X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=524c71c6575e7cd8314fb3fd8013dacb54393a10;hb=e894eb87d40be6e8452d19032ddffe80dad5f804;hp=f322daa78a49e2a44204ce9d06f3db4814fec2c7;hpb=dc1d2d1779b2ccd4d67b2afa094f269db77732e2;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index f322daa..524c71c 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,450 +1,479 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
- *
- * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
- */
-package jalview.gui;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-import java.util.*;
-
-import jalview.bin.Cache;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Preferences extends GPreferences
-{
-    /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
-    public static Vector sequenceURLLinks;
-    static
-    {
-      String string = Cache.getDefault("SEQUENCE_LINKS",
-                                       "SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
-      sequenceURLLinks = new Vector();
-
-      try
-      {
-        StringTokenizer st = new StringTokenizer(string, "|");
-        while (st.hasMoreElements())
-        {
-          sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
-        }
-      }
-      catch (Exception ex)
-      {
-        System.out.println(ex + "\nError parsing sequence links");
-      }
-    }
-    Vector nameLinks, urlLinks;
-
-    JInternalFrame frame;
-
-
-    /**
-     * Creates a new Preferences object.
-     */
-    public Preferences()
-    {
-
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "Preferences", 480, 395);
-        frame.setMinimumSize(new Dimension(480,395));
-
-        seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));
-        fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
-        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
-
-        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
-        quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-        identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-
-        conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
-        quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
-        identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
-
-        for (int i = 0; i < 13; i++)
-        {
-            colour.addItem(ColourSchemeProperty.getColourName(i));
-        }
-
-        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-
-        colour.setSelectedItem(string);
-
-        String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-                                                     .getAvailableFontFamilyNames();
-
-        for (int i = 0; i < fonts.length; i++)
-        {
-            fontNameCB.addItem(fonts[i]);
-        }
-
-        for (int i = 1; i < 31; i++)
-        {
-            fontSizeCB.addItem(i + "");
-        }
-
-        fontStyleCB.addItem("plain");
-        fontStyleCB.addItem("bold");
-        fontStyleCB.addItem("italic");
-
-        fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
-        fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
-        fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
-
-        smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
-
-        gapSymbolCB.addItem("-");
-        gapSymbolCB.addItem(".");
-
-        gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
-
-        startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
-        startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-         "http://www.jalview.org/examples/exampleFile.jar"));
-
-        sortby.addItem("No sort");
-        sortby.addItem("Id");
-        sortby.addItem("Pairwise Identity");
-        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
-
-        epsRendering.addItem("Prompt each time");
-        epsRendering.addItem("Lineart");
-        epsRendering.addItem("Text");
-        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
-
-        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
-        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
-        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
-        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
-        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
-        pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
-        pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
-
-  /****************************************************
-   * Set up Connections
-   */
-        nameLinks = new Vector();
-        urlLinks = new Vector();
-        for(int i=0; i<sequenceURLLinks.size(); i++)
-        {
-          String link = sequenceURLLinks.elementAt(i).toString();
-          nameLinks.addElement(link.substring(0, link.indexOf("|")) );
-          urlLinks.addElement(link.substring(link.indexOf("|")+1));
-        }
-
-        updateLinkData();
-
-        useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
-        proxyServerTB.setEnabled(useProxy.isSelected());
-        proxyPortTB.setEnabled(useProxy.isSelected());
-        proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
-        proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
-
-        defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
-    try
-    {
-      jbInit();
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-
-  }
-
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void ok_actionPerformed(ActionEvent e)
-    {
-
-      Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
-      Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
-
-      Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
-      Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
-      Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
-      Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
-
-      Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
-      Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
-
-      Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
-      Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
-      Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
-
-      Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
-
-      Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
-      Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
-
-      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
-
-      if(epsRendering.getSelectedItem().equals("Prompt each time"))
-        Cache.applicationProperties.remove("EPS_RENDERING");
-      else
-        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
-
-      if(defaultBrowser.getText().trim().length()<1)
-        Cache.applicationProperties.remove("DEFAULT_BROWSER");
-      else
-        Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
-                                                defaultBrowser.getText());
-
-        jalview.util.BrowserLauncher.resetBrowser();
-
-        if(nameLinks.size()>0)
-        {
-          StringBuffer links = new StringBuffer();
-          sequenceURLLinks = new Vector();
-          for (int i = 0; i < nameLinks.size(); i++)
-          {
-            sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
