X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=c9c5f6ddad14d6dc34b59fb2cb4291b90ce10ddc;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=8a3c372dcd2a7b615a883a1dc1c6e8dfc55a7aa6;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 8a3c372..c9c5f6d 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,375 +1,643 @@
-/*
- * 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.bin.*;
-
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import javax.swing.*;
-
-
-/**
- * DOCUMENT ME!
- *
- * @author $author$
- * @version $Revision$
- */
-public class Preferences extends GPreferences
-{
-    static boolean preferencesLoaded = false;
-
-    /** DOCUMENT ME!! */
-    public static boolean showFullscreen = false;
-
-    /** DOCUMENT ME!! */
-    public static boolean showFullId = true;
-
-    /** DOCUMENT ME!! */
-    public static boolean showAnnotation = true;
-
-    /** DOCUMENT ME!! */
-    public static boolean showConservation = true;
-
-    /** DOCUMENT ME!! */
-    public static boolean showQuality = true;
-
-    /** DOCUMENT ME!! */
-    public static boolean showIdentity = true;
-
-    /** DOCUMENT ME!! */
-    public static String fontName = "SansSerif";
-
-    /** DOCUMENT ME!! */
-    public static String fontSize = "10";
-
-    /** DOCUMENT ME!! */
-    public static String fontStyle = Font.PLAIN + "";
-
-    /** DOCUMENT ME!! */
-    public static char gapSymbol = '-';
-
-    /** DOCUMENT ME!! */
-    public static String defaultColour = null;
-
-    /** DOCUMENT ME!! */
-    public static boolean showStartupFile = true;
-
-    /** DOCUMENT ME!! */
-    public static String startupFile = "http://www.jalview.org/examples/exampleFile.jar";
-    JInternalFrame frame;
-
-    /**
-     * Creates a new Preferences object.
-     */
-    public Preferences()
-    {
-        initPreferences();
-
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        Desktop.addInternalFrame(frame, "Preferences", 480, 390);
-
-        fullID.setSelected(showFullId);
-
-        String string = Cache.getProperty("SHOW_FULLSCREEN");
-        boolean value = false;
-
-        if (string != null)
-        {
-            value = Boolean.valueOf(string).booleanValue();
-        }
-
-        fullScreen.setSelected(value);
-        annotations.setSelected(showAnnotation);
-
-        conservation.setEnabled(showAnnotation);
-        quality.setEnabled(showAnnotation);
-        identity.setEnabled(showAnnotation);
-
-        conservation.setSelected(showConservation);
-        quality.setSelected(showQuality);
-        identity.setSelected(showIdentity);
-
-        for (int i = 0; i < 12; i++)
-        {
-            colour.addItem(ColourSchemeProperty.getColourName(i));
-        }
-
-        string = Cache.getProperty("DEFAULT_COLOUR");
-
-        if (string != null)
-        {
-            colour.setSelectedItem(string);
-        }
-        else
-        {
-            colour.setSelectedIndex(11);
-        }
-
-        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(fontName);
-        fontSizeCB.setSelectedItem(fontSize);
-        fontStyleCB.setSelectedItem(fontStyle);
-
-        gapSymbolCB.addItem("-");
-        gapSymbolCB.addItem(".");
-
-        gapSymbolCB.setSelectedItem(gapSymbol + "");
-
-        startupCheckbox.setSelected(showStartupFile);
-        startupFileTextfield.setText(startupFile);
-    }
-
-    /**
-     * DOCUMENT ME!
