X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPreferences.java;h=78a21c82c2e0d5a1f57ffd9eb6b4a8a0a657a06a;hb=a83adb45bdf9554e270921b4baad94defd314b36;hp=398c5bed6d1ee1201fcfae0b5e65bc2e9792f068;hpb=a33d19728e33ab67aacdb990e190cba2ef53e1af;p=jalview.git

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 398c5be..b1206a2 100755
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -1,225 +1,1533 @@
-package jalview.gui;
-
-import jalview.jbgui.*;
-import jalview.schemes.*;
-import jalview.io.*;
-
-import jalview.bin.Cache;
-import javax.swing.*;
-import java.awt.event.ActionEvent;
-import java.awt.*;
-
-
-public class Preferences extends GPreferences
-{
-  static boolean preferencesLoaded=false;
-
-  public static boolean showFullscreen=false;
-  public static boolean showFullId=true;
-  public static boolean showAnnotation=true;
-  public static boolean showConservation=true;
-  public static boolean showQuality=true;
-  public static boolean showIdentity=true;
-  public static String fontName="SansSerif";
-  public static String fontSize="10";
-  public static String fontStyle=Font.PLAIN+"";
-  public static char gapSymbol='-';
-  public static String defaultColour=null;
-  public static boolean showStartupFile=true;
-  public static String startupFile = "http://www.compbio.dundee.ac.uk/~andrew/jalviewTEST/fasta";
-
-  JInternalFrame frame;
-
-  public static void initPreferences()
-  {
-  String string = Cache.getProperty("SHOW_FULL_ID");
-  if(string!=null)
-    showFullId = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_FULLSCREEN");
-  if(string!=null)
-    showFullscreen = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_ANNOTATIONS");
-      if(string!=null)
-    showAnnotation = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("SHOW_CONSERVATION");
-      if(string!=null)
-    showConservation = Boolean.valueOf(string).booleanValue();
-  string = Cache.getProperty("SHOW_QUALITY");
-      if(string!=null)
-    showQuality = Boolean.valueOf(string).booleanValue();
-  string = Cache.getProperty("SHOW_IDENTITY");
-      if(string!=null)
-    showIdentity = Boolean.valueOf(string).booleanValue();
-
-  string = Cache.getProperty("GAP_SYMBOL");
-      if(string!=null)
-    gapSymbol = string.charAt(0);
-
-  string = Cache.getProperty("SHOW_FULL_ID");
-    if(string!=null)
-      showFullId = Boolean.valueOf(string).booleanValue();
-
-    string = Cache.getProperty("FONT_NAME");
-    if (string != null)
-      fontName = string;
-
-    string = Cache.getProperty("FONT_STYLE");
-    if (string != null)
-      fontStyle = string;
-
-    string = Cache.getProperty("FONT_SIZE");
-    if (string != null)
-      fontSize = string;
-
-
-  string = Cache.getProperty("DEFAULT_COLOUR");
-  if(string!=null)
-      defaultColour = string;
-
-  string = Cache.getProperty("STARTUP_FILE");
-    if(string!=null)
-      startupFile = string;
-
-  string = Cache.getProperty("SHOW_STARTUP_FILE");
-        if(string!=null)
-      showStartupFile = Boolean.valueOf(string).booleanValue();
-
-      preferencesLoaded = true;
-  }
-
-  public Preferences()
-  {
-    initPreferences();
-
-    frame = new JInternalFrame();
-    frame.setContentPane(this);
-    Desktop.addInternalFrame(frame, "Preferences", 480,390 );
-
-    fullID.setSelected(showFullId);
-    String string = Cache.getProperty("SHOW_FULLSCREEN");
-    boolean value = false;
-    if(string!=null)
-      value =  Boolean.valueOf(string).booleanValue();
-
-    fullScreen.setSelected(value);
-    annotations.setSelected(showAnnotation);
-
-    conservation.setEnabled(showAnnotation);
-    quality.setEnabled(showAnnotation);
-    identity.setEnabled(showAnnotation);
-
-    conservation.setSelected(showConservation);
-    quality.setSelected(showQuality);
-    identity.setSelected(showIdentity);
-
-    for(int i=0; i<12; i++)
-      colour.addItem( ColourSchemeProperty.getColourName(i) );
-
-    string = Cache.getProperty("DEFAULT_COLOUR");
-    if(string!=null)
-      colour.setSelectedItem( string );
-    else
-      colour.setSelectedIndex( 11 );
-
-    String fonts[] = java.awt.GraphicsEnvironment.getLocalGraphicsEnvironment().getAvailableFontFamilyNames();
-    for(int i=0; i<fonts.length; i++)
-      fontNameCB.addItem(fonts[i]);
-
-    for(int i=1; i<31; i++)
-      fontSizeCB.addItem(i+"");
-
-   fontStyleCB.addItem("plain");
-   fontStyleCB.addItem("bold");
-   fontStyleCB.addItem("italic");
-
-   fontNameCB.setSelectedItem(fontName);
-   fontSizeCB.setSelectedItem(fontSize);
-   fontStyleCB.setSelectedItem(fontStyle);
-
-   gapSymbolCB.addItem("-");
-   gapSymbolCB.addItem(".");
-
-   gapSymbolCB.setSelectedItem( gapSymbol+"" );
-
-   startupCheckbox.setSelected(showStartupFile);
-   startupFileTextfield.setText(startupFile);
-
-  }
-
-  public void ok_actionPerformed(ActionEvent e)
-  {
-    showFullId =  fullID.isSelected() ;
-    showFullscreen = fullScreen.isSelected();
-    showAnnotation = annotations.isSelected();
-    showConservation = conservation.isSelected();
-    showQuality = quality.isSelected();
-    showIdentity = identity.isSelected();
-    defaultColour = colour.getSelectedItem().toString();
-    gapSymbol = gapSymbolCB.getSelectedItem().toString().charAt(0);
-    fontName = fontNameCB.getSelectedItem().toString();
-    fontSize = fontSizeCB.getSelectedItem().toString();
