JAL-1503 update version in GPL header
[jalview.git] / src / jalview / gui / Preferences.java
index bd4c900..51138f2 100755 (executable)
@@ -1,20 +1,20 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
  * 
- * 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 file is part of Jalview.
  * 
- * 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.
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -22,12 +22,14 @@ 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.util.MessageManager;
 
 /**
  * DOCUMENT ME!
@@ -37,17 +39,28 @@ import jalview.schemes.*;
  */
 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");
+                    "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
     sequenceURLLinks = new Vector();
 
     try
@@ -69,6 +82,24 @@ public class Preferences extends GPreferences
     {
       System.out.println(ex + "\nError parsing sequence links");
     }
+    {
+      // upgrade old SRS link
+      int srsPos = sequenceURLLinks
+              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
+      if (srsPos > -1)
+      {
+        sequenceURLLinks.setElementAt(
+                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
+                srsPos);
+      }
+    }
+
+    /**
+     * TODO: reformulate groupURL encoding so two or more can be stored in the
+     * .properties file as '|' separated strings
+     */
+
+    groupURLLinks = new Vector();
   }
 
   Vector nameLinks, urlLinks;
@@ -77,6 +108,8 @@ public class Preferences extends GPreferences
 
   DasSourceBrowser dasSource;
 
+  private WsPreferences wsPrefs;
+
   /**
    * Creates a new Preferences object.
    */
@@ -87,7 +120,8 @@ public class Preferences extends GPreferences
     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())
     {
@@ -95,7 +129,7 @@ public class Preferences extends GPreferences
       height = 460;
     }
 
-    Desktop.addInternalFrame(frame, "Preferences", width, height);
+    Desktop.addInternalFrame(frame, MessageManager.getString("label.preferences"), width, height);
     frame.setMinimumSize(new Dimension(width, height));
 
     seqLimit.setSelected(Cache.getDefault("SHOW_JVSUFFIX", true));
@@ -103,16 +137,18 @@ public class Preferences extends GPreferences
     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));
     openoverv.setSelected(Cache.getDefault("SHOW_OVERVIEW", false));
-
-    for (int i = 0; i < 13; i++)
+    showUnconserved
+            .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+    showNpTooltip.setSelected(Cache
+            .getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
+            true));
+    sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+    for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
     {
       colour.addItem(ColourSchemeProperty.getColourName(i));
     }
@@ -121,6 +157,14 @@ public class Preferences extends GPreferences
 
     colour.setSelectedItem(string);
 
+    /**
+     * default min-max colours for annotation shading
+     */
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+            Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+            Color.red));
+
     String[] fonts = java.awt.GraphicsEnvironment
             .getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
 
@@ -157,7 +201,8 @@ public class Preferences extends GPreferences
     startupCheckbox
             .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
     startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
-            "http://www.jalview.org/examples/exampleFile_2_3.jar"));
+            Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+                    + "/examples/exampleFile_2_3.jar"));
 
     sortby.addItem("No sort");
     sortby.addItem("Id");
@@ -169,7 +214,11 @@ public class Preferences extends GPreferences
     epsRendering.addItem("Text");
     epsRendering.setSelectedItem(Cache.getDefault("EPS_RENDERING",
             "Prompt each time"));
-
+    autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
+    userIdWidth.setEnabled(autoIdWidth.isSelected());
+    userIdWidthlabel.setEnabled(autoIdWidth.isSelected());
+    Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+    userIdWidth.setText(wi == null ? "" : wi.toString());
     blcjv.setSelected(Cache.getDefault("BLC_JVSUFFIX", true));
     clustaljv.setSelected(Cache.getDefault("CLUSTAL_JVSUFFIX", true));
     fastajv.setSelected(Cache.getDefault("FASTA_JVSUFFIX", true));
@@ -182,6 +231,15 @@ public class Preferences extends GPreferences
 
     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));
 
     /***************************************************************************
@@ -205,6 +263,17 @@ public class Preferences extends GPreferences
     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();
@@ -219,27 +288,27 @@ public class Preferences extends GPreferences
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          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("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());
@@ -253,23 +322,41 @@ public class Preferences extends GPreferences
     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("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("SHOW_STARTUP_FILE",
+            Boolean.toString(startupCheckbox.isSelected()));
 
     Cache.applicationProperties.setProperty("SORT_ALIGNMENT", sortby
             .getSelectedItem().toString());
 
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+            minColour.getBackground());
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+            maxColour.getBackground());
+
     if (epsRendering.getSelectedItem().equals("Prompt each time"))
     {
       Cache.applicationProperties.remove("EPS_RENDERING");
@@ -305,16 +392,16 @@ public class Preferences extends GPreferences
       }
       // remove last "|"
       links.setLength(links.length() - 1);
-      Cache.applicationProperties.setProperty("SEQUENCE_LINKS", links
-              .toString());
+      Cache.applicationProperties.setProperty("SEQUENCE_LINKS",
+              links.toString());
     }
     else
     {
       Cache.applicationProperties.remove("SEQUENCE_LINKS");
     }
 
