X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fjbgui%2FGPreferences.java;h=d281c8d824ce70476d2a3184da97d6baf55fbb2a;hb=cb8e52fbbc5f725e3f7f48c672cdddb0690bd978;hp=ca5b203a87d7c8e1f4183c5483046a1229167a39;hpb=e19524773e4547406d2ce5f9c91a536c3bc38f24;p=jalview.git

diff --git a/src/jalview/jbgui/GPreferences.java b/src/jalview/jbgui/GPreferences.java
index ca5b203..d281c8d 100755
--- a/src/jalview/jbgui/GPreferences.java
+++ b/src/jalview/jbgui/GPreferences.java
@@ -43,6 +43,7 @@ import java.util.List;
 
 import javax.swing.AbstractCellEditor;
 import javax.swing.BorderFactory;
+import javax.swing.BoxLayout;
 import javax.swing.ButtonGroup;
 import javax.swing.DefaultListCellRenderer;
 import javax.swing.JButton;
@@ -54,6 +55,7 @@ import javax.swing.JPanel;
 import javax.swing.JPasswordField;
 import javax.swing.JRadioButton;
 import javax.swing.JScrollPane;
+import javax.swing.JSlider;
 import javax.swing.JSpinner;
 import javax.swing.JTabbedPane;
 import javax.swing.JTable;
@@ -69,10 +71,14 @@ import javax.swing.border.EtchedBorder;
 import javax.swing.border.TitledBorder;
 import javax.swing.event.ChangeEvent;
 import javax.swing.event.ChangeListener;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
 import javax.swing.table.TableCellEditor;
 import javax.swing.table.TableCellRenderer;
 
 import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.bin.MemorySetting;
 import jalview.fts.core.FTSDataColumnPreferences;
 import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.service.pdb.PDBFTSRestClient;
@@ -87,6 +93,7 @@ import jalview.io.BackupFilesPresetEntry;
 import jalview.io.IntKeyStringValueEntry;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
+import jalview.util.StringUtils;
 
 /**
  * Base class for the Preferences panel.
@@ -173,8 +180,6 @@ public class GPreferences extends JPanel
 
   protected JCheckBox structFromPdb = new JCheckBox();
 
-  protected JCheckBox useRnaView = new JCheckBox();
-
   protected JCheckBox addSecondaryStructure = new JCheckBox();
 
   protected JCheckBox addTempFactor = new JCheckBox();
@@ -218,6 +223,8 @@ public class GPreferences extends JPanel
   /*
    * Connections tab components
    */
+  protected JPanel connectTab;
+
   protected JTable linkUrlTable = new JTable();
 
   protected JButton editLink = new JButton();
@@ -246,6 +253,8 @@ public class GPreferences extends JPanel
 
   protected JLabel proxyAuthPasswordLabel = new JLabel();
 
+  protected JLabel passwordNotStoredLabel = new JLabel();
+
   protected JTextField proxyServerHttpTB = new JTextField();
 
   protected JTextField proxyPortHttpTB = new JTextField();
@@ -258,7 +267,7 @@ public class GPreferences extends JPanel
 
   protected JTextField proxyAuthUsernameTB = new JTextField();
 
-  protected JTextField proxyAuthPasswordTB = new JPasswordField();
+  protected JPasswordField proxyAuthPasswordPB = new JPasswordField();
 
   protected JTextField defaultBrowser = new JTextField();
 
@@ -270,6 +279,8 @@ public class GPreferences extends JPanel
 
   protected JRadioButton customProxy = new JRadioButton();
 
+  protected JButton applyProxyButton = new JButton();
+
   protected JCheckBox usagestats = new JCheckBox();
 
   protected JCheckBox questionnaire = new JCheckBox();
@@ -369,6 +380,34 @@ public class GPreferences extends JPanel
 
   protected JTextArea backupfilesExampleLabel = new JTextArea();
 