-    fontStyle = fontStyleCB.getSelectedItem().toString();
-    startupFile = startupFileTextfield.getText();
-    showStartupFile = startupCheckbox.isSelected();
-
-    Cache.setProperty("SHOW_FULL_ID", Boolean.toString(showFullId));
-    Cache.setProperty("SHOW_FULLSCREEN", Boolean.toString( showFullscreen ) );
-
-    Cache.setProperty("SHOW_ANNOTATIONS", Boolean.toString( showAnnotation  ));
-    Cache.setProperty("SHOW_CONSERVATION", Boolean.toString( showConservation ));
-    Cache.setProperty("SHOW_QUALITY", Boolean.toString( showQuality ));
-    Cache.setProperty("SHOW_IDENTITY", Boolean.toString( showIdentity ));
-
-    Cache.setProperty("DEFAULT_COLOUR", defaultColour);
-    Cache.setProperty("GAP_SYMBOL", gapSymbol+"");
-
-    Cache.setProperty("FONT_NAME", fontName);
-    Cache.setProperty("FONT_STYLE", fontStyle);
-    Cache.setProperty("FONT_SIZE", fontSize);
-
-    Cache.setProperty("STARTUP_FILE", startupFile);
-    Cache.setProperty("SHOW_STARTUP_FILE", Boolean.toString(showStartupFile));
-
-
-
-    try    {
-      frame.setClosed(true);
-    }    catch (Exception ex)  {}
-
-  }
-
-  public void startupFileTextfield_mouseClicked()
-  {
-    JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),
-        new String[]{"fa, fasta, fastq", "aln",  "pfam", "msf", "pir","blc","jar"},
-        new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}
-       ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));
-   chooser.setFileView(new JalviewFileView());
-   chooser.setDialogTitle("Select startup file");
-   int value = chooser.showOpenDialog(this);
-   if(value == JalviewFileChooser.APPROVE_OPTION)
-   {
-     jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", chooser.getSelectedFormat());
-     startupFileTextfield.setText( chooser.getSelectedFile().getAbsolutePath() );
-   }
-  }
-
-
-  public void cancel_actionPerformed(ActionEvent e)
-  {
-    try{
-      frame.setClosed(true);
-    }catch(Exception ex){}
-  }
-
-  public void annotations_actionPerformed(ActionEvent e)
-  {
-    conservation.setEnabled(annotations.isSelected());
-    quality.setEnabled(annotations.isSelected());
-    identity.setEnabled(annotations.isSelected());
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.analysis.AnnotationSorter.SequenceAnnotationOrder;
+import jalview.bin.Cache;
+import jalview.gui.Help.HelpId;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.BackupFiles;
+import jalview.io.FileFormatI;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GPreferences;
+import jalview.jbgui.GSequenceLink;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.schemes.ResidueColourScheme;
+import jalview.urls.UrlLinkTableModel;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.desktop.DesktopUrlProviderFactory;
+import jalview.util.BrowserLauncher;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.UrlConstants;
+import jalview.ws.sifts.SiftsSettings;
+
+import java.awt.BorderLayout;
+import java.awt.Color;
+import java.awt.Component;
+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.ArrayList;
+import java.util.List;
+
+import javax.help.HelpSetException;
+import javax.swing.JComboBox;
+import javax.swing.JFileChooser;
+import javax.swing.JInternalFrame;
+import javax.swing.JPanel;
+import javax.swing.ListSelectionModel;
+import javax.swing.RowFilter;
+import javax.swing.RowSorter;
+import javax.swing.SortOrder;
+import javax.swing.event.DocumentEvent;
+import javax.swing.event.DocumentListener;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.TableCellRenderer;
+import javax.swing.table.TableColumn;
+import javax.swing.table.TableModel;
+import javax.swing.table.TableRowSorter;
+
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+@SuppressWarnings("serial")
+public class Preferences extends GPreferences
+{
+  public static final String ADD_SS_ANN = "ADD_SS_ANN";
+
+  public static final String ADD_TEMPFACT_ANN = "ADD_TEMPFACT_ANN";
+
+  public static final String ALLOW_UNPUBLISHED_PDB_QUERYING = "ALLOW_UNPUBLISHED_PDB_QUERYING";
+
+  public static final String ANNOTATIONCOLOUR_MAX = "ANNOTATIONCOLOUR_MAX";
+
+  public static final String ANNOTATIONCOLOUR_MIN = "ANNOTATIONCOLOUR_MIN";
+
+  public static final String ANTI_ALIAS = "ANTI_ALIAS";
+
+  public static final String AUTO_CALC_CONSENSUS = "AUTO_CALC_CONSENSUS";
+
+  public static final String AUTOASSOCIATE_PDBANDSEQS = "AUTOASSOCIATE_PDBANDSEQS";
+
+  public static final String CENTRE_COLUMN_LABELS = "CENTRE_COLUMN_LABELS";
+
+  public static final String CHIMERA_PATH = "CHIMERA_PATH";
+
+  public static final String DBREFFETCH_USEPICR = "DBREFFETCH_USEPICR";
+
+  public static final String DEFAULT_COLOUR = "DEFAULT_COLOUR";
+
+  public static final String DEFAULT_COLOUR_NUC = "DEFAULT_COLOUR_NUC";
+
+  public static final String DEFAULT_COLOUR_PROT = "DEFAULT_COLOUR_PROT";
+
+  public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
+
+  public static final String FIGURE_AUTOIDWIDTH = "FIGURE_AUTOIDWIDTH";
+
+  public static final String FIGURE_FIXEDIDWIDTH = "FIGURE_FIXEDIDWIDTH";
+
+  public static final String FOLLOW_SELECTIONS = "FOLLOW_SELECTIONS";
+
+  public static final String FONT_NAME = "FONT_NAME";
+
+  public static final String FONT_SIZE = "FONT_SIZE";
+
+  public static final String FONT_STYLE = "FONT_STYLE";
