X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=bc9584e0678233a6a249ec51735180a5c1b1e60e;hb=419898b96abeb2f9cdc77b22b34d71fff5451fd9;hp=43b521a57232c31a7b05a41a2f787786deb5c34a;hpb=656e362ece73c630f032d8bf30322143a297d92e;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index 43b521a..bc9584e 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -20,16 +20,6 @@
  */
 package jalview.jbgui;
 
-import jalview.fts.core.FTSDataColumnPreferences;
-import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.gui.JalviewBooleanRadioButtons;
-import jalview.gui.JvSwingUtils;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.BackupFilenameFilter;
-import jalview.io.BackupFiles;
-import jalview.util.MessageManager;
-
 import java.awt.BorderLayout;
 import java.awt.Color;
 import java.awt.Component;
@@ -48,8 +38,8 @@ import java.awt.event.KeyEvent;
 import java.awt.event.KeyListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
-import java.util.HashMap;
-import java.util.Map;
+import java.util.Arrays;
+import java.util.List;
 
 import javax.swing.AbstractCellEditor;
 import javax.swing.BorderFactory;
@@ -61,6 +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;
@@ -81,6 +72,22 @@ import javax.swing.event.ChangeListener;
 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.
  * 
@@ -174,7 +181,9 @@ 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();
 
@@ -209,6 +218,8 @@ public class GPreferences extends JPanel
   /*
    * Connections tab components
    */
+  protected JPanel connectTab;
+
   protected JTable linkUrlTable = new JTable();
 
   protected JButton editLink = new JButton();
@@ -221,17 +232,47 @@ 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 JTextField proxyPortTB = new JTextField();
+  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 proxyAuthPasswordTB = 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 JCheckBox usagestats = new JCheckBox();
 
@@ -244,6 +285,10 @@ 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();
@@ -292,7 +337,15 @@ public class GPreferences extends JPanel
 
   protected JPanel presetsPanel = new JPanel();
 
-  protected JComboBox<IntKeyStringValueEntry> backupfilesPresetsCombo = new JComboBox<>();
+  protected JLabel presetsComboLabel = new JLabel();
+
+  protected JCheckBox customiseCheckbox = new JCheckBox();
+
+  protected JButton revertButton = new JButton();
+
+  protected JComboBox<Object> backupfilesPresetsCombo = new JComboBox<>();
+
+  private int backupfilesPresetsComboLastSelected = 0;
 
   protected JPanel suffixPanel = new JPanel();
 
@@ -325,9 +378,14 @@ public class GPreferences extends JPanel
    */
   public GPreferences()
   {
+    new GPreferences(0);
+  }
+
+  public GPreferences(int selectTab)
+  {
     try
     {
-      jbInit();
+      jbInit(selectTab);
     } catch (Exception ex)
     {
       ex.printStackTrace();
@@ -341,6 +399,13 @@ public class GPreferences extends JPanel
    */
   private void jbInit() throws Exception
   {
+    jbInit(0);
+  }
+
+  public final static int CONNECTIONS_TAB = 5;
+
+  private void jbInit(int selectTab) throws Exception
+  {
     final JTabbedPane tabbedPane = new JTabbedPane();
     this.setLayout(new BorderLayout());
     JPanel okCancelPanel = initOkCancelPanel();
@@ -362,8 +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"));
@@ -377,8 +445,11 @@ 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
@@ -404,6 +475,16 @@ public class GPreferences extends JPanel
       }
 
     });
+
+    // select a given tab - currently only for Connections
+    switch (selectTab)
+    {
+    case CONNECTIONS_TAB:
+      tabbedPane.setSelectedComponent(connectTab);
+      break;
+    default:
+    }
+
   }
 
   /**
@@ -436,7 +517,7 @@ public class GPreferences extends JPanel
   }
 
   /**
-   * Initialises the Output tabbed panel.
+   * Initialises the Output tab
    * 
    * @return
    */
@@ -444,18 +525,35 @@ 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") + "     ");
@@ -472,7 +570,7 @@ 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);
@@ -491,7 +589,7 @@ 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()
     {
 
@@ -509,10 +607,10 @@ 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()
     {
 
@@ -525,13 +623,10 @@ 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));
-
-    TitledBorder backupFilesBorder = new TitledBorder(
-            MessageManager.getString("label.backup_files"));
+    embbedBioJSON.setBounds(new Rectangle(228, 248, 250, 23));
 
     jPanel11.add(jLabel1);
     jPanel11.add(blcjv);
@@ -545,9 +640,19 @@ 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;
   }
@@ -559,7 +664,7 @@ public class GPreferences extends JPanel
    */
   private JPanel initConnectionsTab()
   {
-    JPanel connectTab = new JPanel();
+    connectTab = new JPanel();
     connectTab.setLayout(new GridBagLayout());
 