+  private final JTabbedPane tabbedPane = new JTabbedPane();
+
+  private JLabel messageLabel = new JLabel("", JLabel.CENTER);
+
+  /*
+   * Startup tab components
+   */
+
+  protected JCheckBox customiseMemorySetting = new JCheckBox();
+
+  protected JLabel exampleMemoryLabel = new JLabel();
+
+  protected JTextArea exampleMemoryMessageTextArea = new JTextArea();
+
+  protected JLabel maxMemoryLabel = new JLabel();
+
+  protected JLabel jvmMemoryPercentLabel = new JLabel();
+
+  protected JSlider jvmMemoryPercentSlider = new JSlider();
+
+  protected JLabel jvmMemoryPercentDisplay = new JLabel();
+
+  protected JLabel jvmMemoryMaxLabel = new JLabel();
+
+  protected JTextField jvmMemoryMaxTextField = new JTextField(null, 8);
+
+  protected JComboBox<Object> lafCombo = new JComboBox<>();
+
   /**
    * Creates a new GPreferences object.
    */
@@ -390,8 +429,12 @@ public class GPreferences extends JPanel
    */
   private void jbInit() throws Exception
   {
-    final JTabbedPane tabbedPane = new JTabbedPane();
+    // final JTabbedPane tabbedPane = new JTabbedPane();
     this.setLayout(new BorderLayout());
+
+    // message label at top
+    this.add(messageLabel, BorderLayout.NORTH);
+
     JPanel okCancelPanel = initOkCancelPanel();
     this.add(tabbedPane, BorderLayout.CENTER);
     this.add(okCancelPanel, BorderLayout.SOUTH);
@@ -411,11 +454,11 @@ public class GPreferences extends JPanel
     tabbedPane.add(initConnectionsTab(),
             MessageManager.getString("label.connections"));
 
-	if (!Platform.isJS()) 
-	{
-	  tabbedPane.add(initBackupsTab(), 
-			MessageManager.getString("label.backups"));
-	}
+    if (!Platform.isJS())
+    {
+      tabbedPane.add(initBackupsTab(),
+              MessageManager.getString("label.backups"));
+    }
 
     tabbedPane.add(initLinksTab(),
             MessageManager.getString("label.urllinks"));
@@ -426,6 +469,9 @@ public class GPreferences extends JPanel
     tabbedPane.add(initEditingTab(),
             MessageManager.getString("label.editing"));
 
+    tabbedPane.add(initStartupTab(),
+            MessageManager.getString("label.startup"));
+
     /*
      * See WsPreferences for the real work of configuring this tab.
      */
@@ -438,6 +484,7 @@ public class GPreferences extends JPanel
     /*
      * 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()
     {
@@ -456,11 +503,63 @@ 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.
    * 
@@ -638,7 +737,7 @@ public class GPreferences extends JPanel
    */
   private JPanel initConnectionsTab()
   {
-    JPanel connectTab = new JPanel();
+    connectTab = new JPanel();
     connectTab.setLayout(new GridBagLayout());
 
     // Label for browser text box
@@ -927,8 +1026,60 @@ public class GPreferences extends JPanel
     proxyPortHttpsTB.setColumns(4);
     proxyAuthUsernameTB.setFont(LABEL_FONT);
     proxyAuthUsernameTB.setColumns(30);
-    proxyAuthPasswordTB.setFont(LABEL_FONT);
-    proxyAuthPasswordTB.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);
@@ -953,6 +1104,10 @@ public class GPreferences extends JPanel
             .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);
@@ -961,9 +1116,11 @@ public class GPreferences extends JPanel
     systemProxy.setFont(LABEL_FONT);
     systemProxy.setHorizontalAlignment(SwingConstants.LEFT);
     systemProxy.setText(MessageManager.formatMessage("label.system_proxy",
-            displayHostPort(Cache.startupProxyProperties[0],
+            displayUserHostPort(Cache.startupProxyProperties[4],
+                    Cache.startupProxyProperties[0],
                     Cache.startupProxyProperties[1]),
-            displayHostPort(Cache.startupProxyProperties[2],
+            displayUserHostPort(Cache.startupProxyProperties[6],
+                    Cache.startupProxyProperties[2],
                     Cache.startupProxyProperties[3])));
     customProxy.setFont(LABEL_FONT);
     customProxy.setHorizontalAlignment(SwingConstants.LEFT);
@@ -997,117 +1154,196 @@ public class GPreferences extends JPanel
     });
 
     setCustomProxyEnabled();
-    setProxyAuthEnabled();
 