+
+  public static final String GAP_COLOUR = "GAP_COLOUR";
+
+  public static final String GAP_SYMBOL = "GAP_SYMBOL";
+
+  public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
+  public static final String HIDE_INTRONS = "HIDE_INTRONS";
+
+  public static final String ID_ITALICS = "ID_ITALICS";
+
+  public static final String ID_ORG_HOSTURL = "ID_ORG_HOSTURL";
+
+  public static final String MAP_WITH_SIFTS = "MAP_WITH_SIFTS";
+
+  public static final String NOQUESTIONNAIRES = "NOQUESTIONNAIRES";
+
+  public static final String NORMALISE_CONSENSUS_LOGO = "NORMALISE_CONSENSUS_LOGO";
+
+  public static final String NORMALISE_LOGO = "NORMALISE_LOGO";
+
+  public static final String PAD_GAPS = "PAD_GAPS";
+
+  public static final String PDB_DOWNLOAD_FORMAT = "PDB_DOWNLOAD_FORMAT";
+
+  public static final String QUESTIONNAIRE = "QUESTIONNAIRE";
+
+  public static final String RELAXEDSEQIDMATCHING = "RELAXEDSEQIDMATCHING";
+
+  public static final String RIGHT_ALIGN_IDS = "RIGHT_ALIGN_IDS";
+
+  public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
+
+  public static final String SHOW_ANNOTATIONS = "SHOW_ANNOTATIONS";
+
+  public static final String SHOW_AUTOCALC_ABOVE = "SHOW_AUTOCALC_ABOVE";
+
+  public static final String SHOW_CONSENSUS = "SHOW_CONSENSUS";
+
+  public static final String SHOW_CONSENSUS_HISTOGRAM = "SHOW_CONSENSUS_HISTOGRAM";
+
+  public static final String SHOW_CONSENSUS_LOGO = "SHOW_CONSENSUS_LOGO";
+
+  public static final String SHOW_CONSERVATION = "SHOW_CONSERVATION";
+
+  public static final String SHOW_DBREFS_TOOLTIP = "SHOW_DBREFS_TOOLTIP";
+
+  public static final String SHOW_GROUP_CONSENSUS = "SHOW_GROUP_CONSENSUS";
+
+  public static final String SHOW_GROUP_CONSERVATION = "SHOW_GROUP_CONSERVATION";
+
+  public static final String SHOW_JVSUFFIX = "SHOW_JVSUFFIX";
+
+  public static final String SHOW_NPFEATS_TOOLTIP = "SHOW_NPFEATS_TOOLTIP";
+
+  public static final String SHOW_OCCUPANCY = "SHOW_OCCUPANCY";
+
+  public static final String SHOW_OV_HIDDEN_AT_START = "SHOW_OV_HIDDEN_AT_START";
+
+  public static final String SHOW_OVERVIEW = "SHOW_OVERVIEW";
+
+  public static final String SHOW_QUALITY = "SHOW_QUALITY";
+
+  public static final String SHOW_UNCONSERVED = "SHOW_UNCONSERVED";
+
+  public static final String SORT_ALIGNMENT = "SORT_ALIGNMENT";
+
+  public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
+
+  public static final String SORT_BY_TREE = "SORT_BY_TREE";
+
+  public static final String STRUCT_FROM_PDB = "STRUCT_FROM_PDB";
+
+  public static final String STRUCTURE_DISPLAY = "STRUCTURE_DISPLAY";
+
+  public static final String STRUCTURE_DIMENSIONS = "STRUCTURE_DIMENSIONS";
+
+  public static final String UNIPROT_DOMAIN = "UNIPROT_DOMAIN";
+
+  public static final String USE_FULL_SO = "USE_FULL_SO";
+
+  public static final String USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+  public static final String USE_RNAVIEW = "USE_RNAVIEW";
+
+  public static final String USER_DEFINED_COLOURS = "USER_DEFINED_COLOURS";
+
+  public static final String WRAP_ALIGNMENT = "WRAP_ALIGNMENT";
+
+
+  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 UrlProviderI sequenceUrlLinks; // must be nonfinal for test
+
+  public final static UrlLinkTableModel dataModel;
+
+  /**
+   * 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 final List<String> groupURLLinks; // not implemented
+
+  public static final String BLOSUM62_PCA_FOR_NUCLEOTIDE = "BLOSUM62_PCA_FOR_NUCLEOTIDE";
+
+  public static final String SHOW_IDENTITY = "SHOW_IDENTITY";
+
+  public static final String SHOW_FULLSCREEN = "SHOW_FULLSCREEN";
+
+  public static final Dimension DEFAULT_STRUCTURE_DIMENSIONS = new Dimension(
+          600, 600);
+
+  static
+  {
+    // get links selected to be in the menu (SEQUENCE_LINKS)
+    // and links entered by the user but not selected (STORED_LINKS)
+    String inMenuString = Cache.getDefault("SEQUENCE_LINKS", "");
+    String notInMenuString = Cache.getDefault("STORED_LINKS", "");
+    String defaultUrl = Cache.getDefault("DEFAULT_URL",
+            UrlConstants.DEFAULT_LABEL);
+
+    // if both links lists are empty, add the DEFAULT_URL link
+    // otherwise we assume the default link is in one of the lists
+    if (inMenuString.isEmpty() && notInMenuString.isEmpty())
+    {
+      inMenuString = UrlConstants.DEFAULT_STRING;
+    }
+    UrlProviderFactoryI factory = new DesktopUrlProviderFactory(defaultUrl,
+            inMenuString, notInMenuString);
+    sequenceUrlLinks = factory.createUrlProvider();
+    dataModel = new UrlLinkTableModel(sequenceUrlLinks);
+
+    /**
+     * TODO: reformulate groupURL encoding so two or more can be stored in the
+     * .properties file as '|' separated strings
+     */
+
+    groupURLLinks = new ArrayList<>(); // not implemented
+  }
+
+  JInternalFrame frame;
+
+  private WsPreferences wsPrefs;
+
+  private OptionsParam promptEachTimeOpt = new OptionsParam(
+          MessageManager.getString("label.prompt_each_time"),
+          "Prompt each time");
+
+  private OptionsParam lineArtOpt = new OptionsParam(
+          MessageManager.getString("label.lineart"), "Lineart");
+
+  private OptionsParam textOpt = new OptionsParam(
+          MessageManager.getString("action.text"), "Text");
+
+  /**
+   * Creates a new Preferences object.
