X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=78a21c82c2e0d5a1f57ffd9eb6b4a8a0a657a06a;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=6d94687c15a17560ca0ab822b647c8441b6d020a;hpb=27929c642502f19a8f62b1286c7542bb87c35e18;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 6d94687..78a21c8 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,34 +1,57 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 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.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseEvent;
+import java.io.File;
+import java.util.Collection;
+import java.util.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.help.HelpSetException;
+import javax.swing.JColorChooser;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
 
 /**
  * DOCUMENT ME!
@@ -38,16 +61,47 @@ import jalview.schemes.*;
  */
 public class Preferences extends GPreferences
 {
+  public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+  public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+  public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+  public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+  public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
+  public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+  public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+  public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+  public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+  public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+  public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+  public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+  public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+  private static final int MIN_FONT_SIZE = 1;
+
+  private static final int MAX_FONT_SIZE = 30;
 
   /**
    * 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 |,|.
+   * 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
    */
 
@@ -57,9 +111,9 @@ public class Preferences extends GPreferences
     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
     {
       StringTokenizer st = new StringTokenizer(string, "|");
@@ -79,15 +133,25 @@ 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 
+     * 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?workflow=Default&datasetName=JalviewIDs$DATASETID$&input=$SEQUENCEIDS$&inputType=0|,");
-    // TODO: make sequence Group URL links more efficiently generated so popup menu does not take so long. 
-    // groupURLLinks.addElement("Seqs|EnVision2|http://www.ebi.ac.uk/enfin-srv/envision2/pages/linkin.jsf?workflow=Default&datasetName=JalviewSeqs$DATASETID$&input=$SEQUENCES=/([A-Za-z]+)+/=$&inputType=1|,");
-    
   }
 
   Vector nameLinks, urlLinks;
@@ -96,60 +160,66 @@ public class Preferences extends GPreferences
 
   DasSourceBrowser dasSource;
 
+  private WsPreferences wsPrefs;
+
   /**
    * Creates a new Preferences object.
    */
   public Preferences()
   {
-
+    super();
     frame = new JInternalFrame();
     frame.setContentPane(this);
     dasSource = new DasSourceBrowser();
-    dasPanel.add(dasSource, BorderLayout.CENTER);
-
-    int width = 500, height = 420;
+    dasTab.add(dasSource, BorderLayout.CENTER);
+    wsPrefs = new WsPreferences();
+    wsTab.add(wsPrefs, BorderLayout.CENTER);
+    int width = 500, height = 450;
     if (new jalview.util.Platform().isAMac())
     {
       width = 570;
-      height = 460;
+      height = 480;
     }
 
-    Desktop.addInternalFrame(frame, "Preferences", width, height);
+    Desktop.addInternalFrame(frame,
+            MessageManager.getString("label.preferences"), width, height);
     frame.setMinimumSize(new Dimension(width, height));
 
+    /*
+     * Set Visual tab defaults
+     */
     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.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));
-
-    for (int i = 0; i < 13; i++)
-    {
-      colour.addItem(ColourSchemeProperty.getColourName(i));
-    }
-
-    String string = Cache.getDefault("DEFAULT_COLOUR", "None");
-
-    colour.setSelectedItem(string);
+    showUnconserved
+            .setSelected(Cache.getDefault("SHOW_UNCONSERVED", false));
+    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));
+    showNpTooltip.setSelected(Cache
+            .getDefault("SHOW_NPFEATS_TOOLTIP", true));
+    showDbRefTooltip.setSelected(Cache.getDefault("SHOW_DBREFS_TOOLTIP",
+            true));
 
     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++)
+    for (int i = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
     {
       fontSizeCB.addItem(i + "");
     }
@@ -164,6 +234,8 @@ public class Preferences extends GPreferences
             + ""));
 
     smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    scaleProteinToCdna.setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA,
+            false));
 
     idItalics.setSelected(Cache.getDefault("ID_ITALICS", true));
 
@@ -174,38 +246,75 @@ public class Preferences extends GPreferences
 
     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));
+    sortAnnBy.addItem(SequenceAnnotationOrder.NONE.toString());
+    sortAnnBy
+            .addItem(SequenceAnnotationOrder.SEQUENCE_AND_LABEL.toString());
+    sortAnnBy
+            .addItem(SequenceAnnotationOrder.LABEL_AND_SEQUENCE.toString());
+    SequenceAnnotationOrder savedSort = SequenceAnnotationOrder
+            .valueOf(Cache.getDefault(SORT_ANNOTATIONS,
+                    SequenceAnnotationOrder.NONE.name()));
+    sortAnnBy.setSelectedItem(savedSort.toString());
+
+    sortAutocalc.addItem("Autocalculated first");
+    sortAutocalc.addItem("Autocalculated last");
+    final boolean showAbove = Cache.getDefault(SHOW_AUTOCALC_ABOVE, true);
+    sortAutocalc.setSelectedItem(showAbove ? sortAutocalc.getItemAt(0)
+            : sortAutocalc.getItemAt(1));
+    startupCheckbox
+            .setSelected(Cache.getDefault("SHOW_STARTUP_FILE", true));
+    startupFileTextfield.setText(Cache.getDefault("STARTUP_FILE",
+            Cache.getDefault("www.jalview.org", "http://www.jalview.org")
+                    + "/examples/exampleFile_2_3.jar"));
 