-            links.append(sequenceURLLinks.elementAt(i).toString());
-            links.append("|");
-          }
-          // remove last "|"
-          links.setLength( links.length()-1 );
-          Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
-        }
-        else
-          Cache.applicationProperties.remove("SEQUENCE_LINKS");
-
-
-        Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
-
-        if (proxyServerTB.getText().trim().length() < 1)
-          Cache.applicationProperties.remove("PROXY_SERVER");
-        else
-          Cache.applicationProperties.setProperty("PROXY_SERVER",
-                                                  proxyServerTB.getText());
-
-        if (proxyPortTB.getText().trim().length() < 1)
-          Cache.applicationProperties.remove("PROXY_PORT");
-        else
-          Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
-
-        if(useProxy.isSelected())
-        {
-          System.setProperty("http.proxyHost", proxyServerTB.getText());
-          System.setProperty("http.proxyPort", proxyPortTB.getText());
-        }
-        else
-        {
-          System.setProperty("http.proxyHost","");
-          System.setProperty("http.proxyPort","");
-        }
-
-
-        Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
-        Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
-        Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
-        Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
-        Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
-        Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
-        Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
-
-
-        Cache.saveProperties();
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public void startupFileTextfield_mouseClicked()
-    {
-        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
-                    "LAST_DIRECTORY"),
-                new String[]
-                {
-                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
-                    "jar"
-                },
-                new String[]
-                {
-                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
-                }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-        chooser.setFileView(new JalviewFileView());
-        chooser.setDialogTitle("Select startup file");
-
-        int value = chooser.showOpenDialog(this);
-
-        if (value == JalviewFileChooser.APPROVE_OPTION)
-        {
-            jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
-                chooser.getSelectedFormat());
-            startupFileTextfield.setText(chooser.getSelectedFile()
-                                                .getAbsolutePath());
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void cancel_actionPerformed(ActionEvent e)
-    {
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void annotations_actionPerformed(ActionEvent e)
-    {
-        conservation.setEnabled(annotations.isSelected());
-        quality.setEnabled(annotations.isSelected());
-        identity.setEnabled(annotations.isSelected());
-    }
-
-
-    public void newLink_actionPerformed(ActionEvent e) {
-
-      GSequenceLink link = new GSequenceLink();
-      boolean valid = false;
-      while( !valid )
-      {
-        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-                                                  "New sequence URL link",
-                                                  JOptionPane.OK_CANCEL_OPTION
-                                                  ,-1, null)
-            == JOptionPane.OK_OPTION)
-        {
-          if (link.checkValid())
-          {
-            nameLinks.addElement(link.getName());
-            urlLinks.addElement(link.getURL());
-            updateLinkData();
-            valid = true;
-          }
-        }
-        else
-          break;
-      }
-    }
-
-    public void editLink_actionPerformed(ActionEvent e) {
-      GSequenceLink link = new GSequenceLink();
-
-      int index = linkNameList.getSelectedIndex();
-      if(index==-1)
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
-            ,"No link selected", JOptionPane.WARNING_MESSAGE);
-        return;
-      }
-
-      link.setName( nameLinks.elementAt(index).toString() );
-      link.setURL( urlLinks.elementAt(index).toString() );
-
-      boolean valid = false;
-      while (!valid)
-      {
-
-        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-                                                  "New sequence URL link",
-                                                  JOptionPane.OK_CANCEL_OPTION
-                                                  ,-1, null)
-            == JOptionPane.OK_OPTION)
-        {
-          if (link.checkValid())
-          {
-            nameLinks.setElementAt(link.getName(), index);
-            urlLinks.setElementAt(link.getURL(), index);
-            updateLinkData();
-            valid = true;
-          }
-        }
-
-        else
-          break;
-      }
-    }
-
-    public void deleteLink_actionPerformed(ActionEvent e) {
-      int index = linkNameList.getSelectedIndex();
-      if(index==-1)
-      {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
-            ,"No link selected", JOptionPane.WARNING_MESSAGE);
-        return;
-      }
-      nameLinks.removeElementAt(index);
-      urlLinks.removeElementAt(index);
-      updateLinkData();
-    }
-
-    void updateLinkData()
-    {
-      linkNameList.setListData(nameLinks);
-      linkURLList.setListData(urlLinks);
-    }
-
-    public void defaultBrowser_mouseClicked(MouseEvent e)
-    {
-      JFileChooser chooser = new JFileChooser(".");
-      chooser.setDialogTitle("Select default web browser");
-
-      int value = chooser.showOpenDialog(this);
-
-      if (value == JFileChooser.APPROVE_OPTION)
-      {
-        defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
-      }
-
-  }
-
-  private void jbInit()
-      throws Exception
-  {
-  }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ */
+package jalview.gui;
+
+import jalview.io.*;
+
+import jalview.jbgui.*;
+
+import jalview.schemes.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import java.util.*;
+
+import jalview.bin.Cache;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
+{
+    /** Holds name and link separated with | character. Sequence ID must be $SEQUENCE_ID$ */
+    public static Vector sequenceURLLinks;
+    static
+    {
+      String string = Cache.getDefault("SEQUENCE_LINKS",
+                                       "SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      sequenceURLLinks = new Vector();
+
+      try
+      {
+        StringTokenizer st = new StringTokenizer(string, "|");
+        while (st.hasMoreElements())
+        {
+          sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
+        }
+      }
+      catch (Exception ex)
+      {
+        System.out.println(ex + "\nError parsing sequence links");
+      }
+    }
+    Vector nameLinks, urlLinks;
+
+    JInternalFrame frame;
+
+    DasSourceBrowser dasSource;
+
+
+    /**
+     * Creates a new Preferences object.