     // Label for browser text box
@@ -619,6 +724,8 @@ 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,
@@ -640,6 +747,7 @@ public class GPreferences extends JPanel
     linkTab.setLayout(new GridBagLayout());
 
     // Set up table for Url links
+    linkUrlTable.getTableHeader().setReorderingAllowed(false);
     linkUrlTable.setFillsViewportHeight(true);
     linkUrlTable.setAutoResizeMode(JTable.AUTO_RESIZE_ALL_COLUMNS);
     linkUrlTable.setAutoCreateRowSorter(true);
@@ -827,63 +935,255 @@ 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);
+    proxyAuthPasswordTB.setFont(LABEL_FONT);
+    proxyAuthPasswordTB.setColumns(30);
 
     // 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);
+
+    // 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(proxyAuthPasswordTB, c);
+
+    c.gridx++;
+    c.weightx = 0.4;
+    c.anchor = GridBagConstraints.LINE_START;
+    upPanel.add(passwordNotStoredLabel, c);
+
+    gbc.gridy++;
+    proxyPanel.add(upPanel, gbc);
 
     return proxyPanel;
   }
 
+  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
    */
@@ -1182,7 +1482,7 @@ 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;
@@ -1230,13 +1530,19 @@ 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
@@ -1249,35 +1555,38 @@ 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)
         {
           String chosen = openFileChooser();
           if (chosen != null)
           {
-            chimeraPath.setText(chosen);
+            structureViewerPath.setText(chosen);
           }
         }
       }
     });
-    structureTab.add(chimeraPath);
+    structureTab.add(structureViewerPath);
 
     ypos += lineSpacing;
     nwMapping.setFont(LABEL_FONT);
@@ -1292,7 +1601,7 @@ 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);
@@ -1303,9 +1612,20 @@ 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;
   }
 
@@ -1682,10 +2002,67 @@ 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;
   }
 
   /**
+   * Load the saved Backups options EXCEPT "Enabled" and "Scheme"
+   */
+
+  protected void loadLastSavedBackupsOptions()
+  {
+    BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
+            .getSavedBackupEntry();
+    enableBackupFiles
+            .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
+
+    BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
+            .createBackupFilesPresetEntry(Cache
+                    .getDefault(BackupFilesPresetEntry.CUSTOMCONFIG, null));
+    if (backupfilesCustomEntry == null)
+    {
+      backupfilesCustomEntry = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+              .get(BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT);
+    }
+    BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+            BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM,
+            backupfilesCustomEntry);
+
+    setComboIntStringKey(backupfilesPresetsCombo,
+            Cache.getDefault(BackupFiles.NS + "_PRESET",
+                    BackupFilesPresetEntry.BACKUPFILESSCHEMEDEFAULT));
+
+    backupsSetOptions(savedPreset);
+
+    backupsOptionsSetEnabled();
+    updateBackupFilesExampleLabel();
+  }
+
+  private boolean warnAboutSuffixReverseChange()
+  {
+    BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
+            .getSavedBackupEntry();
+    boolean savedSuffixReverse = bfpe.reverse;
+    int savedSuffixDigits = bfpe.digits;
+    String savedSuffixTemplate = bfpe.suffix;
+
+    boolean nowSuffixReverse = suffixReverse.isSelected();
+    int nowSuffixDigits = getSpinnerInt(suffixDigitsSpinner, 3);
+    String nowSuffixTemplate = suffixTemplate.getText();
+    return nowSuffixReverse != savedSuffixReverse
+            && nowSuffixDigits == savedSuffixDigits
+            && nowSuffixTemplate != null
+            && nowSuffixTemplate.equals(savedSuffixTemplate);
+  }
+
+  /**
    * Initialises the Backups tabbed panel.
    * 
    * @return
@@ -1698,9 +2075,9 @@ public class GPreferences extends JPanel
     backupsTab.setLayout(new GridBagLayout());
 
     GridBagConstraints gbc = new GridBagConstraints();
-    gbc.weightx = 1.0;
+    gbc.weightx = 0.0;
     gbc.weighty = 0.0;
-    gbc.anchor = GridBagConstraints.NORTHWEST;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
     gbc.fill = GridBagConstraints.NONE;
 
     initBackupsTabPresetsPanel();
@@ -1708,7 +2085,6 @@ public class GPreferences extends JPanel
     initBackupsTabKeepFilesPanel();
     initBackupsTabFilenameExamplesPanel();
 
-    gbc.weightx = 0.5;
     enableBackupFiles.setFont(LABEL_FONT_BOLD);
     enableBackupFiles
             .setText(MessageManager.getString("label.enable_backupfiles"));
@@ -1717,172 +2093,295 @@ public class GPreferences extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        boolean selected = enableBackupFiles.isSelected();
         // enable other options only when the first is checked
-        backupsOptionsSetEnabled(selected);
+        backupsOptionsSetEnabled();
       }
     });
 