-    autoCalculateConsCheck.setSelected(Cache.getDefault(
-            "AUTO_CALC_CONSENSUS", true));
-    padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+    /*
+     * Set Colours tab defaults
+     */
+    for (int i = ColourSchemeProperty.FIRST_COLOUR; i <= ColourSchemeProperty.LAST_COLOUR; i++)
+    {
+      protColour.addItem(ColourSchemeProperty.getColourName(i));
+      nucColour.addItem(ColourSchemeProperty.getColourName(i));
+    }
+    String oldProp = Cache.getDefault(DEFAULT_COLOUR, "None");
+    String newProp = Cache.getDefault(DEFAULT_COLOUR_PROT, null);
+    protColour.setSelectedItem(newProp != null ? newProp : oldProp);
+    newProp = Cache.getDefault(DEFAULT_COLOUR_NUC, null);
+    nucColour.setSelectedItem(newProp != null ? newProp : oldProp);
+    minColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MIN",
+            Color.orange));
+    maxColour.setBackground(Cache.getDefaultColour("ANNOTATIONCOLOUR_MAX",
+            Color.red));
+
+    /*
+     * Set Structure tab defaults.
+     */
+    final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
+    structFromPdb.setSelected(structSelected);
+    useRnaView.setSelected(Cache.getDefault(USE_RNAVIEW, false));
+    useRnaView.setEnabled(structSelected);
+    addSecondaryStructure.setSelected(Cache.getDefault(ADD_SS_ANN, false));
+    addSecondaryStructure.setEnabled(structSelected);
+    addTempFactor.setSelected(Cache.getDefault(ADD_TEMPFACT_ANN, false));
+    addTempFactor.setEnabled(structSelected);
+    structViewer.setSelectedItem(Cache.getDefault(STRUCTURE_DISPLAY,
+            ViewerType.JMOL.name()));
+    chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+    chimeraPath.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        validateChimeraPath();
+      }
+    });
 
-    /***************************************************************************
-     * Set up Connections
+    /*
+     * Set Connections tab defaults
      */
     nameLinks = new Vector();
     urlLinks = new Vector();
@@ -225,49 +334,83 @@ 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
+    // note antisense here: default is true
+    questionnaire
+            .setSelected(Cache.getProperty("NOQUESTIONNAIRES") == null);
+    versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
 
-    try
-    {
-      jbInit();
-    } catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
+    /*
+     * Set Output tab defaults
+     */
+    epsRendering
+            .addItem(MessageManager.getString("label.prompt_each_time"));
+    epsRendering.addItem(MessageManager.getString("label.lineart"));
+    epsRendering.addItem(MessageManager.getString("action.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));
+    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));
+    embbedBioJSON.setSelected(Cache.getDefault("EXPORT_EMBBED_BIOJSON",
+            true));
 
+    /*
+     * Set Editing tab defaults
+     */
+    autoCalculateConsCheck.setSelected(Cache.getDefault(
+            "AUTO_CALC_CONSENSUS", true));
+    padGaps.setSelected(Cache.getDefault("PAD_GAPS", false));
+    sortByTree.setSelected(Cache.getDefault("SORT_BY_TREE", false));
+
+    annotations_actionPerformed(null); // update the display of the annotation
+                                       // settings
   }
 
   /**
-   * DOCUMENT ME!
+   * Save user selections on the Preferences tabs to the Cache and write out to
+   * file.
    * 
    * @param e
-   *                DOCUMENT ME!
    */
   public void ok_actionPerformed(ActionEvent e)
   {
+    if (!validateSettings())
+    {
+      return;
+    }
+
+    /*
+     * Save Visual settings
+     */
+    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());
     Cache.applicationProperties.setProperty("GAP_SYMBOL", gapSymbolCB
             .getSelectedItem().toString());
 
@@ -278,23 +421,81 @@ 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("SHOW_UNCONSERVED",Boolean.toString(showUnconserved.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(SCALE_PROTEIN_TO_CDNA,
+            Boolean.toString(scaleProteinToCdna.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());
 
