X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=e16aa426e88c3b5d71bfc119250883956df1c0b3;hb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;hp=840598bfd9402db2a9ccb7301d4e3dcc88fd2474;hpb=99bd0585b045d25fa719ee007e3310d27e53ac88;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 840598b..e16aa42 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -18,21 +18,16 @@
  */
 package jalview.gui;
 
-import jalview.io.*;
-
-import jalview.jbgui.*;
-
-import jalview.schemes.*;
+import java.util.*;
 
 import java.awt.*;
 import java.awt.event.*;
-
 import javax.swing.*;
 
-import java.util.*;
-
-import jalview.bin.Cache;
-
+import jalview.bin.*;
+import jalview.io.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
 
 /**
  * DOCUMENT ME!
@@ -40,157 +35,161 @@ import jalview.bin.Cache;
  * @author $author$
  * @version $Revision$
  */
-public class Preferences extends GPreferences
+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();
+  /** 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)
+    try
+    {
+      StringTokenizer st = new StringTokenizer(string, "|");
+      while (st.hasMoreElements())
       {
-        System.out.println(ex + "\nError parsing sequence links");
+        sequenceURLLinks.addElement(st.nextToken() + "|" + st.nextToken());
       }
     }
-    Vector nameLinks, urlLinks;
+    catch (Exception ex)
+    {
+      System.out.println(ex + "\nError parsing sequence links");
+    }
+  }
 
-    JInternalFrame frame;
+  Vector nameLinks, urlLinks;
 
-    DasSourceBrowser dasSource;
+  JInternalFrame frame;
 
+  DasSourceBrowser dasSource;
 
-    /**
-     * Creates a new Preferences object.
-     */
-    public Preferences()
-    {
+  /**
+   * Creates a new Preferences object.
+   */
+  public Preferences()
+  {
 
-        frame = new JInternalFrame();
-        frame.setContentPane(this);
-        dasSource = new DasSourceBrowser();
-        dasPanel.add(dasSource, BorderLayout.CENTER);
+    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;
-        }
+    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));
+    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));
+    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.setEnabled( Cache.getDefault("SHOW_ANNOTATIONS", true));
-        quality.setEnabled(Cache.getDefault("SHOW_ANNOTATIONS", true));
-        identity.setEnabled(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));
+    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));
-        }
+    for (int i = 0; i < 13; i++)
+    {
+      colour.addItem(ColourSchemeProperty.getColourName(i));
+    }
 
-        String string = Cache.getDefault("DEFAULT_COLOUR", "None");
+    String string = Cache.getDefault("DEFAULT_COLOUR", "None");
 
-        colour.setSelectedItem(string);
+    colour.setSelectedItem(string);
 
-        String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
-                                                     .getAvailableFontFamilyNames();
+    String[] fonts = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment()
+        .getAvailableFontFamilyNames();
 
-        for (int i = 0; i < fonts.length; i++)
-        {
-            fontNameCB.addItem(fonts[i]);
-        }
+    for (int i = 0; i < fonts.length; i++)
+    {
+      fontNameCB.addItem(fonts[i]);
+    }
 
-        for (int i = 1; i < 31; i++)
-        {
-            fontSizeCB.addItem(i + "");
-        }
+    for (int i = 1; i < 31; i++)
+    {
+      fontSizeCB.addItem(i + "");
+    }
 
-        fontStyleCB.addItem("plain");
-        fontStyleCB.addItem("bold");
-        fontStyleCB.addItem("italic");
+    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 + "") );
+    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));
+    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
 
-        wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
+    idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
-        gapSymbolCB.addItem("-");
-        gapSymbolCB.addItem(".");
+    wrap.setSelected(Cache.getDefault("WRAP_ALIGNMENT", false));
 
-        gapSymbolCB.setSelectedItem( Cache.getDefault("GAP_SYMBOL", "-"));
+    gapSymbolCB.addItem("-");
+    gapSymbolCB.addItem(".");
 