     // Make proxy server panel
     JPanel proxyPanel = new JPanel();
     TitledBorder titledBorder1 = new TitledBorder(
             MessageManager.getString("label.proxy_servers"));
     proxyPanel.setBorder(titledBorder1);
-    GridBagConstraints gbc = new GridBagConstraints();
     proxyPanel.setLayout(new GridBagLayout());
-
-    gbc.gridx = 0;
-    gbc.gridy = 0;
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.fill = GridBagConstraints.HORIZONTAL;
     gbc.weightx = 1.0;
-    gbc.gridheight = 1;
-    gbc.anchor = GridBagConstraints.WEST;
-    gbc.fill = GridBagConstraints.BOTH;
 
-    gbc.gridwidth = 5;
-    proxyPanel.add(noProxy, gbc);
+    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++;
-    proxyPanel.add(systemProxy, gbc);
-
-    gbc.gridy++;
-    proxyPanel.add(customProxy, gbc);
-
-    gbc.gridwidth = 1;
-    gbc.gridy++;
-    gbc.gridx = 0;
-    gbc.weightx = 0.1;
-    proxyPanel.add(httpLabel, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.EAST;
-    gbc.weightx = 0.15;
-    proxyPanel.add(serverLabel, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.WEST;
-    gbc.weightx = 0.5;
-    proxyPanel.add(proxyServerHttpTB, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.EAST;
-    gbc.weightx = 0.15;
-    proxyPanel.add(portLabel, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.WEST;
-    gbc.weightx = 0.1;
-    proxyPanel.add(proxyPortHttpTB, gbc);
+    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++;
-    gbc.gridx = 0;
-    gbc.anchor = GridBagConstraints.WEST;
-    gbc.weightx = 0.1;
-    proxyPanel.add(httpsLabel, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.EAST;
-    gbc.weightx = 0.15;
-    proxyPanel.add(serverLabel2, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.WEST;
-    gbc.weightx = 0.5;
-    proxyPanel.add(proxyServerHttpsTB, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.EAST;
-    gbc.weightx = 0.15;
-    proxyPanel.add(portLabel2, gbc);
-
-    gbc.gridx++;
-    gbc.anchor = GridBagConstraints.WEST;
-    gbc.weightx = 0.1;
-    proxyPanel.add(proxyPortHttpsTB, gbc);
+    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.gridx = 0;
-    gbc.gridwidth = 5;
-    gbc.anchor = GridBagConstraints.WEST;
-    gbc.weightx = 0.1;
-    proxyPanel.add(proxyAuth, gbc);
+    gbc.fill = GridBagConstraints.NONE;
+    gbc.anchor = GridBagConstraints.LINE_END;
+    proxyPanel.add(applyProxyButton, gbc);
 
-    gbc.gridy++;
-    gbc.gridx = 0;
-    gbc.gridwidth = 1;
-    gbc.anchor = GridBagConstraints.EAST;
-    proxyPanel.add(proxyAuthUsernameLabel, gbc);
+    return proxyPanel;
+  }
 
-    gbc.gridx++;
-    gbc.gridwidth = 4;
-    gbc.anchor = GridBagConstraints.WEST;
-    proxyPanel.add(proxyAuthUsernameTB, gbc);
+  public void proxyAuthPasswordCheckHighlight(boolean enabled)
+  {
+    proxyAuthPasswordCheckHighlight(enabled, false);
+  }
 
-    gbc.gridy++;
-    gbc.gridx = 0;
-    gbc.gridwidth = 1;
-    gbc.anchor = GridBagConstraints.EAST;
-    proxyPanel.add(proxyAuthPasswordLabel, gbc);
+  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);
+    }
+  }
 
-    gbc.gridx++;
-    gbc.gridwidth = 4;
-    gbc.anchor = GridBagConstraints.WEST;
-    proxyPanel.add(proxyAuthPasswordTB, gbc);
+  public void applyProxyButtonEnabled(boolean enabled)
+  {
+    applyProxyButton.setEnabled(enabled);
+  }
 
-    return proxyPanel;
+  public void saveProxySettings()
+  {
+    // overridden in Preferences
   }
 
-  private String displayHostPort(String host, String port)
+  private String displayUserHostPort(String user, String host, String port)
   {
     boolean hostBlank = (host == null || host.isEmpty());
     boolean portBlank = (port == null || port.isEmpty());
@@ -1117,6 +1353,12 @@ public class GPreferences extends JPanel
     }
 