-    // enable checkbox 1 row
+
+    // enable checkbox 1 col
     gbc.gridwidth = 1;
+    gbc.gridheight = 1;
     gbc.gridx = 0;
-    gbc.gridy = 0;
+    gbc.gridy = 0; // row 0
     backupsTab.add(enableBackupFiles, gbc);
 
+    // summary of scheme box (over two rows)
     gbc.gridx = 1;
-    gbc.weightx = 1.0;
+    gbc.weightx = 0.0;
     gbc.gridheight = 2;
-    // gbc.anchor = GridBagConstraints.NORTHEAST;
-    // gbc.fill = GridBagConstraints.HORIZONTAL;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_END;
+    gbc.fill = GridBagConstraints.BOTH;
     backupsTab.add(exampleFilesPanel, gbc);
+    gbc.gridheight = 1;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+    gbc.fill = GridBagConstraints.NONE;
 
+    // fill empty space on right
+    gbc.gridx++;
+    gbc.weightx = 1.0;
+    backupsTab.add(new JPanel(), gbc);
+
+    // schemes box
+    gbc.weightx = 0.0;
     gbc.gridx = 0;
-    gbc.gridy = 1;
+    gbc.gridy++; // row 1
     backupsTab.add(presetsPanel, gbc);
 
-    gbc.anchor = GridBagConstraints.NORTHWEST;
-    gbc.fill = GridBagConstraints.NONE;
+    // now using whole row
     gbc.gridwidth = 2;
     gbc.gridheight = 1;
-    // whole suffix panel next row
+    // keep files box
     gbc.gridx = 0;
-    gbc.gridy = 2;
-    backupsTab.add(suffixPanel, gbc);
-
-    // keep files panel
-    gbc.gridy = 3;
+    gbc.gridy++; // row 2
     backupsTab.add(keepfilesPanel, gbc);
 
-    /*
-    // whole examples panel next row
-    gbc.gridy = 3;
-    backupsTab.add(exampleFilesPanel, gbc);
-    
+    // filename strategy box
+    gbc.gridy++; // row 3
+    backupsTab.add(suffixPanel, gbc);
+
     // fill empty space
-    gbc.gridy = 4;
+    gbc.gridy++; // row 4
     gbc.weighty = 1.0;
     backupsTab.add(new JPanel(), gbc);
-    */
 
-    backupsOptionsSetEnabled(enableBackupFiles.isSelected());
+    backupsOptionsSetEnabled();
     return backupsTab;
   }
 
-  private final IntKeyStringValueEntry[] backupfilesPresetEntries = {
-      new IntKeyStringValueEntry(1,
-              MessageManager.getString("label.default")),
-      new IntKeyStringValueEntry(2,
-              MessageManager.getString("label.single_file")),
-      new IntKeyStringValueEntry(3,
-              MessageManager.getString("label.keep_everything")),
-      new IntKeyStringValueEntry(4,
-              MessageManager.getString("label.rolled_backups")),
-      // ...
-      // IMPORTANT, keep "Custom" entry with key 0 (even though it appears last)
-      new IntKeyStringValueEntry(0,
-              MessageManager.getString("label.custom")) };
-
-  private final Map<Integer, BackupFilesPresetEntry> backupfilesPresetEntriesValues = new HashMap<Integer, BackupFilesPresetEntry>()
-  {
-    {
-      put(1, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
-              3, false, false, 4, false));
-      put(2, new BackupFilesPresetEntry("~", 1, false, false, 1, false));
-      put(3, new BackupFilesPresetEntry(".v" + BackupFiles.NUM_PLACEHOLDER,
-              3, false, true, 10, true));
-      put(4, new BackupFilesPresetEntry(
-              "_bak." + BackupFiles.NUM_PLACEHOLDER, 1, true, false, 9,
-              false));
-    }
-  };
-
   private JPanel initBackupsTabPresetsPanel()
   {
-    presetsPanel.setBorder(
-            new TitledBorder(MessageManager.getString("label.presets")));
 