+     */
+    public Preferences()
+    {
+
+        frame = new JInternalFrame();
+        frame.setContentPane(this);
+        dasSource = new DasSourceBrowser();
+        dasPanel.add(dasSource, BorderLayout.CENTER);
+
+        int width = 500, height = 420;
+        if(System.getProperty("os.name").startsWith("Mac"))
+        {
+          width = 570;
+          height = 460;
+        }
+
+        Desktop.addInternalFrame(frame, "Preferences", width, height);
+        frame.setMinimumSize(new Dimension(width, height));
+
+        seqLimit.setSelected(    Cache.getDefault("SHOW_JVSUFFIX", true));
+        fullScreen.setSelected(  Cache.getDefault("SHOW_FULLSCREEN", false));
+        annotations.setSelected( Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+        conservation.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
+        quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+        identity.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
+
+        conservation.setSelected(Cache.getDefault("SHOW_CONSERVATION", true));
+        quality.setSelected(Cache.getDefault("SHOW_QUALITY", true));
+        identity.setSelected(Cache.getDefault("SHOW_IDENTITY", true));
+
+        for (int i = 0; i < 13; i++)
+        {
+            colour.addItem(ColourSchemeProperty.getColourName(i));
+        }
+
+        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+
+        colour.setSelectedItem(string);
+
+        String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+                                                     .getAvailableFontFamilyNames();
+
+        for (int i = 0; i < fonts.length; i++)
+        {
+            fontNameCB.addItem(fonts[i]);
+        }
+
+        for (int i = 1; i < 31; i++)
+        {
+            fontSizeCB.addItem(i + "");
+        }
+
+        fontStyleCB.addItem("plain");
+        fontStyleCB.addItem("bold");
+        fontStyleCB.addItem("italic");
+
+        fontNameCB.setSelectedItem(Cache.getDefault("FONT_NAME", "SansSerif"));
+        fontSizeCB.setSelectedItem(Cache.getDefault("FONT_SIZE", "10"));
+        fontStyleCB.setSelectedItem(Cache.getDefault("FONT_STYLE", Font.PLAIN + "") );
+
+        smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+
+        wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+
+        gapSymbolCB.addItem("-");
+        gapSymbolCB.addItem(".");
+
+        gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
+
+        startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
+        startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+         "http://www.jalview.org/examples/exampleFile.jar"));
+
+        sortby.addItem("No sort");
+        sortby.addItem("Id");
+        sortby.addItem("Pairwise Identity");
+        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
+
+        epsRendering.addItem("Prompt each time");
+        epsRendering.addItem("Lineart");
+        epsRendering.addItem("Text");
+        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
+
+        blcjv.setSelected( Cache.getDefault("BLC_JVSUFFIX", true) );
+        clustaljv.setSelected( Cache.getDefault("CLUSTAL_JVSUFFIX", true) );
+        fastajv.setSelected( Cache.getDefault("FASTA_JVSUFFIX", true) );
+        msfjv.setSelected( Cache.getDefault("MSF_JVSUFFIX", true) );
+        pfamjv.setSelected( Cache.getDefault("PFAM_JVSUFFIX", true) );
+        pileupjv.setSelected( Cache.getDefault("PILEUP_JVSUFFIX", true) );
+        pirjv.setSelected( Cache.getDefault("PIR_JVSUFFIX", true) );
+
+        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+
+        autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
+        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
+
+  /****************************************************
+   * Set up Connections
+   */
+        nameLinks = new Vector();
+        urlLinks = new Vector();
+        for(int i=0; i<sequenceURLLinks.size(); i++)
+        {
+          String link = sequenceURLLinks.elementAt(i).toString();
+          nameLinks.addElement(link.substring(0, link.indexOf("|")) );
+          urlLinks.addElement(link.substring(link.indexOf("|")+1));
+        }
+
+        updateLinkData();
+
+        useProxy.setSelected( Cache.getDefault("USE_PROXY", false));
+        proxyServerTB.setEnabled(useProxy.isSelected());
+        proxyPortTB.setEnabled(useProxy.isSelected());
+        proxyServerTB.setText( Cache.getDefault("PROXY_SERVER", ""));
+        proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+
+        defaultBrowser.setText( Cache.getDefault("DEFAULT_BROWSER",""));
+    try
+    {
+      jbInit();
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+
+  }
+
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void ok_actionPerformed(ActionEvent e)