-        startupCheckbox.setSelected( Cache.getDefault("SHOW_STARTUP_FILE", true) );
-        startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-         "http://www.jalview.org/examples/exampleFile.jar"));
+    gapSymbolCB.setSelectedItem(Cache.getDefault("GAP_SYMBOL", "-"));
 
-        sortby.addItem("No sort");
-        sortby.addItem("Id");
-        sortby.addItem("Pairwise Identity");
-        sortby.setSelectedItem( Cache.getDefault("SORT_ALIGNMENT", "No sort") );
+    startupCheckbox.setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+    startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+                                                  "http://www.jalview.org/examples/exampleFile.jar"));
 
-        epsRendering.addItem("Prompt each time");
-        epsRendering.addItem("Lineart");
-        epsRendering.addItem("Text");
-        epsRendering.setSelectedItem( Cache.getDefault("EPS_RENDERING", "Prompt each time"));
+    sortby.addItem("No sort");
+    sortby.addItem("Id");
+    sortby.addItem("Pairwise Identity");
+    sortby.setSelectedItem(Cache.getDefault("SORT_ALIGNMENT", "No sort"));
 
-        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) );
+    epsRendering.addItem("Prompt each time");
+    epsRendering.addItem("Lineart");
+    epsRendering.addItem("Text");
+    epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
+                                                  "Prompt each time"));
 
-        modellerOutput.setSelected( Cache.getDefault("PIR_MODELLER", false));
+    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));
 
-        autoCalculateConsCheck.setSelected( Cache.getDefault("AUTO_CALC_CONSENSUS", true));
-        padGaps.setSelected( Cache.getDefault("PAD_GAPS", false));
+    modellerOutput.setSelected(Cache.getDefault("PIR_MODELLER", 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));
-        }
+    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();
+    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", ""));
+    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",""));
+    defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
     try
     {
       jbInit();
@@ -202,275 +201,351 @@ public class Preferences extends GPreferences
 
   }
 
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void ok_actionPerformed(ActionEvent e)
+  {
 
-    /**
-     * 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_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("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());
+    }
 
-      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_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());
+    }
 
-      if(defaultBrowser.getText().trim().length()<1)
-        Cache.applicationProperties.remove("DEFAULT_BROWSER");
-      else
-        Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
-                                                defaultBrowser.getText());
+    jalview.util.BrowserLauncher.resetBrowser();
 
-        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");
+    }
 
-        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());
+    }
 
-        Cache.applicationProperties.setProperty("USE_PROXY", Boolean.toString(useProxy.isSelected()));
+    if (proxyPortTB.getText().trim().length() < 1)
+    {
+      Cache.applicationProperties.remove("PROXY_PORT");
+    }
+    else
+    {
+      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+    }
 
-        if (proxyServerTB.getText().trim().length() < 1)
-          Cache.applicationProperties.remove("PROXY_SERVER");
-        else
-          Cache.applicationProperties.setProperty("PROXY_SERVER",
-                                                  proxyServerTB.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", "");
+    }
 
-        if (proxyPortTB.getText().trim().length() < 1)
-          Cache.applicationProperties.remove("PROXY_PORT");
-        else
-          Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB.getText());
+    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)
+    {
+    }
+  }
 
-        if(useProxy.isSelected())
+  /**
+   * DOCUMENT ME!
+   */
+  public void startupFileTextfield_mouseClicked()
+  {
+    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.
+        getProperty(
+            "LAST_DIRECTORY"),
+        new String[]
         {
-          System.setProperty("http.proxyHost", proxyServerTB.getText());
-          System.setProperty("http.proxyPort", proxyPortTB.getText());
-        }
-        else
+        "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",
+        "jar"
+    },
+        new String[]
         {
-          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();
+        "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"
+    }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle("Select startup file");
 
-        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)
-        {
-        }
-    }
+    int value = chooser.showOpenDialog(this);
 