-    for (int i = 0; i < backupfilesPresetEntries.length; i++)
+    String title = MessageManager.getString("label.schemes");
+
+    presetsPanel.setLayout(new GridBagLayout());
+
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.weightx = 0.0;
+    gbc.weighty = 0.0;
+    gbc.anchor = GridBagConstraints.BASELINE_LEADING;
+    gbc.fill = GridBagConstraints.NONE;
+    gbc.gridwidth = 1;
+    gbc.gridheight = 1;
+
+    // "Scheme: "
+    gbc.gridx = 0;
+    gbc.gridy = 0;
+
+    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(backupfilesPresetEntries[i]);
+      backupfilesPresetsCombo
+              .addItem(BackupFilesPresetEntry.backupfilesPresetEntries[i]);
     }
+    */
 
     backupfilesPresetsCombo.addActionListener(new ActionListener()
     {
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        backupsTabUpdatePresets();
+        int key = getComboIntStringKey(backupfilesPresetsCombo);
+        if (!customiseCheckbox.isSelected())
+        {
+          backupfilesPresetsComboLastSelected = key;
+        }
+        if (key == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+        {
+          if (customiseCheckbox.isSelected())
+          {
+            // got here by clicking on customiseCheckbox so don't change the values
+            backupfilesCustomOptionsSetEnabled();
+          }
+          else
+          {
+            backupsTabUpdatePresets();
+            backupfilesCustomOptionsSetEnabled();
+          }
+        }
+        else
+        {
+          customiseCheckbox.setSelected(false);
+          backupsTabUpdatePresets();
+          backupfilesCustomOptionsSetEnabled();
+        }
       }
     });
 
-    presetsPanel.add(backupfilesPresetsCombo);
+    // dropdown list of preset schemes
+    gbc.gridx = 1;
+    presetsPanel.add(backupfilesPresetsCombo, gbc);
+
+    revertButton.setText(MessageManager.getString("label.cancel_changes"));
+    revertButton.setToolTipText(
+            MessageManager.getString("label.cancel_changes_description"));
+    revertButton.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        backupsSetOptions(
+                BackupFilesPresetEntry.backupfilesPresetEntriesValues.get(
+                        BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM));
+        backupfilesCustomOptionsSetEnabled();
+      }
+
+    });
+    revertButton.setFont(LABEL_FONT);
+
+    customiseCheckbox.setFont(LABEL_FONT);
+    customiseCheckbox.setText(MessageManager.getString("label.customise"));
+    customiseCheckbox.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        int currently = getComboIntStringKey(backupfilesPresetsCombo);
+        if (customiseCheckbox.isSelected())
+        {
+          backupfilesPresetsComboLastSelected = currently;
+          setComboIntStringKey(backupfilesPresetsCombo,
+                  BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+        }
+        else
+        {
+          setComboIntStringKey(backupfilesPresetsCombo,
+                  backupfilesPresetsComboLastSelected);
+
+        }
+        backupfilesCustomOptionsSetEnabled();
+      }
+    });
+    customiseCheckbox.setToolTipText(
+            MessageManager.getString("label.customise_description"));
+
+    // customise checkbox
+    gbc.gridx = 0;
+    gbc.gridy++;
+    presetsPanel.add(customiseCheckbox, gbc);
+
+    // "Cancel changes" button (aligned with combo box above)
+    gbc.gridx = 1;
+    presetsPanel.add(revertButton, gbc);
+
     return presetsPanel;
   }
 
+  private JPanel initBackupsTabFilenameExamplesPanel()
+  {
+    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());
+
+    updateBackupFilesExampleLabel();
+
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.weightx = 1.0;
+    gbc.weighty = 1.0;
+    gbc.fill = GridBagConstraints.NONE;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+
+    exampleFilesPanel.add(backupfilesExampleLabel, gbc);
+    return exampleFilesPanel;
+  }
+
   private void backupsTabUpdatePresets()
   {
     IntKeyStringValueEntry entry = (IntKeyStringValueEntry) backupfilesPresetsCombo
             .getSelectedItem();
-    int key = entry.getKey();
-    String value = entry.getValue();
-    boolean custom = key == 0;
+    int key = entry.k;
+    String value = entry.v;
 
-    if (custom)
+    if (BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .containsKey(key))
     {
-      // backupsSetCustomOptions();
+      backupsSetOptions(
+              BackupFilesPresetEntry.backupfilesPresetEntriesValues
+                      .get(key));
     }
     else
     {
-      if (backupfilesPresetEntriesValues.containsKey(key))
-      {
-        backupsSetOptions(backupfilesPresetEntriesValues.get(key));
-      }
-      else
-      {
-        System.out.println("Preset '" + value + "' not implemented yet");
-      }
+      Cache.log.error(
+              "Preset '" + value + "' [key:" + key + "] not implemented");
     }
 
+    // Custom options will now be enabled when the customiseCheckbox is checked
+    // (performed above)
+    // backupfilesCustomOptionsSetEnabled();
     updateBackupFilesExampleLabel();
-    backupsCustomOptionsSetEnabled(custom);
   }
 