+   */
+  public Preferences()
+  {
+    super();
+    frame = new JInternalFrame();
+    frame.setContentPane(this);
+    if (!Platform.isJS())
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      wsPrefs = new WsPreferences();
+      wsTab.add(wsPrefs, BorderLayout.CENTER);
+    }
+    int width = 500, height = 510; // BH 2019.07.12 added 60 to height
+    // (structure panel was too small anyway, and I added a default dimension
+    // for Jmol
+    if (Platform.isAMacAndNotJS())
+    {
+      width = 570;
+      height = 540; // BH 2019.07.12 added 30
+    }
+
+    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.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));
+    showOccupancy.setSelected(Cache.getDefault(SHOW_OCCUPANCY, 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 = MIN_FONT_SIZE; i <= MAX_FONT_SIZE; i++)
+    {
+      fontSizeCB.addItem(i + "");
+    }
+
+    fontStyleCB.addItem("plain");
+    fontStyleCB.addItem("bold");
+    fontStyleCB.addItem("italic");
+
+    fontNameCB.setSelectedItem(Cache.getDefault(FONT_NAME, "SansSerif"));
+    fontSizeCB.setSelectedItem(Cache.getDefault(FONT_SIZE, "10"));
+    fontStyleCB.setSelectedItem(
+            Cache.getDefault(FONT_STYLE, Font.PLAIN + ""));
+
+    smoothFont.setSelected(Cache.getDefault(ANTI_ALIAS, false));
+    scaleProteinToCdna
+            .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
+
+    idItalics.setSelected(Cache.getDefault(ID_ITALICS, true));
+
+    wrap.setSelected(Cache.getDefault(WRAP_ALIGNMENT, false));
+
+    gapSymbolCB.addItem("-");
+    gapSymbolCB.addItem(".");
+
+    gapSymbolCB.setSelectedItem(Cache.getDefault(GAP_SYMBOL, "-"));
+
+    sortby.addItem("No sort");
+    sortby.addItem("Id");
+    sortby.addItem("Pairwise Identity");
+    sortby.setSelectedItem(Cache.getDefault(SORT_ALIGNMENT, "No sort"));
+
+    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"));
+
+    /*
+     * Set Colours tab defaults
+     */
+    protColour.addItem(ResidueColourScheme.NONE);
+    nucColour.addItem(ResidueColourScheme.NONE);
+    for (ColourSchemeI cs : ColourSchemes.getInstance().getColourSchemes())
+    {
+      String name = cs.getSchemeName();
+      protColour.addItem(name);
+      nucColour.addItem(name);
+    }
+    String oldProp = Cache.getDefault(DEFAULT_COLOUR,
+            ResidueColourScheme.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 overview panel defaults
+     */
+    gapColour.setBackground(
+            Cache.getDefaultColour(GAP_COLOUR,
+                    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP));
+    hiddenColour.setBackground(
+            Cache.getDefaultColour(HIDDEN_COLOUR,
+                    jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN));
+    useLegacyGap.setSelected(Cache.getDefault(USE_LEGACY_GAP, false));
+    gapLabel.setEnabled(!useLegacyGap.isSelected());
+    gapColour.setEnabled(!useLegacyGap.isSelected());
+    showHiddenAtStart
+            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
+
+    /*
+     * 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()));
+    Dimension d = Cache.getDefaultDim(STRUCTURE_DIMENSIONS,
+            DEFAULT_STRUCTURE_DIMENSIONS);
+    String s = d.width + "," + d.height;
+    structureDimensions.setText(s);
+    chimeraPath.setText(Cache.getDefault(CHIMERA_PATH, ""));
+    chimeraPath.addActionListener(new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        validateChimeraPath();
+      }
+    });
+
+    if (Cache.getDefault(MAP_WITH_SIFTS, false))
+    {
+      siftsMapping.setSelected(true);
+    }
+    else
+    {
+      nwMapping.setSelected(true);
+    }
+
+    SiftsSettings
+            .setMapWithSifts(Cache.getDefault(MAP_WITH_SIFTS, false));
+
+    /*
+     * Set Connections tab defaults
+     */
+
+    // set up sorting
+    linkUrlTable.setModel(dataModel);
+    final TableRowSorter<TableModel> sorter = new TableRowSorter<>(
+            linkUrlTable.getModel());
+    linkUrlTable.setRowSorter(sorter);
+    List<RowSorter.SortKey> sortKeys = new ArrayList<>();
+
+    UrlLinkTableModel m = (UrlLinkTableModel) linkUrlTable.getModel();
+    sortKeys.add(new RowSorter.SortKey(m.getPrimaryColumn(),
+            SortOrder.DESCENDING));
+    sortKeys.add(new RowSorter.SortKey(m.getSelectedColumn(),
+            SortOrder.DESCENDING));
+    sortKeys.add(
+            new RowSorter.SortKey(m.getNameColumn(), SortOrder.ASCENDING));
+
+    sorter.setSortKeys(sortKeys);
+    // BH 2018 setSortKeys will do the sort
+    // sorter.sort();
+
+    // set up filtering
+    ActionListener onReset;
+    onReset = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        filterTB.setText("");
+        sorter.setRowFilter(RowFilter.regexFilter(""));
+      }
+
+    };
+    doReset.addActionListener(onReset);
+
+    // filter to display only custom urls
+    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+    {
+      @Override
+      public boolean include(
+              Entry<? extends TableModel, ? extends Object> entry)