     StringBuilder sb = new StringBuilder();
+    if (user != null)
+    {
+      sb.append(user.isEmpty() || user.indexOf(" ") > -1 ? '"' + user + '"'
+              : user);
+      sb.append("@");
+    }
     sb.append(hostBlank ? "" : host);
     if (!portBlank)
     {
@@ -1440,7 +1682,6 @@ 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);
       }
@@ -1449,12 +1690,6 @@ public class GPreferences extends JPanel
 
     // 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);
     addSecondaryStructure
             .setText(MessageManager.getString("label.autoadd_secstr"));
@@ -1498,11 +1733,13 @@ public class GPreferences extends JPanel
 
     ypos += lineSpacing;
     structureViewerPathLabel = new JLabel();
-    structureViewerPathLabel.setFont(LABEL_FONT);// new Font("SansSerif", 0, 11));
+    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
+            .setBounds(new Rectangle(10, ypos, 170, height));
     structureViewerPathLabel.setEnabled(false);
     structureTab.add(structureViewerPathLabel);
 
@@ -1560,14 +1797,14 @@ public class GPreferences extends JPanel
     /*
      * hide Chimera options in JalviewJS
      */
-    if (Platform.isJS()) 
+    if (Platform.isJS())
     {
       structureViewerPathLabel.setVisible(false);
       structureViewerPath.setVisible(false);
       viewerLabel.setVisible(false);
       structViewer.setVisible(false);
     }
-    
+
     return structureTab;
   }
 
@@ -1581,8 +1818,8 @@ 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
    */
@@ -1591,6 +1828,14 @@ public class GPreferences extends JPanel
     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);
+    }
+
     // chooser.setFileView(new JalviewFileView());
     chooser.setDialogTitle(
             MessageManager.getString("label.open_local_file"));
@@ -1944,13 +2189,13 @@ 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;
   }
 
@@ -1962,8 +2207,8 @@ public class GPreferences extends JPanel
   {
     BackupFilesPresetEntry savedPreset = BackupFilesPresetEntry
             .getSavedBackupEntry();
-    enableBackupFiles
-            .setSelected(Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
+    enableBackupFiles.setSelected(
+            Cache.getDefault(BackupFiles.ENABLED, !Platform.isJS()));
 
     BackupFilesPresetEntry backupfilesCustomEntry = BackupFilesPresetEntry
             .createBackupFilesPresetEntry(Cache
@@ -1987,6 +2232,19 @@ public class GPreferences extends JPanel
     updateBackupFilesExampleLabel();
   }
 
+  /*
+   * Load the saved Memory settings
+   */
+  protected void loadLastSavedMemorySettings()
+  {
+    customiseMemorySetting.setSelected(
+            Cache.getDefault(MemorySetting.CUSTOMISED_SETTINGS, false));
+    jvmMemoryPercentSlider
+            .setValue(Cache.getDefault(MemorySetting.MEMORY_JVMMEMPC, 90));
+    jvmMemoryMaxTextField.setText(
+            Cache.getDefault(MemorySetting.MEMORY_JVMMEMMAX, "32g"));
+  }
+
   private boolean warnAboutSuffixReverseChange()
   {
     BackupFilesPresetEntry bfpe = BackupFilesPresetEntry
@@ -2004,6 +2262,285 @@ public class GPreferences extends JPanel
             && nowSuffixTemplate.equals(savedSuffixTemplate);
   }
 