-  protected int getComboIntStringKey(JComboBox 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);
-      int k = e.getKey();
-      String v = e.getValue();
-      if (e.getKey() == key)
+      IntKeyStringValueEntry e;
+      try
       {
-        c.setSelectedIndex(i);
+        e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
+      } catch (Exception ex)
+      {
+        Cache.log.error(
+                "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
+        continue;
+      }
+      if (e.k == key)
+      {
+        backupfilesPresetsCombo2.setSelectedIndex(i);
         break;
       }
     }
-    backupsTabUpdatePresets();
+    // backupsTabUpdatePresets();
   }
 
   private JPanel initBackupsTabSuffixPanel()
   {
     suffixPanel.setBorder(new TitledBorder(
-            MessageManager.getString("label.suffix_format")));
+            MessageManager.getString("label.backup_filename_strategy")));
     suffixPanel.setLayout(new GridBagLayout());
 
     suffixTemplateLabel
-            .setText(MessageManager.getString("label.suffix_template"));
+            .setText(MessageManager.getString("label.append_to_filename"));
     suffixTemplateLabel.setHorizontalAlignment(SwingConstants.LEFT);
     suffixTemplateLabel.setFont(LABEL_FONT);
 
     final String tooltip = JvSwingUtils.wrapTooltip(true,
-            MessageManager.getString("label.suffix_template_tooltip"));
+            MessageManager.getString("label.append_to_filename_tooltip"));
     suffixTemplate.setToolTipText(tooltip);
     suffixTemplate.addActionListener(new ActionListener()
     {
@@ -1890,15 +2389,19 @@ public class GPreferences extends JPanel
       public void actionPerformed(ActionEvent e)
       {
         updateBackupFilesExampleLabel();
+        backupfilesCustomOptionsSetEnabled();
+        backupfilesRevertButtonSetEnabled(true);
       }
 
     });
-    KeyListener kl = new KeyListener()
+    suffixTemplate.addKeyListener(new KeyListener()
     {
       @Override
       public void keyReleased(KeyEvent e)
       {
         updateBackupFilesExampleLabel();
+        backupfilesCustomOptionsSetEnabled();
+        backupfilesRevertButtonSetEnabled(true);
       }
 
       @Override
@@ -1906,38 +2409,37 @@ public class GPreferences extends JPanel
       {
       }
 
-      // disable use of ':'
+      // disable use of ':' or '/' or '\'
       @Override
       public void keyTyped(KeyEvent e)
       {
         char c = e.getKeyChar();
-        if (c == ':')
+        if (c == ':' || c == '/' || c == '\\')
         {
-          // don't process ':'
+          // don't process ':' or '/' or '\'
           e.consume();
         }
       }
 
-    };
-    suffixTemplate.addKeyListener(kl);
+    });
 
     // digits spinner
     suffixDigitsLabel
             .setText(MessageManager.getString("label.index_digits"));
     suffixDigitsLabel.setHorizontalAlignment(SwingConstants.LEFT);
     suffixDigitsLabel.setFont(LABEL_FONT);
-    int defaultmin = 1;
-    int defaultmax = 6;
     ChangeListener c = new ChangeListener()
     {
       @Override
       public void stateChanged(ChangeEvent e)
       {
+        backupfilesRevertButtonSetEnabled(true);
         updateBackupFilesExampleLabel();
       }
 
     };
-    setIntegerSpinner(suffixDigitsSpinner, defaultmin, defaultmax, 3, c);
+    setIntegerSpinner(suffixDigitsSpinner, BackupFilesPresetEntry.DIGITSMIN,
+            BackupFilesPresetEntry.DIGITSMAX, 3, c);
 
     suffixReverse.setLabels(MessageManager.getString("label.reverse_roll"),
             MessageManager.getString("label.increment_index"));
@@ -1946,7 +2448,23 @@ public class GPreferences extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        updateBackupFilesExampleLabel();
+        boolean okay = true;
+        if (warnAboutSuffixReverseChange())
+        {
+          // Warning popup
+          okay = confirmSuffixReverseChange();
+        }
+        if (okay)
+        {
+          backupfilesRevertButtonSetEnabled(true);
+          updateBackupFilesExampleLabel();
+        }
+        else
+        {
+          boolean savedSuffixReverse = BackupFilesPresetEntry
+                  .getSavedBackupEntry().reverse;
+          suffixReverse.setSelected(savedSuffixReverse);
+        }
       }
     });
 
@@ -1991,10 +2509,18 @@ public class GPreferences extends JPanel
     return suffixPanel;
   }
 