+      {
+        return ((UrlLinkTableModel) entry.getModel()).isUserEntry(entry);
+      }
+    };
+
+    final TableRowSorter<TableModel> customSorter = new TableRowSorter<>(
+            linkUrlTable.getModel());
+    customSorter.setRowFilter(customUrlFilter);
+
+    ActionListener onCustomOnly;
+    onCustomOnly = new ActionListener()
+    {
+      @Override
+      public void actionPerformed(ActionEvent e)
+      {
+        filterTB.setText("");
+        sorter.setRowFilter(customUrlFilter);
+      }
+    };
+    userOnly.addActionListener(onCustomOnly);
+
+    filterTB.getDocument().addDocumentListener(new DocumentListener()
+    {
+      String caseInsensitiveFlag = "(?i)";
+
+      @Override
+      public void changedUpdate(DocumentEvent e)
+      {
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+      }
+
+      @Override
+      public void removeUpdate(DocumentEvent e)
+      {
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+      }
+
+      @Override
+      public void insertUpdate(DocumentEvent e)
+      {
+        sorter.setRowFilter(RowFilter
+                .regexFilter(caseInsensitiveFlag + filterTB.getText()));
+      }
+    });
+
+    // set up list selection functionality
+    linkUrlTable.getSelectionModel()
+            .addListSelectionListener(new UrlListSelectionHandler());
+
+    // set up radio buttons
+    int onClickCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getPrimaryColumn();
+    String onClickName = linkUrlTable.getColumnName(onClickCol);
+    linkUrlTable.getColumn(onClickName)
+            .setCellRenderer(new RadioButtonRenderer());
+    linkUrlTable.getColumn(onClickName)
+            .setCellEditor(new RadioButtonEditor());
+
+    // get boolean columns and resize those to min possible
+    for (int column = 0; column < linkUrlTable.getColumnCount(); column++)
+    {
+      if (linkUrlTable.getModel().getColumnClass(column)
+              .equals(Boolean.class))
+      {
+        TableColumn tableColumn = linkUrlTable.getColumnModel()
+                .getColumn(column);
+        int preferredWidth = tableColumn.getMinWidth();
+
+        TableCellRenderer cellRenderer = linkUrlTable.getCellRenderer(0,
+                column);
+        Component c = linkUrlTable.prepareRenderer(cellRenderer, 0, column);
+        int cwidth = c.getPreferredSize().width
+                + linkUrlTable.getIntercellSpacing().width;
+        preferredWidth = Math.max(preferredWidth, cwidth);
+
+        tableColumn.setPreferredWidth(preferredWidth);
+      }
+    }
+
+    useProxy.setSelected(Cache.getDefault("USE_PROXY", false));
+    useProxy_actionPerformed(); // make sure useProxy is correctly initialised
+    proxyServerTB.setText(Cache.getDefault("PROXY_SERVER", ""));
+    proxyPortTB.setText(Cache.getDefault("PROXY_PORT", ""));
+
+    defaultBrowser.setText(Cache.getDefault("DEFAULT_BROWSER", ""));
+
+    usagestats.setSelected(Cache.getDefault("USAGESTATS", false));
+    // note antisense here: default is true
+    questionnaire
+            .setSelected(Cache.getProperty(NOQUESTIONNAIRES) == null);
+    versioncheck.setSelected(Cache.getDefault("VERSION_CHECK", true));
+
+    /*
+     * Set Output tab defaults
+     */
+    setupOutputCombo(epsRendering, "EPS_RENDERING");
+    setupOutputCombo(htmlRendering, "HTML_RENDERING");
+    setupOutputCombo(svgRendering, "SVG_RENDERING");
+    autoIdWidth.setSelected(Cache.getDefault(FIGURE_AUTOIDWIDTH, false));
+    userIdWidth.setEnabled(!autoIdWidth.isSelected());
+    userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
+    Integer wi = Cache.getIntegerProperty(FIGURE_FIXEDIDWIDTH);
+    userIdWidth.setText(wi == null ? "" : wi.toString());
+    // TODO: refactor to use common enum via FormatAdapter and allow extension
+    // for new flat file formats
+    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
+    
+    
+    /*
+     * Set Backups tab defaults
+     */
+    loadLastSavedBackupsOptions();
+  }
+
+  /**
+   * A helper method that sets the items and initial selection in a character
+   * rendering option list (Prompt each time/Lineart/Text)
+   * 
+   * @param comboBox
+   * @param propertyKey
+   */
+  protected void setupOutputCombo(JComboBox<Object> comboBox,
+          String propertyKey)
+  {
+    comboBox.addItem(promptEachTimeOpt);
+    comboBox.addItem(lineArtOpt);
+    comboBox.addItem(textOpt);
+    
+    /*
+     * JalviewJS doesn't support Lineart so force it to Text
+     */
+    String defaultOption = Platform.isJS() ? "Text"
+            : Cache.getDefault(propertyKey, "Prompt each time");
+    if (defaultOption.equalsIgnoreCase("Text"))
+    {
+      comboBox.setSelectedItem(textOpt);
+    }
+    else if (defaultOption.equalsIgnoreCase("Lineart"))
+    {
+      comboBox.setSelectedItem(lineArtOpt);
+    }
+    else
+    {
+      comboBox.setSelectedItem(promptEachTimeOpt);
+    }
+  }
+
+  /**
+   * Save user selections on the Preferences tabs to the Cache and write out to
+   * file.