+  /* Initialises the Startup tabbed panel.
+   * 
+   * @return
+   * */
+
+  private JPanel initStartupTab()
+  {
+    JPanel startupTab = new JPanel();
+    startupTab.setBorder(
+            new TitledBorder(MessageManager.getString("label.memory")));
+    startupTab.setLayout(new GridBagLayout());
+
+    GridBagConstraints gbc = new GridBagConstraints();
+    gbc.weightx = 0.0;
+    gbc.weighty = 0.0;
+    gbc.anchor = GridBagConstraints.FIRST_LINE_START;
+    gbc.fill = GridBagConstraints.NONE;
+
+    initMemoryPanel();
+
+    gbc.gridheight = 1;
+    gbc.gridwidth = 3;
+
+    gbc.gridy = 0; // row 1
+    gbc.gridx = 0;
+    JLabel memoryText = new JLabel();
+    memoryText.setFont(LABEL_FONT_ITALIC);
+    memoryText
+            .setText(MessageManager.getString("label.memory_setting_text"));
+    startupTab.add(memoryText, gbc);
+
+    gbc.gridy++; // row 2
+    gbc.gridx = 0;
+    JPanel exampleMemoryPanel = new JPanel();
+    exampleMemoryPanel
+            .setLayout(new BoxLayout(exampleMemoryPanel, BoxLayout.Y_AXIS));
+    exampleMemoryPanel.setToolTipText(JvSwingUtils.wrapTooltip(true,
+            MessageManager.getString("label.memory_example_tooltip")));
+    JLabel exampleTextLabel = new JLabel();
+    exampleTextLabel
+            .setText(MessageManager.getString("label.memory_example_text"));
+    exampleTextLabel.setForeground(Color.GRAY);
+    exampleTextLabel.setFont(LABEL_FONT);
+    exampleMemoryPanel.add(exampleTextLabel);
+    exampleMemoryPanel.add(exampleMemoryLabel);
+    exampleMemoryPanel.setBackground(Color.WHITE);
+    exampleMemoryPanel.setBorder(BorderFactory.createEtchedBorder());
+    startupTab.add(exampleMemoryPanel, gbc);
+
+    gbc.gridy++; // row 3
+    gbc.gridx = 0;
+    startupTab.add(customiseMemorySetting, gbc);
+
+    gbc.gridy += 2; // row 4 with a gap
+    gbc.gridx = 0;
+    startupTab.add(maxMemoryLabel, gbc);
+
+    gbc.gridy += 2; // row 5
+    gbc.gridx = 0;
+    gbc.gridwidth = 1;
+    startupTab.add(jvmMemoryPercentLabel, gbc);
+    gbc.gridx++;
+    startupTab.add(jvmMemoryPercentSlider, gbc);
+    gbc.gridx++;
+    // gbc.weightx = 0.1;
+    startupTab.add(jvmMemoryPercentDisplay, gbc);
+    // gbc.weightx = 1.0;
+    gbc.gridwidth = 3;
+
+    gbc.gridy++; // row 6
+    gbc.gridx = 0;
+    startupTab.add(jvmMemoryMaxLabel, gbc);
+    gbc.gridx++;
+    startupTab.add(jvmMemoryMaxTextField, gbc);
+
+    gbc.gridy++; // row 7
+    gbc.gridx = 0;
+    gbc.gridwidth = 4;
+    exampleMemoryMessageTextArea.setBackground(startupTab.getBackground());
+    JScrollPane sp = new JScrollPane(exampleMemoryMessageTextArea);
+    sp.setBorder(BorderFactory.createEmptyBorder());
+    sp.setHorizontalScrollBarPolicy(JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
+    sp.setVerticalScrollBarPolicy(JScrollPane.VERTICAL_SCROLLBAR_NEVER);
+    startupTab.add(sp, gbc);
+
+    // fill empty space to push widget to top left
+    gbc.gridy++;
+    gbc.weighty = 1.0;
+    gbc.gridx = 100;
+    gbc.gridwidth = 1;
+    gbc.weightx = 1.0;
+    startupTab.add(new JPanel(), gbc);
+
+    setMemoryPercentDisplay();
+    memoryOptionsSetEnabled();
+    return startupTab;
+  }
+
+  private void initMemoryPanel()
+  {
+    // Enable memory settings checkbox
+    customiseMemorySetting.setFont(LABEL_FONT_BOLD);
+    customiseMemorySetting.setText(
+            MessageManager.getString("label.customise_memory_settings"));
+    customiseMemorySetting.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        memoryOptionsSetEnabled();
+      }
+    });
+
+    loadLastSavedMemorySettings();
+
+    exampleMemoryLabel.setFont(LABEL_FONT_BOLD);
+    exampleMemoryLabel.setBackground(Color.WHITE);
+
+    maxMemoryLabel = new JLabel(
+            MessageManager.getString("label.maximum_memory_used"));
+    maxMemoryLabel.setFont(LABEL_FONT_BOLD);
+
+    // Maximum memory percentage slider
+    jvmMemoryPercentLabel.setFont(LABEL_FONT);
+    jvmMemoryPercentLabel.setText(
+            MessageManager.getString("label.percent_of_physical_memory"));
+    jvmMemoryPercentSlider.setPaintLabels(true);
+    jvmMemoryPercentSlider.setPaintTicks(true);
+    jvmMemoryPercentSlider.setPaintTrack(true);
+    jvmMemoryPercentSlider.setMajorTickSpacing(50);
+    jvmMemoryPercentSlider.setMinorTickSpacing(10);
+    jvmMemoryPercentSlider.addChangeListener(new ChangeListener()
+    {
+      @Override
+      public void stateChanged(ChangeEvent e)
+      {
+        setMemoryPercentDisplay();
+      }
+    });
+    jvmMemoryPercentDisplay.setFont(LABEL_FONT);