-  private void backupfilesKeepAllEnabled(boolean enabled)
+  private boolean confirmSuffixReverseChange()
   {
-    backupfilesKeepAll.setEnabled(enabled);
-    keepRollMaxOptionsEnabled();
+    boolean ret = false;
+    String warningMessage = MessageManager
+            .getString("label.warning_confirm_change_reverse");
+    int confirm = JvOptionPane.showConfirmDialog(Desktop.desktop,
+            warningMessage,
+            MessageManager.getString("label.change_increment_decrement"),
+            JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE);
+
+    ret = (confirm == JvOptionPane.YES_OPTION);
+    return ret;
   }
 
   private JPanel initBackupsTabKeepFilesPanel()
@@ -2012,6 +2538,7 @@ public class GPreferences extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
+        backupfilesRevertButtonSetEnabled(true);
         updateBackupFilesExampleLabel();
       }
     });
@@ -2020,7 +2547,7 @@ public class GPreferences extends JPanel
       @Override
       public void actionPerformed(ActionEvent e)
       {
-        boolean selected = backupfilesKeepAll.isSelected();
+        backupfilesRevertButtonSetEnabled(true);
         keepRollMaxOptionsEnabled();
         updateBackupFilesExampleLabel();
       }
@@ -2031,15 +2558,26 @@ public class GPreferences extends JPanel
       @Override
       public void stateChanged(ChangeEvent e)
       {
+        backupfilesRevertButtonSetEnabled(true);
         updateBackupFilesExampleLabel();
       }
 
     };
-    setIntegerSpinner(backupfilesRollMaxSpinner, 1, 999, 4, true, c);
+    setIntegerSpinner(backupfilesRollMaxSpinner,
+            BackupFilesPresetEntry.ROLLMAXMIN,
+            BackupFilesPresetEntry.ROLLMAXMAX, 4, true, c);
 
     backupfilesConfirmDelete.setLabels(
-            MessageManager.getString("label.confirm_delete"),
+            MessageManager.getString("label.always_ask"),
             MessageManager.getString("label.auto_delete"));
+    backupfilesConfirmDelete.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        backupfilesRevertButtonSetEnabled(true);
+      }
+    });
     // update the enabled section
     keepRollMaxOptionsEnabled();
 
@@ -2075,18 +2613,12 @@ 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());
     oldBackupFilesLabel
-            .setText(MessageManager.getString("label.old_backup_files"));
+            .setText(MessageManager
+                    .getString("label.autodelete_old_backup_files"));
     oldBackupFilesLabel.setFont(LABEL_FONT);
     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
     jp.add(oldBackupFilesLabel);
@@ -2097,76 +2629,46 @@ public class GPreferences extends JPanel
     return keepfilesPanel;
   }
 
-  private JPanel initBackupsTabFilenameExamplesPanel()
-  {
-    String title = MessageManager.getString("label.example_filenames");
-    TitledBorder tb = new TitledBorder(title);
-    // tb.setTitleFont(LABEL_FONT);
-    exampleFilesPanel.setBorder(tb);
-    exampleFilesPanel.setLayout(new GridBagLayout());
-
-    // inordinately difficult to get this titledborder the right size for the
-    // title
-
-    backupfilesExampleLabel.setEditable(false);
-    backupfilesExampleLabel.setPreferredSize(new Dimension(280, 85));
-    backupfilesExampleLabel.setAlignmentX(LEFT_ALIGNMENT);
-    backupfilesExampleLabel.setAlignmentY(TOP_ALIGNMENT);
-
-    backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
-    backupfilesExampleLabel
-            .setBackground(exampleFilesPanel.getBackground());
-
-    updateBackupFilesExampleLabel();
-    exampleFilesPanel.setMinimumSize(new Dimension(280, 85));
-
-    GridBagConstraints gbc = new GridBagConstraints();
-    gbc.anchor = GridBagConstraints.EAST;
-
-    gbc.gridy = 0;
-    exampleFilesPanel.add(backupfilesExampleLabel, gbc);
-    return exampleFilesPanel;
-  }
-
   protected void updateBackupFilesExampleLabel()
   {
     int exampleindex = 12;
-    String base = MessageManager.getString("label.filename");
-    if (base == null || base.length() > 0)
+    String base = MessageManager.getString("label.filename") + ".fa";
+    if (base == null || base.length() == 0)
     {
-      base = "filename.fa";
+      base = "file_name.fa";
     }
 
-    String suffix = suffixTemplate.getText();
-    int digits = 3;
-    try
-    {
-      suffixDigitsSpinner.commitEdit();
-      digits = (Integer) suffixDigitsSpinner.getValue();
-      digits = digits < 1 ? 1 : digits;
-    } catch (Exception e)
-    {
-      System.out.println(
-              "Failed casting (Integer) suffixTemplateSpinner.getValue()");
-    }
     boolean reverse = suffixReverse.isSelected();
     boolean keepAll = backupfilesKeepAll.isSelected();
     int rollMax = 4;
-    try
+    String suffix = suffixTemplate.getText();
+    int digits = 3;
+
+    backupfilesExampleLabel.setFont(LABEL_FONT_ITALIC);
+    if (suffix == null || suffix.length() == 0)
     {
-      backupfilesRollMaxSpinner.commitEdit();
-      rollMax = (Integer) backupfilesRollMaxSpinner.getValue();
-      rollMax = rollMax < 1 ? 1 : rollMax;
-    } catch (Exception e)
+      backupfilesExampleLabel
+              .setText(MessageManager.getString("label.no_backup_files"));
+      backupfilesExampleLabel.setFont(LABEL_FONT_BOLD);
+      return;
+    }
+
+    rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 4);
+    rollMax = rollMax < 1 ? 1 : rollMax;
+
+    if (suffix.indexOf(BackupFiles.NUM_PLACEHOLDER) == -1)
     {
-      System.out.println(
-              "Failed casting (Integer) backupfilesRollMaxSpinner.getValue()");
+      rollMax = 1;
     }
 
