinLocation);
+      installationPanel.add(cygwinPath);
+    }
+
+    /*
+     * preferences for hmmalign
+     */
+    JPanel alignOptionsPanel = new JPanel(new MigLayout());
+    // new FlowLayout(FlowLayout.LEFT));
+    JvSwingUtils.createTitledBorder(alignOptionsPanel,
+            MessageManager.getString("label.hmmalign_options"), true);
+    hmmerTab.add(alignOptionsPanel);
+    hmmrTrimTermini = new JCheckBox();
+    hmmrTrimTermini.setFont(LABEL_FONT);
+    hmmrTrimTermini.setText(MessageManager.getString("label.trim_termini"));
+    alignOptionsPanel.add(hmmrTrimTermini);
+
+    /*
+     * preferences for hmmsearch
+     */
+    JPanel searchOptions = new JPanel(new MigLayout());
+    // FlowLayout(FlowLayout.LEFT));
+    JvSwingUtils.createTitledBorder(searchOptions,
+            MessageManager.getString("label.hmmsearch_options"), true);
+    hmmerTab.add(searchOptions);
+    JLabel sequencesToKeep = new JLabel(
+            MessageManager.getString("label.no_of_sequences"));
+    sequencesToKeep.setFont(LABEL_FONT);
+    searchOptions.add(sequencesToKeep);
+    hmmerSequenceCount = new JTextField(5);
+    searchOptions.add(hmmerSequenceCount);
+
+    /*
+     * preferences for Information Content annotation
+     */
+    // JPanel dummy = new JPanel(new FlowLayout(FlowLayout.LEFT));
+    JPanel annotationOptions = new JPanel(new MigLayout("left"));
+    JvSwingUtils.createTitledBorder(annotationOptions,
+            MessageManager.getString("label.information_annotation"), true);
+    // dummy.add(annotationOptions);
+    hmmerTab.add(annotationOptions);
+    ButtonGroup backgroundOptions = new ButtonGroup();
+    hmmerBackgroundUniprot = new JRadioButton(
+            MessageManager.getString("label.freq_uniprot"));
+    hmmerBackgroundUniprot.setFont(LABEL_FONT);
+    hmmerBackgroundAlignment = new JRadioButton(
+            MessageManager.getString("label.freq_alignment"));
+    hmmerBackgroundAlignment.setFont(LABEL_FONT);
+    backgroundOptions.add(hmmerBackgroundUniprot);
+    backgroundOptions.add(hmmerBackgroundAlignment);
+    backgroundOptions.setSelected(hmmerBackgroundUniprot.getModel(), true);
+    // disable buttons for now as annotation only uses Uniprot background
+    hmmerBackgroundAlignment.setEnabled(false);
+    hmmerBackgroundUniprot.setEnabled(false);
+    annotationOptions.add(hmmerBackgroundUniprot, "wrap");
+    annotationOptions.add(hmmerBackgroundAlignment);
+
+    return hmmerTab;
+  }
+
+  /**
    * Initialises the Output tabbed panel.
    * 
    * @return
@@ -455,18 +718,35 @@ 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") + "     ");
@@ -483,7 +763,7 @@ 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);
@@ -502,7 +782,7 @@ 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()
     {
 
@@ -520,10 +800,10 @@ 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()
     {
 
@@ -536,10 +816,10 @@ 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);
@@ -553,9 +833,19 @@ 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;
   }
@@ -567,7 +857,7 @@ public class GPreferences extends JPanel
    */
   private JPanel initConnectionsTab()
   {
-    JPanel connectTab = new JPanel();
+    connectTab = new JPanel();
     connectTab.setLayout(new GridBagLayout());
 
     // Label for browser text box
@@ -627,6 +917,8 @@ public class GPreferences extends JPanel
                     GridBagConstraints.WEST, GridBagConstraints.HORIZONTAL,
                     new Insets(0, 2, 5, 5), 70, 1));
 