+   * 
+   * @param e
+   */
+  @Override
+  public void ok_actionPerformed(ActionEvent e)
+  {
+    if (!validateSettings())
+    {
+      return;
+    }
+
+    /*
+     * Save Visual settings
+     */
+    Cache.setPropertyNoSave(SHOW_JVSUFFIX,
+            Boolean.toString(seqLimit.isSelected()));
+    Cache.setPropertyNoSave(RIGHT_ALIGN_IDS,
+            Boolean.toString(rightAlign.isSelected()));
+    Cache.setPropertyNoSave(SHOW_FULLSCREEN,
+            Boolean.toString(fullScreen.isSelected()));
+    Cache.setPropertyNoSave(SHOW_OVERVIEW,
+            Boolean.toString(openoverv.isSelected()));
+    Cache.setPropertyNoSave(SHOW_ANNOTATIONS,
+            Boolean.toString(annotations.isSelected()));
+    Cache.setPropertyNoSave(SHOW_CONSERVATION,
+            Boolean.toString(conservation.isSelected()));
+    Cache.setPropertyNoSave(SHOW_QUALITY,
+            Boolean.toString(quality.isSelected()));
+    Cache.setPropertyNoSave(SHOW_IDENTITY,
+            Boolean.toString(identity.isSelected()));
+
+    Cache.setPropertyNoSave(GAP_SYMBOL,
+            gapSymbolCB.getSelectedItem().toString());
+
+    Cache.setPropertyNoSave(FONT_NAME,
+            fontNameCB.getSelectedItem().toString());
+    Cache.setPropertyNoSave(FONT_STYLE,
+            fontStyleCB.getSelectedItem().toString());
+    Cache.setPropertyNoSave(FONT_SIZE,
+            fontSizeCB.getSelectedItem().toString());
+
+    Cache.setPropertyNoSave(ID_ITALICS,
+            Boolean.toString(idItalics.isSelected()));
+    Cache.setPropertyNoSave(SHOW_UNCONSERVED,
+            Boolean.toString(showUnconserved.isSelected()));
+    Cache.setPropertyNoSave(SHOW_OCCUPANCY,
+            Boolean.toString(showOccupancy.isSelected()));
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS,
+            Boolean.toString(showGroupConsensus.isSelected()));
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION,
+            Boolean.toString(showGroupConservation.isSelected()));
+    Cache.setPropertyNoSave(SHOW_CONSENSUS_HISTOGRAM,
+            Boolean.toString(showConsensHistogram.isSelected()));
+    Cache.setPropertyNoSave(SHOW_CONSENSUS_LOGO,
+            Boolean.toString(showConsensLogo.isSelected()));
+    Cache.setPropertyNoSave(ANTI_ALIAS,
+            Boolean.toString(smoothFont.isSelected()));
+    Cache.setPropertyNoSave(SCALE_PROTEIN_TO_CDNA,
+            Boolean.toString(scaleProteinToCdna.isSelected()));
+    Cache.setPropertyNoSave(SHOW_NPFEATS_TOOLTIP,
+            Boolean.toString(showNpTooltip.isSelected()));
+    Cache.setPropertyNoSave(SHOW_DBREFS_TOOLTIP,
+            Boolean.toString(showDbRefTooltip.isSelected()));
+
+    Cache.setPropertyNoSave(WRAP_ALIGNMENT,
+            Boolean.toString(wrap.isSelected()));
+
+    Cache.setPropertyNoSave("STARTUP_FILE",
+            startupFileTextfield.getText());
+    Cache.setPropertyNoSave("SHOW_STARTUP_FILE",
+            Boolean.toString(startupCheckbox.isSelected()));
+
+    Cache.setPropertyNoSave(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.setPropertyNoSave(SORT_ANNOTATIONS,
+              annSortOrder.name());
+    }
+
+    final boolean showAutocalcFirst = sortAutocalc.getSelectedIndex() == 0;
+    Cache.setPropertyNoSave(SHOW_AUTOCALC_ABOVE,
+            Boolean.valueOf(showAutocalcFirst).toString());
+
+    /*
+     * Save Colours settings
+     */
+    Cache.setPropertyNoSave(DEFAULT_COLOUR_PROT,
+            protColour.getSelectedItem().toString());
+    Cache.setPropertyNoSave(DEFAULT_COLOUR_NUC,
+            nucColour.getSelectedItem().toString());
+    Cache.setColourProperty(ANNOTATIONCOLOUR_MIN,
+            minColour.getBackground());
+    Cache.setColourProperty(ANNOTATIONCOLOUR_MAX,
+            maxColour.getBackground());
+
+    /*
+     * Save Overview settings
+     */
+    Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+    Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+    Cache.setPropertyNoSave(USE_LEGACY_GAP,
+            Boolean.toString(useLegacyGap.isSelected()));
+    Cache.setPropertyNoSave(SHOW_OV_HIDDEN_AT_START,
+            Boolean.toString(showHiddenAtStart.isSelected()));
+
+    /*
+     * Save Structure settings
+     */
+    Cache.setPropertyNoSave(ADD_TEMPFACT_ANN,
+            Boolean.toString(addTempFactor.isSelected()));
+    Cache.setPropertyNoSave(ADD_SS_ANN,
+            Boolean.toString(addSecondaryStructure.isSelected()));
+    Cache.setPropertyNoSave(USE_RNAVIEW,
+            Boolean.toString(useRnaView.isSelected()));
+    Cache.setPropertyNoSave(STRUCT_FROM_PDB,
+            Boolean.toString(structFromPdb.isSelected()));