-     */
-    public static void initPreferences()
-    {
-        String string = Cache.getProperty("SHOW_FULL_ID");
-
-        if (string != null)
-        {
-            showFullId = Boolean.valueOf(string).booleanValue();
-        }
-
-        string = Cache.getProperty("SHOW_FULLSCREEN");
-
-        if (string != null)
-        {
-            showFullscreen = Boolean.valueOf(string).booleanValue();
-        }
-
-        string = Cache.getProperty("SHOW_ANNOTATIONS");
-
-        if (string != null)
-        {
-            showAnnotation = Boolean.valueOf(string).booleanValue();
-        }
-
-        string = Cache.getProperty("SHOW_CONSERVATION");
-
-        if (string != null)
-        {
-            showConservation = Boolean.valueOf(string).booleanValue();
-        }
-
-        string = Cache.getProperty("SHOW_QUALITY");
-
-        if (string != null)
-        {
-            showQuality = Boolean.valueOf(string).booleanValue();
-        }
-
-        string = Cache.getProperty("SHOW_IDENTITY");
-
-        if (string != null)
-        {
-            showIdentity = Boolean.valueOf(string).booleanValue();
-        }
-
-        string = Cache.getProperty("GAP_SYMBOL");
-
-        if (string != null)
-        {
-            gapSymbol = string.charAt(0);
-        }
-
-        string = Cache.getProperty("SHOW_FULL_ID");
-
-        if (string != null)
-        {
-            showFullId = Boolean.valueOf(string).booleanValue();
-        }
-
-        string = Cache.getProperty("FONT_NAME");
-
-        if (string != null)
-        {
-            fontName = string;
-        }
-
-        string = Cache.getProperty("FONT_STYLE");
-
-        if (string != null)
-        {
-            fontStyle = string;
-        }
-
-        string = Cache.getProperty("FONT_SIZE");
-
-        if (string != null)
-        {
-            fontSize = string;
-        }
-
-        string = Cache.getProperty("DEFAULT_COLOUR");
-
-        if (string != null)
-        {
-            defaultColour = string;
-        }
-
-        string = Cache.getProperty("STARTUP_FILE");
-
-        if (string != null)
-        {
-            startupFile = string;
-        }
-
-        string = Cache.getProperty("SHOW_STARTUP_FILE");
-
-        if (string != null)
-        {
-            showStartupFile = Boolean.valueOf(string).booleanValue();
-        }
-
-        preferencesLoaded = true;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void ok_actionPerformed(ActionEvent e)
-    {
-        showFullId = fullID.isSelected();
-        showFullscreen = fullScreen.isSelected();
-        showAnnotation = annotations.isSelected();
-        showConservation = conservation.isSelected();
-        showQuality = quality.isSelected();
-        showIdentity = identity.isSelected();
-        defaultColour = colour.getSelectedItem().toString();
-        gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);
-        fontName = fontNameCB.getSelectedItem().toString();
-        fontSize = fontSizeCB.getSelectedItem().toString();
-        fontStyle = fontStyleCB.getSelectedItem().toString();
-        startupFile = startupFileTextfield.getText();
-        showStartupFile = startupCheckbox.isSelected();
-
-        Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));
-        Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString(showFullscreen));
-
-        Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString(showAnnotation));
-        Cache.setProperty("SHOW_CONSERVATION",
-            Boolean.toString(showConservation));
-        Cache.setProperty("SHOW_QUALITY", Boolean.toString(showQuality));
-        Cache.setProperty("SHOW_IDENTITY", Boolean.toString(showIdentity));
-
-        Cache.setProperty("DEFAULT_COLOUR", defaultColour);
-        Cache.setProperty("GAP_SYMBOL", gapSymbol + "");
-
-        Cache.setProperty("FONT_NAME", fontName);
-        Cache.setProperty("FONT_STYLE", fontStyle);
-        Cache.setProperty("FONT_SIZE", fontSize);
-
-        Cache.setProperty("STARTUP_FILE", startupFile);
-        Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));
-
-        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.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());
-    }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ * 
+ * Jalview 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+import jalview.bin.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+import jalview.ws.EnfinEnvision2OneWay;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class Preferences extends GPreferences
+{
+
+  /**
+   * Holds name and link separated with | character. Sequence ID must be
+   * $SEQUENCE_ID$ or $SEQUENCE_ID=/.possible | chars ./=$
+   */
+  public static Vector sequenceURLLinks;
+
+  /**
+   * Holds name and link separated with | character. Sequence IDS and Sequences
+   * must be $SEQUENCEIDS$ or $SEQUENCEIDS=/.possible | chars ./=$ and
+   * $SEQUENCES$ or $SEQUENCES=/.possible | chars ./=$ and separation character
+   * for first and second token specified after a pipe character at end |,|.
+   * (TODO: proper escape for using | to separate ids or sequences
+   */
+
+  public static Vector groupURLLinks;
+  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())
+      {
+        String name = st.nextToken();
+        String url = st.nextToken();
+        // check for '|' within a regex
+        int rxstart = url.indexOf("$SEQUENCE_ID$");
+        while (rxstart == -1 && url.indexOf("/=$") == -1)
+        {
+          url = url + "|" + st.nextToken();
+        }
+        sequenceURLLinks.addElement(name + "|" + url);
+      }
+    } catch (Exception ex)
+    {
+      System.out.println(ex + "\nError parsing sequence links");
+    }
+    /**
+     * TODO: reformulate groupURL encoding so two or more can be stored in the
+     * .properties file as '|' separated strings
+     */
+
+    groupURLLinks = new Vector();
+    // groupURLLinks.addElement("UNIPROT|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
+    // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?tool=Jalview&workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
+
+  }
+
+  Vector nameLinks, urlLinks;
+
+  JInternalFrame frame;
+
+  DasSourceBrowser dasSource;
+
+  private WsPreferences wsPrefs;
+
+  /**
+   * Creates a new Preferences object.