+    versioncheck.setVisible(false);
+
     // Add padding so the panel doesn't look ridiculous
     JPanel spacePanel = new JPanel();
     connectTab.add(spacePanel,
@@ -836,63 +1128,365 @@ 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
    */
@@ -1002,7 +1596,7 @@ public class GPreferences extends JPanel
     protColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
     protColourLabel.setText(
             MessageManager.getString("label.prot_alignment_colour") + " ");
-    JvSwingUtils.addtoLayout(coloursTab,
+    GPreferences.addtoLayout(coloursTab,
             MessageManager
                     .getString("label.default_colour_scheme_for_alignment"),
             protColourLabel, protColour);
@@ -1014,7 +1608,7 @@ public class GPreferences extends JPanel
     nucColourLabel.setHorizontalAlignment(SwingConstants.LEFT);
     nucColourLabel.setText(
             MessageManager.getString("label.nuc_alignment_colour") + " ");
-    JvSwingUtils.addtoLayout(coloursTab,
+    GPreferences.addtoLayout(coloursTab,
             MessageManager
                     .getString("label.default_colour_scheme_for_alignment"),
             nucColourLabel, nucColour);
@@ -1023,11 +1617,11 @@ public class GPreferences extends JPanel
     annotationShding.setBorder(new TitledBorder(
             MessageManager.getString("label.annotation_shading_default")));
     annotationShding.setLayout(new GridLayout(1, 2));
-    JvSwingUtils.addtoLayout(annotationShding,
+    GPreferences.addtoLayout(annotationShding,
             MessageManager.getString(
                     "label.default_minimum_colour_annotation_shading"),
             mincolourLabel, minColour);
-    JvSwingUtils.addtoLayout(annotationShding,
+    GPreferences.addtoLayout(annotationShding,
             MessageManager.getString(
                     "label.default_maximum_colour_annotation_shading"),
             maxcolourLabel, maxColour);
@@ -1191,7 +1785,7 @@ public class GPreferences extends JPanel
     structureTab.setBorder(new TitledBorder(
             MessageManager.getString("label.structure_options")));
     structureTab.setLayout(null);
-    final int width = 400;
+    final int width = 420;
     final int height = 22;
     final int lineSpacing = 25;
     int ypos = 15;
@@ -1207,7 +1801,6 @@ public class GPreferences extends JPanel
       {
         boolean selected = structFromPdb.isSelected();
         // enable other options only when the first is checked
-        useRnaView.setEnabled(selected);
         addSecondaryStructure.setEnabled(selected);
         addTempFactor.setEnabled(selected);
       }
@@ -1215,11 +1808,6 @@ public class GPreferences extends JPanel
     structureTab.add(structFromPdb);
 
     // indent checkboxes that are conditional on the first one
-    ypos += lineSpacing;
-    useRnaView.setFont(LABEL_FONT);
-    useRnaView.setText(MessageManager.getString("label.use_rnaview"));
-    useRnaView.setBounds(new Rectangle(25, ypos, width, height));
-    structureTab.add(useRnaView);
 
     ypos += lineSpacing;
     addSecondaryStructure.setFont(LABEL_FONT);
@@ -1239,13 +1827,19 @@ public class GPreferences extends JPanel
     viewerLabel.setFont(LABEL_FONT);
     viewerLabel.setHorizontalAlignment(SwingConstants.LEFT);
     viewerLabel.setText(MessageManager.getString("label.structure_viewer"));
-    viewerLabel.setBounds(new Rectangle(10, ypos, 200, height));
+    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(160, ypos, 120, height));
+    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
@@ -1258,35 +1852,68 @@ public class GPreferences extends JPanel
     structureTab.add(structViewer);
 
     ypos += lineSpacing;
-    JLabel pathLabel = new JLabel();
-    pathLabel.setFont(new java.awt.Font("SansSerif", 0, 11));
-    pathLabel.setHorizontalAlignment(SwingConstants.LEFT);
-    pathLabel.setText(MessageManager.getString("label.chimera_path"));
-    pathLabel.setBounds(new Rectangle(10, ypos, 140, height));
-    structureTab.add(pathLabel);
-
-    chimeraPath.setFont(LABEL_FONT);
-    chimeraPath.setText("");
+    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(160, ypos, 300, 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 (e.getClickCount() == 2)
+        if (structureViewerPath.isEnabled() && e.getClickCount() == 2)
+        {
+          structureViewer_actionPerformed(
+                  (String) structViewer.getSelectedItem());
+        }
+      });
+      structureTab.add(structViewer);
+      ypos += lineSpacing;
+      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.viewer_path_tip"));
+      structureViewerPath.setToolTipText(tooltip);
+      structureViewerPath.setBounds(new Rectangle(190, ypos, 290, height));
+      structureViewerPath.addMouseListener(new MouseAdapter()
+      {
+        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);
@@ -1301,7 +1928,7 @@ public class GPreferences extends JPanel
             MessageManager.getString("label.mapping_method"));
     mmTitledBorder.setTitleFont(LABEL_FONT);
     mappingPanel.setBorder(mmTitledBorder);
-    mappingPanel.setBounds(new Rectangle(10, ypos, 452, 45));
+    mappingPanel.setBounds(new Rectangle(10, ypos, 472, 45));
     // GridLayout mappingLayout = new GridLayout();
     mappingPanel.setLayout(new GridLayout());
     mappingPanel.add(nwMapping);
@@ -1312,9 +1939,19 @@ public class GPreferences extends JPanel
     ypos += lineSpacing;
     FTSDataColumnPreferences docFieldPref = new FTSDataColumnPreferences(
             PreferenceSource.PREFERENCES, PDBFTSRestClient.getInstance());
-    docFieldPref.setBounds(new Rectangle(10, ypos, 450, 120));
+    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;
   }
 