+    setMemoryPercentDisplay();
+
+    // Maximum memory cap textbox
+    jvmMemoryMaxLabel.setFont(LABEL_FONT);
+    jvmMemoryMaxLabel
+            .setText(MessageManager.getString("label.maximum_memory"));
+    initMemoryMaxTextField();
+
+    exampleMemoryMessageTextArea.setFont(LABEL_FONT_ITALIC);
+    exampleMemoryMessageTextArea.setForeground(Color.GRAY);
+    exampleMemoryMessageTextArea.setEditable(false);
+    exampleMemoryMessageTextArea.setLineWrap(true);
+    exampleMemoryMessageTextArea.setWrapStyleWord(true);
+    exampleMemoryMessageTextArea.setText(" ");
+    exampleMemoryMessageTextArea.setRows(2);
+    exampleMemoryMessageTextArea.setColumns(40);
+
+    setExampleMemoryLabel();
+  }
+
+  private void initMemoryMaxTextField()
+  {
+    jvmMemoryMaxTextField.setToolTipText(
+            MessageManager.getString("label.maximum_memory_tooltip"));
+    jvmMemoryMaxTextField.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent arg0)
+      {
+        validateMemoryMaxTextField();
+        setExampleMemoryLabel();
+      }
+    });
+
+    jvmMemoryMaxTextField.addKeyListener(new KeyListener()
+    {
+      @Override
+      public void keyReleased(KeyEvent e)
+      {
+        validateMemoryMaxTextField();
+        setExampleMemoryLabel();
+      }
+
+      @Override
+      public void keyPressed(KeyEvent e)
+      {
+      }
+
+      // try and stop invalid typing
+      @Override
+      public void keyTyped(KeyEvent e)
+      {
+        char c = Character.toLowerCase(e.getKeyChar());
+        String text = jvmMemoryMaxTextField.getText();
+        String suffixes = "tgmkb";
+        int pos = jvmMemoryMaxTextField.getCaretPosition();
+        int suffixPos = StringUtils.firstCharPosIgnoreCase(text, suffixes);
+        if (!((('0' <= c && c <= '9')
+                && (suffixPos == -1 || pos <= suffixPos)) // digits only allowed
+                // before suffix
+                || (suffixes.indexOf(Character.toLowerCase(c)) >= 0 // valid
+                                                                    // suffix
+                        && pos == text.length() // at end of text and
+                        && suffixPos == -1) // there isn't already one
+        ))
+        {
+          // don't process
+          e.consume();
+        }
+      }
+    });
+  }
+
+  private boolean isMemoryMaxTextFieldValid()
+  {
+    return MemorySetting
+            .isValidMemoryString(jvmMemoryMaxTextField.getText());
+  }
+
+  private void validateMemoryMaxTextField()
+  {
+    if (isMemoryMaxTextFieldValid())
+    {
+      jvmMemoryMaxTextField.setBackground(Color.WHITE);
+    }
+    else
+    {
+      jvmMemoryMaxTextField.setBackground(Color.PINK);
+    }
+  }
+
+  private void setMemoryPercentDisplay()
+  {
+    jvmMemoryPercentDisplay
+            .setText(jvmMemoryPercentSlider.getValue() + "%");
+    setExampleMemoryLabel();
+  }
+
+  private void setExampleMemoryLabel()
+  {
+    boolean selected = customiseMemorySetting.isSelected();
+    int jvmmempc = jvmMemoryPercentSlider.getValue();
+    String jvmmemmax = jvmMemoryMaxTextField.getText();
+
+    long mem;
+    if (selected && (0 <= jvmmempc && jvmmempc <= 100)
+            && MemorySetting.isValidMemoryString(jvmmemmax))
+    {
+      mem = MemorySetting.getMemorySetting(jvmmemmax,
+              String.valueOf(jvmmempc), false, true);
+    }
+    else
+    {
+      mem = MemorySetting.getMemorySetting(null, null, false, true);
+    }
+    exampleMemoryLabel.setText(MemorySetting.memoryLongToString(mem));
+    String message = MemorySetting.getAdjustmentMessage();
+    exampleMemoryMessageTextArea.setText(
+            MessageManager.getString("label.adjustments_for_this_computer")
+                    + ": "
+                    + (message == null
+                            ? MessageManager.getString("label.none")
+                            : message));
+  }
+
+  private void memoryOptionsSetEnabled()
+  {
+    boolean enabled = customiseMemorySetting.isSelected();
+    // leave exampleMemoryLabel enabled always
+    maxMemoryLabel.setEnabled(enabled);
+    jvmMemoryPercentLabel.setEnabled(enabled);
+    jvmMemoryPercentSlider.setEnabled(enabled);
+    jvmMemoryPercentDisplay.setEnabled(enabled);
+    jvmMemoryMaxLabel.setEnabled(enabled);
+    jvmMemoryMaxTextField.setEnabled(enabled);
+    exampleMemoryMessageTextArea.setEnabled(enabled);
+    setExampleMemoryLabel();
+  }
+
   /**
    * Initialises the Backups tabbed panel.
    * 
@@ -2040,7 +2577,6 @@ public class GPreferences extends JPanel
       }
     });
 