+    {
+
+      Cache.applicationProperties.setProperty("SHOW_JVSUFFIX", Boolean.toString(seqLimit.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean.toString(fullScreen.isSelected()));
+
+      Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS", Boolean.toString(annotations.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_CONSERVATION", Boolean.toString(conservation.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_QUALITY", Boolean.toString(quality.isSelected()));
+      Cache.applicationProperties.setProperty("SHOW_IDENTITY", Boolean.toString(identity.isSelected()));
+
+      Cache.applicationProperties.setProperty("DEFAULT_COLOUR", colour.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB.getSelectedItem().toString());
+
+      Cache.applicationProperties.setProperty("FONT_NAME", fontNameCB.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("FONT_STYLE", fontStyleCB.getSelectedItem().toString());
+      Cache.applicationProperties.setProperty("FONT_SIZE", fontSizeCB.getSelectedItem().toString());
+
+      Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean.toString(smoothFont.isSelected()));
+
+      Cache.applicationProperties.setProperty("WRAP_ALIGNMENT", Boolean.toString(wrap.isSelected()));
+
+      Cache.applicationProperties.setProperty("STARTUP_FILE", startupFileTextfield.getText());
+      Cache.applicationProperties.setProperty("SHOW_STARTUP_FILE",  Boolean.toString(startupCheckbox.isSelected()));
+
+      Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby.getSelectedItem().toString() );
+
+      if(epsRendering.getSelectedItem().equals("Prompt each time"))
+        Cache.applicationProperties.remove("EPS_RENDERING");
+      else
+        Cache.applicationProperties.setProperty("EPS_RENDERING", epsRendering.getSelectedItem().toString());
+
+      if(defaultBrowser.getText().trim().length()<1)
+        Cache.applicationProperties.remove("DEFAULT_BROWSER");
+      else
+        Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
+                                                defaultBrowser.getText());
+
+        jalview.util.BrowserLauncher.resetBrowser();
+
+        if(nameLinks.size()>0)
+        {
+          StringBuffer links = new StringBuffer();
+          sequenceURLLinks = new Vector();
+          for (int i = 0; i < nameLinks.size(); i++)
+          {
+            sequenceURLLinks.addElement(nameLinks.elementAt(i)+"|"+urlLinks.elementAt(i));
+            links.append(sequenceURLLinks.elementAt(i).toString());
+            links.append("|");
+          }
+          // remove last "|"
+          links.setLength( links.length()-1 );
+          Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links.toString());
+        }
+        else
+          Cache.applicationProperties.remove("SEQUENCE_LINKS");
+
+
+        Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
+
+        if (proxyServerTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_SERVER");
+        else
+          Cache.applicationProperties.setProperty("PROXY_SERVER",
+                                                  proxyServerTB.getText());
+
+        if (proxyPortTB.getText().trim().length() < 1)
+          Cache.applicationProperties.remove("PROXY_PORT");
+        else
+          Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+
+        if(useProxy.isSelected())
+        {
+          System.setProperty("http.proxyHost", proxyServerTB.getText());
+          System.setProperty("http.proxyPort", proxyPortTB.getText());
+        }
+        else
+        {
+          System.setProperty("http.proxyHost","");
+          System.setProperty("http.proxyPort","");
+        }
+
+
+        Cache.applicationProperties.setProperty("BLC_JVSUFFIX", Boolean.toString(blcjv.isSelected()) );
+        Cache.applicationProperties.setProperty("CLUSTAL_JVSUFFIX", Boolean.toString(clustaljv.isSelected()) );
+        Cache.applicationProperties.setProperty("FASTA_JVSUFFIX", Boolean.toString(fastajv.isSelected()) );
+        Cache.applicationProperties.setProperty("MSF_JVSUFFIX", Boolean.toString(msfjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PFAM_JVSUFFIX", Boolean.toString(pfamjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PILEUP_JVSUFFIX", Boolean.toString(pileupjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_JVSUFFIX", Boolean.toString(pirjv.isSelected()) );
+        Cache.applicationProperties.setProperty("PIR_MODELLER", Boolean.toString(modellerOutput.isSelected()) );
+        jalview.io.PIRFile.useModellerOutput = modellerOutput.isSelected();
+
+        Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+                                                Boolean.toString(autoCalculateConsCheck.isSelected()));