@@ -1328,16 +1965,29 @@ public class GPreferences extends JPanel
   }
 
   /**
-   * Show a dialog for the user to choose a file. Returns the chosen path, or
-   * null on Cancel.
+   * Show a dialog for the user to choose a file. Returns the chosen path, or null
+   * on Cancel.
    * 
    * @return
    */
-  protected String openFileChooser()
+  protected String openFileChooser(boolean forFolder)
   {
     String choice = null;
     JFileChooser chooser = new JFileChooser();
 
+    // Enable appBundleIsTraversable in macOS FileChooser to allow selecting
+    // hidden executables within .app dirs
+    if (Platform.isMac())
+    {
+      chooser.putClientProperty("JFileChooser.appBundleIsTraversable",
+              true);
+    }
+
+    if (forFolder)
+    {
+      chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
+    }
+
     // chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.open_local_file"));
@@ -1691,6 +2341,13 @@ 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;
   }
 
@@ -1703,7 +2360,7 @@ public class GPreferences extends JPanel
     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
             .getSavedBackupEntry();
     enableBackupFiles
-            .setSelected(Cache.getDefault(BackupFiles.ENABLED, true));
+            .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
 
     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
             .createBackupFilesPresetEntry(Cache
@@ -1720,27 +2377,13 @@ public class GPreferences extends JPanel
     setComboIntStringKey(backupfilesPresetsCombo,
             Cache.getDefault(BackupFiles.NS + "_PRESET",
                     BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
-    // backupsTabUpdatePresets();
 
-    System.out
-            .println("LOADLASTSAVEDBACKUPSOPTIONS SETTING BACKUPS OPTIONS");
     backupsSetOptions(savedPreset);
 
     backupsOptionsSetEnabled();
     updateBackupFilesExampleLabel();
   }
 
-  private void setBackupfilesCustomPreset()
-  {
-    if (customiseCheckbox.isSelected() && getComboIntStringKey(
-            backupfilesPresetsCombo) == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
-    {
-      BackupFilesPresetEntry.backupfilesPresetEntriesValues
-              .put(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
-                      getBackupfilesCurrentEntry());
-    }
-  }
-
   private boolean warnAboutSuffixReverseChange()
   {
     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
@@ -1824,7 +2467,6 @@ public class GPreferences extends JPanel
     gbc.gridy++; // row 1
     backupsTab.add(presetsPanel, gbc);
 
-    // gbc.anchor = GridBagConstraints.NORTHWEST;
     // now using whole row
     gbc.gridwidth = 2;
     gbc.gridheight = 1;
@@ -1850,10 +2492,6 @@ public class GPreferences extends JPanel
   {
 
     String title = MessageManager.getString("label.schemes");
-    // TitledBorder tb = new TitledBorder(new EmptyBorder(0, 0, 0, 0), title);
-    // TitledBorder tb = new TitledBorder(title);
-    // tb.setTitleFont(LABEL_FONT);
-    // presetsPanel.setBorder(tb);
 
     presetsPanel.setLayout(new GridBagLayout());
 
@@ -1872,11 +2510,19 @@ public class GPreferences extends JPanel
     presetsComboLabel = new JLabel(title + ":");
     presetsPanel.add(presetsComboLabel, gbc);
 
+    List<Object> entries = Arrays
+            .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+    List<String> tooltips = Arrays.asList(
+            BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
+    backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
+            tooltips);
+    /*
     for (int i = 0; i < BackupFilesPresetEntry.backupfilesPresetEntries.length; i++)
     {
       backupfilesPresetsCombo
               .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
     }
+    */
 
     backupfilesPresetsCombo.addActionListener(new ActionListener()
     {
@@ -1915,6 +2561,8 @@ public class GPreferences extends JPanel
     presetsPanel.add(backupfilesPresetsCombo, gbc);
 
     revertButton.setText(MessageManager.getString("label.cancel_changes"));
+    revertButton.setToolTipText(
+            MessageManager.getString("label.cancel_changes_description"));
     revertButton.addActionListener(new ActionListener()
     {
       @Override
@@ -1952,6 +2600,8 @@ public class GPreferences extends JPanel
         backupfilesCustomOptionsSetEnabled();
       }
     });
+    customiseCheckbox.setToolTipText(
+            MessageManager.getString("label.customise_description"));
 