+    digits = getSpinnerInt(suffixDigitsSpinner, 3);
+    digits = digits < 1 ? 1 : digits;
+
     int lowersurround = 2;
     int uppersurround = 0;
     StringBuilder exampleSB = new StringBuilder();
     boolean firstLine = true;
+    int lineNumber = 0;
     if (reverse)
     {
 
@@ -2177,6 +2679,7 @@ 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)
         {
@@ -2191,8 +2694,9 @@ public class GPreferences extends JPanel
           else
           {
             exampleSB.append("\n");
+            lineNumber++;
           }
-          exampleSB.append(BackupFilenameFilter.getBackupFilename(index,
+          exampleSB.append(BackupFilenameParts.getBackupFilename(index,
                   base, suffix, digits));
           if (min == max)
           {
@@ -2230,6 +2734,7 @@ 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)
         {
@@ -2244,8 +2749,9 @@ public class GPreferences extends JPanel
           else
           {
             exampleSB.append("\n");
+            lineNumber++;
           }
-          exampleSB.append(BackupFilenameFilter.getBackupFilename(index,
+          exampleSB.append(BackupFilenameParts.getBackupFilename(index,
                   base, suffix, digits));
           if (min == max)
           {
@@ -2272,6 +2778,18 @@ 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());
   }
 
@@ -2283,10 +2801,10 @@ 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()");
       }
     }
@@ -2302,6 +2820,10 @@ public class GPreferences extends JPanel
     {
       max = def;
     }
+    if (def < min)
+    {
+      def = min;
+    }
     SpinnerModel sModel = new SpinnerNumberModel(def, min, max, 1);
     s.setModel(sModel);
 
@@ -2318,60 +2840,112 @@ 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;
   }
 
-  protected void keepRollMaxOptionsEnabled()
+  private void keepRollMaxOptionsEnabled()
   {
-    keepRollMaxOptionsEnabled(backupfilesKeepAll.isEnabled());
+    boolean enabled = backupfilesKeepAll.isEnabled()
+            && !backupfilesKeepAll.isSelected();
+    oldBackupFilesLabel.setEnabled(enabled);
+    backupfilesRollMaxSpinner.setEnabled(enabled);
+    backupfilesConfirmDelete.setEnabled(enabled);
   }
 
-  protected void keepRollMaxOptionsEnabled(boolean tryEnabled)
+  private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
   {
-    boolean enabled = tryEnabled && !backupfilesKeepAll.isSelected();
+    boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+            && customiseCheckbox.isSelected()
+            && suffixTemplate.getText()
+                    .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+    keepfilesPanel.setEnabled(enabled);
+    backupfilesKeepAll.setEnabled(enabled);
     oldBackupFilesLabel.setEnabled(enabled);
-    backupfilesRollMaxSpinner.setEnabled(enabled);
-    backupfilesConfirmDelete.setEnabled(enabled);
+    keepRollMaxOptionsEnabled();
   }
 
-  protected void backupsCustomOptionsSetEnabled(boolean enabled)
+  private void backupfilesSuffixTemplateDigitsSetEnabled()
   {
-    backupsOptionsSetEnabled(enabled, false);
+    boolean enabled = suffixTemplate.isEnabled() && suffixTemplate.getText()
+            .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
+    suffixDigitsLabel.setEnabled(enabled);
+    suffixDigitsSpinner.setEnabled(enabled);
+    suffixReverse.setEnabled(enabled);
   }
 
-  protected void backupsOptionsSetEnabled(boolean enabled)
+  private void backupfilesSuffixTemplateSetEnabled(boolean tryEnabled)
   {
-    backupsOptionsSetEnabled(enabled, true);
+    boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+            && customiseCheckbox.isSelected();
+    suffixPanel.setEnabled(enabled);
+    suffixTemplateLabel.setEnabled(enabled);
+    suffixTemplate.setEnabled(enabled);
+    backupfilesSuffixTemplateDigitsSetEnabled();
   }
 