-
     // enable checkbox 1 col
     gbc.gridwidth = 1;
     gbc.gridheight = 1;
@@ -2113,8 +2649,8 @@ public class GPreferences extends JPanel
     presetsComboLabel = new JLabel(title + ":");
     presetsPanel.add(presetsComboLabel, gbc);
 
-    List<Object> entries = Arrays
-            .asList((Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
+    List<Object> entries = Arrays.asList(
+            (Object[]) BackupFilesPresetEntry.backupfilesPresetEntries);
     List<String> tooltips = Arrays.asList(
             BackupFilesPresetEntry.backupfilesPresetEntryDescriptions);
     backupfilesPresetsCombo = JvSwingUtils.buildComboWithTooltips(entries,
@@ -2141,7 +2677,8 @@ public class GPreferences extends JPanel
         {
           if (customiseCheckbox.isSelected())
           {
-            // got here by clicking on customiseCheckbox so don't change the values
+            // got here by clicking on customiseCheckbox so don't change the
+            // values
             backupfilesCustomOptionsSetEnabled();
           }
           else
@@ -2220,13 +2757,11 @@ public class GPreferences extends JPanel
 
   private JPanel initBackupsTabFilenameExamplesPanel()
   {
-    String title = MessageManager
-            .getString("label.scheme_examples");
+    String title = MessageManager.getString("label.scheme_examples");
     TitledBorder tb = new TitledBorder(title);
     exampleFilesPanel.setBorder(tb);
     exampleFilesPanel.setLayout(new GridBagLayout());
 
-
     backupfilesExampleLabel.setEditable(false);
     backupfilesExampleLabel
             .setBackground(exampleFilesPanel.getBackground());
@@ -2259,7 +2794,7 @@ public class GPreferences extends JPanel
     }
     else
     {
-      Cache.log.error(
+      Console.error(
               "Preset '" + value + "' [key:" + key + "] not implemented");
     }
 
@@ -2279,7 +2814,7 @@ public class GPreferences extends JPanel
               .getSelectedItem();
     } catch (Exception ex)
     {
-      Cache.log.error(
+      Console.error(
               "Problem casting Combo entry to IntKeyStringValueEntry.");
       e = null;
     }
@@ -2287,8 +2822,7 @@ public class GPreferences extends JPanel
   }
 
   protected void setComboIntStringKey(
-          JComboBox<Object> backupfilesPresetsCombo2,
-          int key)
+          JComboBox<Object> backupfilesPresetsCombo2, int key)
   {
     for (int i = 0; i < backupfilesPresetsCombo2.getItemCount(); i++)
     {
@@ -2298,7 +2832,7 @@ public class GPreferences extends JPanel
         e = (IntKeyStringValueEntry) backupfilesPresetsCombo2.getItemAt(i);
       } catch (Exception ex)
       {
-        Cache.log.error(
+        Console.error(
                 "Problem casting Combo entry to IntKeyStringValueEntry. Skipping item. ");
         continue;
       }
@@ -2558,9 +3092,8 @@ public class GPreferences extends JPanel
 