     // customise checkbox
     gbc.gridx = 0;
@@ -1968,7 +2618,7 @@ public class GPreferences extends JPanel
   private JPanel initBackupsTabFilenameExamplesPanel()
   {
     String title = MessageManager
-            .getString("label.summary_of_backups_scheme");
+            .getString("label.scheme_examples");
     TitledBorder tb = new TitledBorder(title);
     exampleFilesPanel.setBorder(tb);
     exampleFilesPanel.setLayout(new GridBagLayout());
@@ -1994,8 +2644,8 @@ public class GPreferences extends JPanel
   {
     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
             .getSelectedItem();
-    int key = entry.getKey();
-    String value = entry.getValue();
+    int key = entry.k;
+    String value = entry.v;
 
     if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
             .containsKey(key))
@@ -2006,7 +2656,7 @@ public class GPreferences extends JPanel
     }
     else
     {
-      System.out.println(
+      Cache.log.error(
               "Preset '" + value + "' [key:" + key + "] not implemented");
     }
 
@@ -2016,21 +2666,42 @@ public class GPreferences extends JPanel
     updateBackupFilesExampleLabel();
   }
 
-  protected int getComboIntStringKey(JComboBox<IntKeyStringValueEntry> c)
+  protected int getComboIntStringKey(
+          JComboBox<Object> backupfilesPresetsCombo2)
   {
-    IntKeyStringValueEntry e = (IntKeyStringValueEntry) c.getSelectedItem();
-    return e != null ? e.getKey() : 0;
+    IntKeyStringValueEntry e;
+    try
+    {
+      e = (IntKeyStringValueEntry) backupfilesPresetsCombo2
+              .getSelectedItem();
+    } catch (Exception ex)
+    {
+      Cache.log.error(
+              "Problem casting Combo entry to IntKeyStringValueEntry.");
+      e = null;
+    }
+    return e != null ? e.k : 0;
   }
 
-  protected void setComboIntStringKey(JComboBox<IntKeyStringValueEntry> c,
+  protected void setComboIntStringKey(
+          JComboBox<Object> backupfilesPresetsCombo2,
           int key)
   {
-    for (int i = 0; i < c.getItemCount(); i++)
+    for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
     {
-      IntKeyStringValueEntry e = c.getItemAt(i);
-      if (e.getKey() == key)
+      IntKeyStringValueEntry e;
+      try
+      {
+        e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+      } catch (Exception ex)
+      {
+        Cache.log.error(
+                "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
+        continue;
+      }
+      if (e.k == key)
       {
-        c.setSelectedIndex(i);
+        backupfilesPresetsCombo2.setSelectedIndex(i);
         break;
       }
     }
@@ -2081,7 +2752,6 @@ public class GPreferences extends JPanel
       @Override
       public void keyTyped(KeyEvent e)
       {
-        int count = 300;
         char c = e.getKeyChar();
         if (c == ':' || c == '/' || c == '\\')
         {
@@ -2183,7 +2853,7 @@ public class GPreferences extends JPanel
     boolean ret = false;
     String warningMessage = MessageManager
             .getString("label.warning_confirm_change_reverse");
-    int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+    int confirm = JvOptionPane.showConfirmDialog(Desktop.getDesktopPane(),
             warningMessage,
             MessageManager.getString("label.change_increment_decrement"),
             JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
@@ -2282,13 +2952,6 @@ public class GPreferences extends JPanel
     kgbc.gridwidth = GridBagConstraints.REMAINDER;
     kgbc.fill = GridBagConstraints.HORIZONTAL;
     kgbc.weightx = 1.0;
-    /*
-    keepfilesPanel.add(backupfilesConfirmDelete.getTrueButton(), kgbc);
-    
-    // fourth row (indented)
-    kgbc.gridy = 3;
-    keepfilesPanel.add(backupfilesConfirmDelete.getFalseButton(), kgbc);
-    */
 
     JPanel jp = new JPanel();
     jp.setLayout(new FlowLayout());
@@ -2344,6 +3007,7 @@ public class GPreferences extends JPanel
     int uppersurround = 0;
     StringBuilder exampleSB = new StringBuilder();
     boolean firstLine = true;
+    int lineNumber = 0;
     if (reverse)
     {
 