+        Cache.applicationProperties.setProperty("PAD_GAPS",
+                                                Boolean.toString(padGaps.isSelected()));
+
+        dasSource.saveProperties(Cache.applicationProperties);
+
+        Cache.saveProperties();
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     */
+    public void startupFileTextfield_mouseClicked()
+    {
+        JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(
+                    "LAST_DIRECTORY"),
+                new String[]
+                {
+                    "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+                    "jar"
+                },
+                new String[]
+                {
+                    "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+                }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+        chooser.setFileView(new JalviewFileView());
+        chooser.setDialogTitle("Select startup file");
+
+        int value = chooser.showOpenDialog(this);
+
+        if (value == JalviewFileChooser.APPROVE_OPTION)
+        {
+            jalview.bin.Cache.applicationProperties.setProperty("DEFAULT_FILE_FORMAT",
+                chooser.getSelectedFormat());
+            startupFileTextfield.setText(chooser.getSelectedFile()
+                                                .getAbsolutePath());
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void cancel_actionPerformed(ActionEvent e)
+    {
+        try
+        {
+            frame.setClosed(true);
+        }
+        catch (Exception ex)
+        {
+        }
+    }
+
+    /**
+     * DOCUMENT ME!
+     *
+     * @param e DOCUMENT ME!
+     */
+    public void annotations_actionPerformed(ActionEvent e)
+    {
+        conservation.setEnabled(annotations.isSelected());
+        quality.setEnabled(annotations.isSelected());
+        identity.setEnabled(annotations.isSelected());
+    }
+
+
+    public void newLink_actionPerformed(ActionEvent e) {
+
+      GSequenceLink link = new GSequenceLink();
+      boolean valid = false;
+      while( !valid )
+      {
+        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+                                                  "New sequence URL link",
+                                                  JOptionPane.OK_CANCEL_OPTION
+                                                  ,-1, null)
+            == JOptionPane.OK_OPTION)
+        {
+          if (link.checkValid())
+          {
+            nameLinks.addElement(link.getName());
+            urlLinks.addElement(link.getURL());
+            updateLinkData();
+            valid = true;
+          }
+        }
+        else
+          break;
+      }
+    }
+
+    public void editLink_actionPerformed(ActionEvent e) {
+      GSequenceLink link = new GSequenceLink();
+
+      int index = linkNameList.getSelectedIndex();
+      if(index==-1)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
+            ,"No link selected", JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+
+      link.setName( nameLinks.elementAt(index).toString() );
+      link.setURL( urlLinks.elementAt(index).toString() );
+
+      boolean valid = false;
+      while (!valid)
+      {
+
+        if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+                                                  "New sequence URL link",
+                                                  JOptionPane.OK_CANCEL_OPTION
+                                                  ,-1, null)
+            == JOptionPane.OK_OPTION)
+        {
+          if (link.checkValid())
+          {
+            nameLinks.setElementAt(link.getName(), index);
+            urlLinks.setElementAt(link.getURL(), index);
+            updateLinkData();
+            valid = true;
+          }
+        }
+
+        else
+          break;
+      }
+    }
+
+    public void deleteLink_actionPerformed(ActionEvent e) {
+      int index = linkNameList.getSelectedIndex();
+      if(index==-1)
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
+            ,"No link selected", JOptionPane.WARNING_MESSAGE);
+        return;
+      }
+      nameLinks.removeElementAt(index);
+      urlLinks.removeElementAt(index);
+      updateLinkData();
+    }
+
+    void updateLinkData()
+    {
+      linkNameList.setListData(nameLinks);
+      linkURLList.setListData(urlLinks);
+    }
+
+    public void defaultBrowser_mouseClicked(MouseEvent e)
+    {
+      JFileChooser chooser = new JFileChooser(".");
+      chooser.setDialogTitle("Select default web browser");
+
+      int value = chooser.showOpenDialog(this);
+
+      if (value == JFileChooser.APPROVE_OPTION)
+      {
+        defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+      }
+
+  }
+
+  private void jbInit()
+      throws Exception
+  {
+  }
+}