-    /**
-     * DOCUMENT ME!
-     */
-    public void startupFileTextfield_mouseClicked()
+    if (value == JalviewFileChooser.APPROVE_OPTION)
     {
-        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());
-        }
+      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)
+  /**
+   * DOCUMENT ME!
+   *
+   * @param e DOCUMENT ME!
+   */
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try
     {
-        try
-        {
-            frame.setClosed(true);
-        }
-        catch (Exception ex)
-        {
-        }
+      frame.setClosed(true);
     }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param e DOCUMENT ME!
-     */
-    public void annotations_actionPerformed(ActionEvent e)
+    catch (Exception ex)
     {
-        conservation.setEnabled(annotations.isSelected());
-        quality.setEnabled(annotations.isSelected());
-        identity.setEnabled(annotations.isSelected());
     }
+  }
 
+  /**
+   * 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) {
+  public void newLink_actionPerformed(ActionEvent e)
+  {
 
-      GSequenceLink link = new GSequenceLink();
-      boolean valid = false;
-      while( !valid )
+    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 (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-                                                  "New sequence URL link",
-                                                  JOptionPane.OK_CANCEL_OPTION
-                                                  ,-1, null)
-            == JOptionPane.OK_OPTION)
+        if (link.checkValid())
         {
-          if (link.checkValid())
-          {
-            nameLinks.addElement(link.getName());
-            urlLinks.addElement(link.getURL());
-            updateLinkData();
-            valid = true;
-          }
+          nameLinks.addElement(link.getName());
+          urlLinks.addElement(link.getURL());
+          updateLinkData();
+          valid = true;
         }
-        else
-          break;
+      }
+      else
+      {
+        break;
       }
     }
+  }
 
-    public void editLink_actionPerformed(ActionEvent e) {
-      GSequenceLink link = new GSequenceLink();
+  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;
-      }
+    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() );
+    link.setName(nameLinks.elementAt(index).toString());
+    link.setURL(urlLinks.elementAt(index).toString());
 
-      boolean valid = false;
-      while (!valid)
-      {
+    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 (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
+                                                "New sequence URL link",
+                                                JOptionPane.OK_CANCEL_OPTION
+                                                , -1, null)
+          == JOptionPane.OK_OPTION)
+      {
+        if (link.checkValid())
         {
-          if (link.checkValid())
-          {
-            nameLinks.setElementAt(link.getName(), index);
-            urlLinks.setElementAt(link.getURL(), index);
-            updateLinkData();
-            valid = true;
-          }
+          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)
+      else
       {
-        JOptionPane.showInternalMessageDialog(Desktop.desktop, "No link selected!"
-            ,"No link selected", JOptionPane.WARNING_MESSAGE);
-        return;
+        break;
       }
-      nameLinks.removeElementAt(index);
-      urlLinks.removeElementAt(index);
-      updateLinkData();
     }
+  }
 
-    void updateLinkData()
+  public void deleteLink_actionPerformed(ActionEvent e)
+  {
+    int index = linkNameList.getSelectedIndex();
+    if (index == -1)
     {
-      linkNameList.setListData(nameLinks);
-      linkURLList.setListData(urlLinks);
+      JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                                            "No link selected!"
+                                            , "No link selected",
+                                            JOptionPane.WARNING_MESSAGE);
+      return;
     }
+    nameLinks.removeElementAt(index);
+    urlLinks.removeElementAt(index);
+    updateLinkData();
+  }
 
-    public void defaultBrowser_mouseClicked(MouseEvent e)
-    {
-      JFileChooser chooser = new JFileChooser(".");
-      chooser.setDialogTitle("Select default web browser");
+  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);
+    int value = chooser.showOpenDialog(this);
 
-      if (value == JFileChooser.APPROVE_OPTION)
-      {
-        defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
-      }
+    if (value == JFileChooser.APPROVE_OPTION)
+    {
+      defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+    }
 
   }