+    Cache.setPropertyNoSave(STRUCTURE_DISPLAY,
+            structViewer.getSelectedItem().toString());
+    Cache.setPropertyNoSave(STRUCTURE_DIMENSIONS,
+            structureDimensions.getText()); // BH 2019.07.12
+    Cache.setOrRemove(CHIMERA_PATH, chimeraPath.getText());
+    Cache.setPropertyNoSave(MAP_WITH_SIFTS,
+            Boolean.toString(siftsMapping.isSelected()));
+    SiftsSettings.setMapWithSifts(siftsMapping.isSelected());
+
+    /*
+     * Save Output settings
+     */
+    Cache.setPropertyNoSave("EPS_RENDERING",
+            ((OptionsParam) epsRendering.getSelectedItem()).getCode());
+    Cache.setPropertyNoSave("HTML_RENDERING",
+            ((OptionsParam) htmlRendering.getSelectedItem()).getCode());
+    Cache.setPropertyNoSave("SVG_RENDERING",
+            ((OptionsParam) svgRendering.getSelectedItem()).getCode());
+
+    if (!Platform.isJS())
+    /**
+     * @j2sNative
+     */
+    {
+      // Java only
+      // Save Connections settings
+      Cache.setOrRemove("DEFAULT_BROWSER", defaultBrowser.getText());
+      BrowserLauncher.resetBrowser();
+    }
+
+    // save user-defined and selected links
+    String menuLinks = sequenceUrlLinks.writeUrlsAsString(true);
+    if (menuLinks.isEmpty())
+    {
+      Cache.removePropertyNoSave("SEQUENCE_LINKS");
+    }
+    else
+    {
+      Cache.setPropertyNoSave("SEQUENCE_LINKS",
+              menuLinks.toString());
+    }
+
+    String nonMenuLinks = sequenceUrlLinks.writeUrlsAsString(false);
+    if (nonMenuLinks.isEmpty())
+    {
+      Cache.removePropertyNoSave("STORED_LINKS");
+    }
+    else
+    {
+      Cache.setPropertyNoSave("STORED_LINKS",
+              nonMenuLinks.toString());
+    }
+
+    Cache.setPropertyNoSave("DEFAULT_URL",
+            sequenceUrlLinks.getPrimaryUrlId());
+
+    Cache.setPropertyNoSave("USE_PROXY",
+            Boolean.toString(useProxy.isSelected()));
+
+    Cache.setOrRemove("PROXY_SERVER", proxyServerTB.getText());
+
+    Cache.setOrRemove("PROXY_PORT", proxyPortTB.getText());
+
+    if (useProxy.isSelected())
+    {
+      System.setProperty("http.proxyHost", proxyServerTB.getText());
+      System.setProperty("http.proxyPort", proxyPortTB.getText());
+    }
+    else
+    {
+      System.setProperty("http.proxyHost", "");
+      System.setProperty("http.proxyPort", "");
+    }
+    Cache.setProperty("VERSION_CHECK",
+            Boolean.toString(versioncheck.isSelected()));
+    if (Cache.getProperty("USAGESTATS") != null || usagestats.isSelected())
+    {
+      // default is false - we only set this if the user has actively agreed
+      Cache.setProperty("USAGESTATS",
+              Boolean.toString(usagestats.isSelected()));
+    }
+    if (!questionnaire.isSelected())
+    {
+      Cache.setProperty(NOQUESTIONNAIRES, "true");
+    }
+    else
+    {
+      // special - made easy to edit a property file to disable questionnaires
+      // by just adding the given line
+      Cache.removeProperty(NOQUESTIONNAIRES);
+    }
+
+    /*
+     * Save Output settings
+     */
+    Cache.setPropertyNoSave("BLC_JVSUFFIX",
+            Boolean.toString(blcjv.isSelected()));
+    Cache.setPropertyNoSave("CLUSTAL_JVSUFFIX",
+            Boolean.toString(clustaljv.isSelected()));
+    Cache.setPropertyNoSave("FASTA_JVSUFFIX",
+            Boolean.toString(fastajv.isSelected()));
+    Cache.setPropertyNoSave("MSF_JVSUFFIX",
+            Boolean.toString(msfjv.isSelected()));
+    Cache.setPropertyNoSave("PFAM_JVSUFFIX",
+            Boolean.toString(pfamjv.isSelected()));
+    Cache.setPropertyNoSave("PILEUP_JVSUFFIX",
+            Boolean.toString(pileupjv.isSelected()));
+    Cache.setPropertyNoSave("PIR_JVSUFFIX",
+            Boolean.toString(pirjv.isSelected()));
+    Cache.setPropertyNoSave("PIR_MODELLER",
+            Boolean.toString(modellerOutput.isSelected()));
+    Cache.setPropertyNoSave("EXPORT_EMBBED_BIOJSON",
+            Boolean.toString(embbedBioJSON.isSelected()));
+    Cache.setPropertyNoSave(FIGURE_AUTOIDWIDTH,
+            Boolean.toString(autoIdWidth.isSelected()));
+    userIdWidth_actionPerformed();
+    Cache.setPropertyNoSave("FIGURE_FIXEDIDWIDTH",
+            userIdWidth.getText());
+
+    /*
+     * Save Editing settings
+     */
+    Cache.setPropertyNoSave(AUTO_CALC_CONSENSUS,
+            Boolean.toString(autoCalculateConsCheck.isSelected()));
+    Cache.setPropertyNoSave(SORT_BY_TREE,
+            Boolean.toString(sortByTree.isSelected()));
+    Cache.setPropertyNoSave(PAD_GAPS,
+            Boolean.toString(padGaps.isSelected()));
+
+    if (!Platform.isJS())
+    {