     JPanel jp = new JPanel();
     jp.setLayout(new FlowLayout());
-    oldBackupFilesLabel
-            .setText(MessageManager
-                    .getString("label.autodelete_old_backup_files"));
+    oldBackupFilesLabel.setText(
+            MessageManager.getString("label.autodelete_old_backup_files"));
     oldBackupFilesLabel.setFont(LABEL_FONT);
     oldBackupFilesLabel.setHorizontalAlignment(SwingConstants.LEFT);
     jp.add(oldBackupFilesLabel);
@@ -2720,7 +3253,8 @@ public class GPreferences extends JPanel
 
     }
 
-    // add some extra empty lines to pad out the example files box. ugh, please tell
+    // add some extra empty lines to pad out the example files box. ugh, please
+    // tell
     // me how to do this better
     int remainingLines = lowersurround + uppersurround + 1 - lineNumber;
     if (remainingLines > 0)
@@ -2746,7 +3280,7 @@ public class GPreferences extends JPanel
         i = ((Integer) s.getValue()).intValue();
       } catch (Exception e)
       {
-        Cache.log.error(
+        Console.error(
                 "Exception casting the initial value of s.getValue()");
       }
     }
@@ -2782,7 +3316,7 @@ public class GPreferences extends JPanel
       i = (Integer) s.getValue();
     } catch (Exception e)
     {
-      Cache.log.error("Failed casting (Integer) JSpinner s.getValue()");
+      Console.error("Failed casting (Integer) JSpinner s.getValue()");
     }
     return i;
   }
@@ -2799,8 +3333,7 @@ public class GPreferences extends JPanel
   private void backupfilesKeepAllSetEnabled(boolean tryEnabled)
   {
     boolean enabled = tryEnabled && enableBackupFiles.isSelected()
-            && customiseCheckbox.isSelected()
-            && suffixTemplate.getText()
+            && customiseCheckbox.isSelected() && suffixTemplate.getText()
                     .indexOf(BackupFiles.NUM_PLACEHOLDER) > -1;
     keepfilesPanel.setEnabled(enabled);
     backupfilesKeepAll.setEnabled(enabled);
@@ -2954,7 +3487,7 @@ public class GPreferences extends JPanel
    * DOCUMENT ME!
    * 
    * @param e
-   *          DOCUMENT ME!
+   *            DOCUMENT ME!
    */
   public void ok_actionPerformed(ActionEvent e)
   {
@@ -2964,7 +3497,7 @@ public class GPreferences extends JPanel
    * DOCUMENT ME!
    * 
    * @param e
-   *          DOCUMENT ME!
+   *            DOCUMENT ME!
    */
   public void cancel_actionPerformed(ActionEvent e)
   {
@@ -2974,7 +3507,7 @@ public class GPreferences extends JPanel
    * DOCUMENT ME!
    * 
    * @param e
-   *          DOCUMENT ME!
+   *            DOCUMENT ME!
    */
   public void annotations_actionPerformed(ActionEvent e)
   {
@@ -3017,8 +3550,9 @@ public class GPreferences extends JPanel
     boolean enabled = proxyAuth.isSelected() && proxyAuth.isEnabled();
     proxyAuthUsernameLabel.setEnabled(enabled);
     proxyAuthPasswordLabel.setEnabled(enabled);
+    passwordNotStoredLabel.setEnabled(enabled);
     proxyAuthUsernameTB.setEnabled(enabled);
-    proxyAuthPasswordTB.setEnabled(enabled);
+    proxyAuthPasswordPB.setEnabled(enabled);
   }
 
   public void setCustomProxyEnabled()
@@ -3041,11 +3575,15 @@ public class GPreferences extends JPanel
   public void proxyType_actionPerformed()
   {
     setCustomProxyEnabled();
+    proxyAuthPasswordCheckHighlight(true);
+    applyProxyButtonEnabled(true);
   }
 
   public void proxyAuth_actionPerformed()
   {
     setProxyAuthEnabled();
+    proxyAuthPasswordCheckHighlight(true);
+    applyProxyButtonEnabled(true);
   }
 
   /**
@@ -3120,4 +3658,3 @@ public class GPreferences extends JPanel
 
   }
 }
-