+    // convert description of sort order to enum name for save
+    SequenceAnnotationOrder annSortOrder = SequenceAnnotationOrder
+            .forDescription(sortAnnBy.getSelectedItem().toString());
+    if (annSortOrder != null)
+    {
+      Cache.applicationProperties.setProperty(SORT_ANNOTATIONS,
+              annSortOrder.name());
+    }
+
+    final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+    Cache.applicationProperties.setProperty(SHOW_AUTOCALC_ABOVE, Boolean
+            .valueOf(showAutocalcFirst).toString());
+
+    /*
+     * Save Colours settings
+     */
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_PROT, protColour
+            .getSelectedItem().toString());
+    Cache.applicationProperties.setProperty(DEFAULT_COLOUR_NUC, nucColour
+            .getSelectedItem().toString());
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MIN",
+            minColour.getBackground());
+    Cache.setColourProperty("ANNOTATIONCOLOUR_MAX",
+            maxColour.getBackground());
+
+    /*
+     * Save Structure settings
+     */
+    Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
+            Boolean.toString(addTempFactor.isSelected()));
+    Cache.applicationProperties.setProperty(ADD_SS_ANN,
+            Boolean.toString(addSecondaryStructure.isSelected()));
+    Cache.applicationProperties.setProperty(USE_RNAVIEW,
+            Boolean.toString(useRnaView.isSelected()));
+    Cache.applicationProperties.setProperty(STRUCT_FROM_PDB,
+            Boolean.toString(structFromPdb.isSelected()));
+    Cache.applicationProperties.setProperty(STRUCTURE_DISPLAY, structViewer
+            .getSelectedItem().toString());
+    Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+
+    /*
+     * Save Output settings
+     */
     if (epsRendering.getSelectedItem().equals("Prompt each time"))
     {
       Cache.applicationProperties.remove("EPS_RENDERING");
@@ -305,15 +506,10 @@ public class Preferences extends GPreferences
               .getSelectedItem().toString());
     }
 
-    if (defaultBrowser.getText().trim().length() < 1)
-    {
-      Cache.applicationProperties.remove("DEFAULT_BROWSER");
-    }
-    else
-    {
-      Cache.applicationProperties.setProperty("DEFAULT_BROWSER",
-              defaultBrowser.getText());
-    }
+    /*
+     * Save Connections settings
+     */
+    Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
 
     jalview.util.BrowserLauncher.resetBrowser();
 
@@ -330,36 +526,20 @@ 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)
-    {
-      Cache.applicationProperties.remove("PROXY_SERVER");
-    }
-    else
-    {
-      Cache.applicationProperties.setProperty("PROXY_SERVER", proxyServerTB
-              .getText());
-    }
+    Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
 
-    if (proxyPortTB.getText().trim().length() < 1)
-    {
-      Cache.applicationProperties.remove("PROXY_PORT");
-    }
-    else
-    {
-      Cache.applicationProperties.setProperty("PROXY_PORT", proxyPortTB
-              .getText());
-    }
+    Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
 
     if (useProxy.isSelected())
     {
@@ -371,46 +551,68 @@ public class Preferences extends GPreferences
       System.setProperty("http.proxyHost", "");
       System.setProperty("http.proxyPort", "");
     }
-    Cache.setProperty("VERSION_CHECK", Boolean
-            .toString(versioncheck.isSelected()));
-    if (Cache.getProperty("USAGESTATS")!=null || usagestats.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()));
+      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
+    }
+    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()));
+
+    /*
+     * Save Output settings
+     */
+    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.applicationProperties.setProperty("EXPORT_EMBBED_BIOJSON",
+            Boolean.toString(embbedBioJSON.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);
+    /*
+     * Save Editing settings
+     */
+    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();
+    Desktop.instance.doConfigureStructurePrefs();
     try
     {
       frame.setClosed(true);
@@ -420,18 +622,42 @@ public class Preferences extends GPreferences
   }
 
   /**
+   * Do any necessary validation before saving settings. Return focus to the
+   * first tab which fails validation.
+   * 
+   * @return
+   */
+  private boolean validateSettings()
+  {
+    if (!validateStructure())
+    {
+      structureTab.requestFocusInWindow();
+      return false;
+    }
+    return true;
+  }
+
+  @Override
+  protected boolean validateStructure()
+  {
+    return validateChimeraPath();
+
+  }
+
+  /**
    * 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" },
+    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");
+    chooser.setDialogTitle(MessageManager
+            .getString("label.select_startup_file"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -448,12 +674,14 @@ 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)
     {
@@ -464,13 +692,19 @@ 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)
@@ -481,8 +715,8 @@ public class Preferences extends GPreferences
     while (!valid)
     {
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
-              null) == JOptionPane.OK_OPTION)
+              MessageManager.getString("label.new_sequence_url_link"),
+              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -507,7 +741,8 @@ 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;
     }
@@ -520,8 +755,8 @@ public class Preferences extends GPreferences
     {
 