-    Cache.applicationProperties.setProperty("USE_PROXY", Boolean
-            .toString(useProxy.isSelected()));
+    Cache.applicationProperties.setProperty("USE_PROXY",
+            Boolean.toString(useProxy.isSelected()));
 
     if (proxyServerTB.getText().trim().length() < 1)
     {
@@ -322,8 +409,8 @@ public class Preferences extends GPreferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
-              .getText());
+      Cache.applicationProperties.setProperty("PROXY_SERVER",
+              proxyServerTB.getText());
     }
 
     if (proxyPortTB.getText().trim().length() < 1)
@@ -332,8 +419,8 @@ public class Preferences extends GPreferences
     }
     else
     {
-      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
-              .getText());
+      Cache.applicationProperties.setProperty("PROXY_PORT",
+              proxyPortTB.getText());
     }
 
     if (useProxy.isSelected())
@@ -346,32 +433,57 @@ public class Preferences extends GPreferences
       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()));
+    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()));
+    Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
+            Boolean.toString(autoIdWidth.isSelected()));
+    userIdWidth_actionPerformed();
+    Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+            userIdWidth.getText());
 
-    dasSource.saveProperties(Cache.applicationProperties);
+    Cache.applicationProperties.setProperty("AUTO_CALC_CONSENSUS",
+            Boolean.toString(autoCalculateConsCheck.isSelected()));
+    Cache.applicationProperties.setProperty("SORT_BY_TREE",
+            Boolean.toString(sortByTree.isSelected()));
+    Cache.applicationProperties.setProperty("PAD_GAPS",
+            Boolean.toString(padGaps.isSelected()));
 
+    dasSource.saveProperties(Cache.applicationProperties);
+    wsPrefs.updateAndRefreshWsMenuConfig(false);
     Cache.saveProperties();
     try
     {
@@ -386,9 +498,10 @@ public class Preferences extends GPreferences
    */
   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" },
+    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"));
@@ -410,12 +523,14 @@ public class Preferences extends GPreferences
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void cancel_actionPerformed(ActionEvent e)
   {
     try
     {
+      wsPrefs.updateWsMenuConfig(true);
+      wsPrefs.refreshWs_actionPerformed(e);
       frame.setClosed(true);
     } catch (Exception ex)
     {
@@ -426,13 +541,19 @@ public class Preferences extends GPreferences
    * DOCUMENT ME!
    * 
    * @param e
-   *                DOCUMENT ME!
+   *          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)
@@ -443,7 +564,7 @@ public class Preferences extends GPreferences
     while (!valid)
     {
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+              MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
               null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
@@ -469,7 +590,7 @@ public class Preferences extends GPreferences
     if (index == -1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "No link selected!", "No link selected",
+              MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
               JOptionPane.WARNING_MESSAGE);
       return;
     }
@@ -482,7 +603,7 @@ public class Preferences extends GPreferences
     {
 
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
+              MessageManager.getString("label.new_sequence_url_link"), JOptionPane.OK_CANCEL_OPTION, -1,
               null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
@@ -507,7 +628,7 @@ public class Preferences extends GPreferences
     if (index == -1)
     {
       JOptionPane.showInternalMessageDialog(Desktop.desktop,
-              "No link selected!", "No link selected",
+              MessageManager.getString("label.no_link_selected"), MessageManager.getString("label.no_link_selected"),
               JOptionPane.WARNING_MESSAGE);
       return;
     }
@@ -536,7 +657,82 @@ public class Preferences extends GPreferences
 
   }
 
+  /*
+   * (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;
+  }
+
+  public void minColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Minimum Value", minColour.getBackground());
+    if (col != null)
+    {
+      minColour.setBackground(col);
+    }
+    minColour.repaint();
+  }
+
+  public void maxColour_actionPerformed()
+  {
+    Color col = JColorChooser.showDialog(this,
+            "Select Colour for Maximum Value", maxColour.getBackground());
+    if (col != null)
+    {
+      maxColour.setBackground(col);
+    }
+    maxColour.repaint();
+  }
+
+  @Override
+  protected void userIdWidth_actionPerformed()
+  {
+    try
+    {
+      String val = userIdWidth.getText().trim();
+      if (val.length() > 0)
+      {
+        Integer iw = Integer.parseInt(val);
+        if (iw.intValue() < 12)
+        {
+          throw new NumberFormatException();
+        }
+        userIdWidth.setText(iw.toString());
+      }
+    } catch (NumberFormatException x)
+    {
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+                      "The user defined width for the\nannotation and sequence ID columns\nin exported figures must be\nat least 12 pixels wide.",
+                      "Invalid ID Column width",
+                      JOptionPane.WARNING_MESSAGE);
+      userIdWidth.setText("");
+    }
+  }
+
+  @Override
+  protected void autoIdWidth_actionPerformed()
+  {
+    userIdWidth.setEnabled(!autoIdWidth.isSelected());
+    userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+  }
+
 }