@@ -2354,6 +3018,7 @@ public class GPreferences extends JPanel
         if (index == min + lowersurround && index < max - uppersurround - 1)
         {
           exampleSB.append("\n...");
+          lineNumber++;
         }
         else if (index > min + lowersurround && index < max - uppersurround)
         {
@@ -2368,6 +3033,7 @@ public class GPreferences extends JPanel
           else
           {
             exampleSB.append("\n");
+            lineNumber++;
           }
           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
                   base, suffix, digits));
@@ -2407,6 +3073,7 @@ public class GPreferences extends JPanel
         if (index == min + lowersurround && index < max - uppersurround - 1)
         {
           exampleSB.append("\n...");
+          lineNumber++;
         }
         else if (index > min + lowersurround && index < max - uppersurround)
         {
@@ -2421,6 +3088,7 @@ public class GPreferences extends JPanel
           else
           {
             exampleSB.append("\n");
+            lineNumber++;
           }
           exampleSB.append(BackupFilenameParts.getBackupFilename(index,
                   base, suffix, digits));
@@ -2449,6 +3117,18 @@ public class GPreferences extends JPanel
 
     }
 
+    // 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)
+    {
+      for (int i = 0; i < remainingLines; i++)
+      {
+        exampleSB.append("\n ");
+        lineNumber++;
+      }
+    }
+
     backupfilesExampleLabel.setText(exampleSB.toString());
   }
 
@@ -2460,10 +3140,10 @@ public class GPreferences extends JPanel
     {
       try
       {
-        i = Integer.parseInt((String) s.getValue());
+        i = ((Integer) s.getValue()).intValue();
       } catch (Exception e)
       {
-        System.out.println(
+        Cache.log.error(
                 "Exception casting the initial value of s.getValue()");
       }
     }
@@ -2479,6 +3159,10 @@ public class GPreferences extends JPanel
     {
       max = def;
     }
+    if (def < min)
+    {
+      def = min;
+    }
     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
     s.setModel(sModel);
 
@@ -2495,7 +3179,7 @@ public class GPreferences extends JPanel
       i = (Integer) s.getValue();
     } catch (Exception e)
     {
-      System.out.println("Failed casting (Integer) JSpinner s.getValue()");
+      Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
     }
     return i;
   }
@@ -2572,11 +3256,7 @@ public class GPreferences extends JPanel
 
   protected void backupfilesCustomOptionsSetEnabled()
   {
-    // int scheme = getComboIntStringKey(backupfilesPresetsCombo);
-    // boolean enabled = scheme == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM &&
-    // enableBackupFiles.isSelected();
     boolean enabled = customiseCheckbox.isSelected();
-    //boolean enabled = customiseCheckbox.isSelected() && enableBackupFiles.isSelected();
 
     backupfilesRevertButtonSetEnabled(enabled);
     backupfilesSuffixTemplateSetEnabled(enabled);
@@ -2729,13 +3409,45 @@ public class GPreferences extends JPanel
 
   }
 
-  public void useProxy_actionPerformed()
+  public void setProxyAuthEnabled()
   {
-    boolean enabled = useProxy.isSelected();
+    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 = 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);
   }
 
   /**
@@ -2809,5 +3521,41 @@ public class GPreferences extends JPanel
     }
 
   }
+
+  protected void validateHmmerPath()
+  {
+  }
+
+  protected void validateCygwinPath()
+  {
+  }
+
+  /**
+   * A helper method to add a panel containing a label and a component to a
+   * panel
+   * 
+   * @param panel
+   * @param tooltip
+   * @param label
+   * @param valBox
+   */
+  protected static void addtoLayout(JPanel panel, String tooltip,
+          JComponent label, JComponent valBox)
+  {
+    JPanel laypanel = new JPanel(new GridLayout(1, 2));
+    JPanel labPanel = new JPanel(new BorderLayout());
+    JPanel valPanel = new JPanel();
+    labPanel.setBounds(new Rectangle(7, 7, 158, 23));
+    valPanel.setBounds(new Rectangle(172, 7, 270, 23));
+    labPanel.add(label, BorderLayout.WEST);
+    valPanel.add(valBox);
+    laypanel.add(labPanel);
+    laypanel.add(valPanel);
+    valPanel.setToolTipText(tooltip);
+    labPanel.setToolTipText(tooltip);
+    valBox.setToolTipText(tooltip);
+    panel.add(laypanel);
+    panel.validate();
+  }
 }