       if (JOptionPane.showInternalConfirmDialog(Desktop.desktop, link,
-              "New sequence URL link", JOptionPane.OK_CANCEL_OPTION, -1,
-              null) == JOptionPane.OK_OPTION)
+              MessageManager.getString("label.new_sequence_url_link"),
+              JOptionPane.OK_CANCEL_OPTION, -1, null) == JOptionPane.OK_OPTION)
       {
         if (link.checkValid())
         {
@@ -545,7 +780,8 @@ 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;
     }
@@ -563,7 +799,8 @@ public class Preferences extends GPreferences
   public void defaultBrowser_mouseClicked(MouseEvent e)
   {
     JFileChooser chooser = new JFileChooser(".");
-    chooser.setDialogTitle("Select default web browser");
+    chooser.setDialogTitle(MessageManager
+            .getString("label.select_default_browser"));
 
     int value = chooser.showOpenDialog(this);
 
@@ -573,8 +810,13 @@ public class Preferences extends GPreferences
     }
 
   }
-  /* (non-Javadoc)
-   * @see jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event.ActionEvent)
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
+   * .ActionEvent)
    */
   protected void showunconserved_actionPerformed(ActionEvent e)
   {
@@ -582,7 +824,136 @@ public class Preferences extends GPreferences
     super.showunconserved_actionPerformed(e);
   }
 
-  private void jbInit() throws Exception
+  public static Collection getGroupURLLinks()
   {
+    return groupURLLinks;
   }
+
+  @Override
+  public void minColour_actionPerformed(JPanel panel)
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_colour_minimum_value"),
+            minColour.getBackground());
+    if (col != null)
+    {
+      panel.setBackground(col);
+    }
+    panel.repaint();
+  }
+
+  @Override
+  public void maxColour_actionPerformed(JPanel panel)
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_colour_maximum_value"),
+            maxColour.getBackground());
+    if (col != null)
+    {
+      panel.setBackground(col);
+    }
+    panel.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, MessageManager
+              .getString("warn.user_defined_width_requirements"),
+              MessageManager.getString("label.invalid_id_column_width"),
+              JOptionPane.WARNING_MESSAGE);
+      userIdWidth.setText("");
+    }
+  }
+
+  @Override
+  protected void autoIdWidth_actionPerformed()
+  {
+    userIdWidth.setEnabled(!autoIdWidth.isSelected());
+    userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+  }
+
+  /**
+   * Returns true if chimera path is to a valid executable, else show an error
+   * dialog.
+   */
+  private boolean validateChimeraPath()
+  {
+    if (chimeraPath.getText().trim().length() > 0)
+    {
+      File f = new File(chimeraPath.getText());
+      if (!f.canExecute())
+      {
+        JOptionPane.showInternalMessageDialog(Desktop.desktop,
+                MessageManager.getString("label.invalid_chimera_path"),
+                MessageManager.getString("label.invalid_name"),
+                JOptionPane.ERROR_MESSAGE);
+        return false;
+      }
+    }
+    return true;
+  }
+
+  /**
+   * If Chimera is selected, check it can be found on default or user-specified
+   * path, if not show a warning/help dialog.
+   */
+  @Override
+  protected void structureViewer_actionPerformed(String selectedItem)
+  {
+    if (!selectedItem.equals(ViewerType.CHIMERA.name()))
+    {
+      return;
+    }
+    boolean found = false;
+
+    /*
+     * Try user-specified and standard paths for Chimera executable.
+     */
+    List<String> paths = StructureManager.getChimeraPaths();
+    paths.add(0, chimeraPath.getText());
+    for (String path : paths)
+    {
+      if (new File(path.trim()).canExecute())
+      {
+        found = true;
+        break;
+      }
+    }
+    if (!found)
+    {
+      String[] options = { "OK", "Help" };
+      int showHelp = JOptionPane.showInternalOptionDialog(
+              Desktop.desktop,
+              JvSwingUtils.wrapTooltip(true,
+                      MessageManager.getString("label.chimera_missing")),
+              "", JOptionPane.YES_NO_OPTION, JOptionPane.WARNING_MESSAGE,
+              null, options, options[0]);
+      if (showHelp == JOptionPane.NO_OPTION)
+      {
+        try
+        {
+          Help.showHelpWindow(HelpId.StructureViewer);
+        } catch (HelpSetException e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }
+  }
+
 }