+   */
+  public Preferences()
+  {
+
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    dasSource = new DasSourceBrowser();
+    dasPanel.add(dasSource, BorderLayout.CENTER);
+    wsPrefs = new WsPreferences();
+    wsPanel.add(wsPrefs, BorderLayout.CENTER);
+    int width = 500, height = 420;
+    if (new jalview.util.Platform().isAMac())
+    {
+      width = 570;
+      height = 460;
+    }
+
+    Desktop.addInternalFrame(frame, "Preferences", width, height);
+    frame.setMinimumSize(new Dimension(width, height));
+
+    seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
+    rightAlign.setSelected(Cache.getDefault("RIGHT_ALIGN_IDS", false));
+    fullScreen.setSelected(Cache.getDefault("SHOW_FULLSCREEN", false));
+    annotations.setSelected(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));
+    openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
+    showUnconserved
+            .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+    showNpTooltip.setSelected(Cache
+            .getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
+            true));
+
+    for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; 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));
+
+    idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
+
+    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_2_3.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));
+    showGroupConsensus.setSelected(Cache.getDefault("SHOW_GROUP_CONSENSUS",
+            false));
+    showGroupConservation.setSelected(Cache.getDefault(
+            "SHOW_GROUP_CONSERVATION", false));
+    showConsensHistogram.setSelected(Cache.getDefault(
+            "SHOW_CONSENSUS_HISTOGRAM", true));
+    showConsensLogo.setSelected(Cache.getDefault("SHOW_CONSENSUS_LOGO",
+            false));
+
+    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", ""));
+
+    usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+    questionnaire
+            .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null); // note
+                                                                         // antisense
+                                                                         // here
+    versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true)); // default
+                                                                       // is
+                                                                       // true
+    annotations_actionPerformed(null); // update the display of the annotation
+                                       // settings
+    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("RIGHT_ALIGN_IDS", Boolean
+            .toString(rightAlign.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_FULLSCREEN", Boolean
+            .toString(fullScreen.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_OVERVIEW", Boolean
+            .toString(openoverv.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("ID_ITALICS", Boolean
+            .toString(idItalics.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_UNCONSERVED", Boolean
+            .toString(showUnconserved.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSENSUS", Boolean
+            .toString(showGroupConsensus.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_GROUP_CONSERVATION",
+            Boolean.toString(showGroupConservation.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_HISTOGRAM",
+            Boolean.toString(showConsensHistogram.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_CONSENSUS_LOGO", Boolean
+            .toString(showConsensLogo.isSelected()));
+    Cache.applicationProperties.setProperty("ANTI_ALIAS", Boolean
+            .toString(smoothFont.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_NPFEATS_TOOLTIP", Boolean
+            .toString(showNpTooltip.isSelected()));
+    Cache.applicationProperties.setProperty("SHOW_DBREFS_TOOLTIP", Boolean
+            .toString(showDbRefTooltip.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.setProperty("VERSION_CHECK", Boolean.toString(versioncheck
+            .isSelected()));
+    if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
+    {
+      // default is false - we only set this if the user has actively agreed
+      Cache.setProperty("USAGESTATS", Boolean.toString(usagestats
+              .isSelected()));
+    }
+    if (!questionnaire.isSelected())
+    {
+      Cache.setProperty("NOQUESTIONNAIRES", "true");
+    }
+    else
+    {
+      // special - made easy to edit a property file to disable questionnaires
+      // by just adding the given line
+      Cache.removeProperty("NOQUESTIONNAIRES");
+    }
+    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);
+    wsPrefs.updateAndRefreshWsMenuConfig(false);
+    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
+    {
+      wsPrefs.updateWsMenuConfig(true);
+      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());
+    showGroupConsensus.setEnabled(annotations.isSelected());
+    showGroupConservation.setEnabled(annotations.isSelected());
+    showConsensHistogram.setEnabled(annotations.isSelected()
+            && (identity.isSelected() || showGroupConsensus.isSelected()));
+    showConsensLogo.setEnabled(annotations.isSelected()
+            && (identity.isSelected() || showGroupConsensus.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());
+    }
+
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
+   * .ActionEvent)
+   */
+  protected void showunconserved_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    super.showunconserved_actionPerformed(e);
+  }
+
+  private void jbInit() throws Exception
+  {
+  }
+
+  public static Collection getGroupURLLinks()
+  {
+    return groupURLLinks;
+  }
+}