-  protected void backupsOptionsSetEnabled(boolean enabled, boolean all)
+  private void backupfilesRevertButtonSetEnabled(boolean tryEnabled)
   {
+    boolean enabled = tryEnabled && enableBackupFiles.isSelected()
+            && customiseCheckbox.isSelected() && backupfilesCustomChanged();
+    revertButton.setEnabled(enabled);
+  }
 
-    if (all)
-    {
-      presetsPanel.setEnabled(enabled);
-      exampleFilesPanel.setEnabled(enabled);
+  private boolean backupfilesCustomChanged()
+  {
+    BackupFilesPresetEntry custom = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .get(BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM);
+    BackupFilesPresetEntry current = getBackupfilesCurrentEntry();
+    return !custom.equals(current);
+  }
 
-      backupfilesPresetsCombo.setEnabled(enabled);
-      backupfilesExampleLabel.setEnabled(enabled);
-    }
-    suffixPanel.setEnabled(enabled);
-    keepfilesPanel.setEnabled(enabled);
+  protected BackupFilesPresetEntry getBackupfilesCurrentEntry()
+  {
+    String suffix = suffixTemplate.getText();
+    int digits = getSpinnerInt(suffixDigitsSpinner, 3);
+    boolean reverse = suffixReverse.isSelected();
+    boolean keepAll = backupfilesKeepAll.isSelected();
+    int rollMax = getSpinnerInt(backupfilesRollMaxSpinner, 3);
+    boolean confirmDelete = backupfilesConfirmDelete.isSelected();
 
-    suffixTemplate.setEnabled(enabled);
-    suffixTemplateLabel.setEnabled(enabled);
-    suffixDigitsLabel.setEnabled(enabled);
-    suffixDigitsSpinner.setEnabled(enabled);
-    suffixReverse.setEnabled(enabled);
-    oldBackupFilesLabel.setEnabled(enabled);
-    backupfilesKeepAllEnabled(enabled);
+    BackupFilesPresetEntry bfpe = new BackupFilesPresetEntry(suffix, digits,
+            reverse, keepAll, rollMax, confirmDelete);
 
-    if (enabled && all)
-    {
-      backupsTabUpdatePresets();
-    }
+    return bfpe;
+  }
+
+  protected void backupfilesCustomOptionsSetEnabled()
+  {
+    boolean enabled = customiseCheckbox.isSelected();
+
+    backupfilesRevertButtonSetEnabled(enabled);
+    backupfilesSuffixTemplateSetEnabled(enabled);
+    backupfilesKeepAllSetEnabled(enabled);
+  }
+
+  private void backupfilesSummarySetEnabled()
+  {
+    boolean enabled = enableBackupFiles.isSelected();
+    backupfilesExampleLabel.setEnabled(enabled);
+    exampleFilesPanel.setEnabled(enabled);
+  }
+
+  private void backupfilesPresetsSetEnabled()
+  {
+    boolean enabled = enableBackupFiles.isSelected();
+    presetsPanel.setEnabled(enabled);
+    presetsComboLabel.setEnabled(enabled);
+    backupfilesPresetsCombo.setEnabled(enabled);
+    customiseCheckbox.setEnabled(enabled);
+    revertButton.setEnabled(enabled);
+  }
+
+  protected void backupsOptionsSetEnabled()
+  {
+    backupfilesPresetsSetEnabled();
+    backupfilesSummarySetEnabled();
+    backupfilesCustomOptionsSetEnabled();
   }
 
   protected void backupsSetOptions(String suffix, int digits,
@@ -2496,13 +3070,41 @@ 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);
+    proxyAuthPasswordTB.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();
+  }
+
+  public void proxyAuth_actionPerformed()
+  {
+    setProxyAuthEnabled();
   }
 
   /**
@@ -2578,57 +3180,3 @@ public class GPreferences extends JPanel
   }
 }
 
-class IntKeyStringValueEntry
-{
-  int k;
-
-  String v;
-
-  public IntKeyStringValueEntry(int k, String v)
-  {
-    this.k = k;
-    this.v = v;
-  }
-
-  @Override
-  public String toString()
-  {
-    return this.getValue();
-  }
-
-  public int getKey()
-  {
-    return k;
-  }
-
-  public String getValue()
-  {
-    return v;
-  }
-}
-
-class BackupFilesPresetEntry
-{
-  String suffix;
-
-  int digits;
-
-  boolean reverse;
-
-  boolean keepAll;
-
-  int rollMax;
-
-  boolean confirmDelete;
-
-  public BackupFilesPresetEntry(String suffix, int digits, boolean reverse,
-          boolean keepAll, int rollMax, boolean confirmDelete)
-  {
-    this.suffix = suffix;
-    this.digits = digits;
-    this.reverse = reverse;
-    this.keepAll = keepAll;
-    this.rollMax = rollMax;
-    this.confirmDelete = confirmDelete;
-  }
-}