+      wsPrefs.updateAndRefreshWsMenuConfig(false);
+    }
+
+    /*
+     * Save Backups settings
+     */
+    Cache.setPropertyNoSave(BackupFiles.CONFIRM_DELETE_OLD,
+            Boolean.toString(backupfilesConfirmDelete.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.ENABLED,
+            Boolean.toString(enableBackupFiles.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.NO_MAX,
+            Boolean.toString(backupfilesKeepAll.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.REVERSE_ORDER,
+            Boolean.toString(suffixReverse.isSelected()));
+    Cache.setPropertyNoSave(BackupFiles.SUFFIX,
+            suffixTemplate.getText());
+    Cache.setPropertyNoSave(BackupFiles.ROLL_MAX,
+            Integer.toString(getSpinnerInt(backupfilesRollMaxSpinner, 4)));
+    Cache.setPropertyNoSave(BackupFiles.SUFFIX_DIGITS,
+            Integer.toString(getSpinnerInt(suffixDigitsSpinner, 3)));
+    Cache.setPropertyNoSave(BackupFiles.NS + "_PRESET",
+            Integer.toString(getComboIntStringKey(backupfilesPresetsCombo)));
+
+    Cache.saveProperties();
+    Desktop.getInstance().doConfigureStructurePrefs();
+    try
+    {
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  public static void setAppletDefaults()
+  {
+
+    // http://www.jalview.org/old/v2_8/examples/appletParameters.html
+
+    // showConservation true or false Default is true.
+    // showQuality true or false Default is true.
+    // showConsensus true or false Default is true.
+    // showFeatureSettings true or false Shows the feature settings window when
+    // startin
+    // showTreeBootstraps true or false (default is true) show or hide branch
+    // bootstraps
+    // showTreeDistances true or false (default is true) show or hide branch
+    // lengths
+    // showUnlinkedTreeNodes true or false (default is false) indicate if
+    // unassociated nodes should be highlighted in the tree view
+    // showUnconserved true of false (default is false) When true, only gaps and
+    // symbols different to the consensus sequence ions of the alignment
+    // showGroupConsensus true of false (default is false) When true, shows
+    // consensus annotation row for any groups on the alignment. (since 2.7)
+    // showGroupConservation true of false (default is false) When true, shows
+    // amino-acid property conservation annotation row for any groups on the
+    // showConsensusHistogram true of false (default is true) When true, shows
+    // the percentage occurence of the consensus symbol for each column as a
+    // showSequenceLogo true of false (default is false) When true, shows a
+    // sequence logo above the consensus sequence (overlaid above the Consensus
+
+    Cache.setPropertyNoSave(SHOW_CONSERVATION, "true");
+    Cache.setPropertyNoSave(SHOW_QUALITY, "false");
+    Cache.setPropertyNoSave(SHOW_CONSENSUS, "true");
+    Cache.setPropertyNoSave(SHOW_UNCONSERVED, "false");
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSERVATION, "false");
+    Cache.setPropertyNoSave(SHOW_GROUP_CONSENSUS, "false");
+
+    // TODO -- just a start here
+  }
+
+  /**
+   * 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!
+   */
+  @Override
+  public void startupFileTextfield_mouseClicked()
+  {
+    // TODO: JAL-3048 not needed for Jalview-JS
+    String fileFormat = Cache.getProperty("DEFAULT_FILE_FORMAT");
+    JalviewFileChooser chooser = JalviewFileChooser
+            .forRead(Cache.getProperty("LAST_DIRECTORY"), fileFormat);
+    chooser.setFileView(new JalviewFileView());
+    chooser.setDialogTitle(
+            MessageManager.getString("label.select_startup_file"));
+
+    int value = chooser.showOpenDialog(this);
+
+    if (value == JalviewFileChooser.APPROVE_OPTION)
+    {
+      FileFormatI format = chooser.getSelectedFormat();
+      if (format != null)
+      {
+        Cache.setPropertyNoSave("DEFAULT_FILE_FORMAT",
+                format.getName());
+      }
+      startupFileTextfield
+              .setText(chooser.getSelectedFile().getAbsolutePath());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void cancel_actionPerformed(ActionEvent e)
+  {
+    try
+    {
+      if (!Platform.isJS())
+      {
+        wsPrefs.updateWsMenuConfig(true);
+        wsPrefs.refreshWs_actionPerformed(e);
+      }
+      frame.setClosed(true);
+    } catch (Exception ex)
+    {
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void annotations_actionPerformed(ActionEvent e)
+  {
+    conservation.setEnabled(annotations.isSelected());
+    quality.setEnabled(annotations.isSelected());
+    identity.setEnabled(annotations.isSelected());
+    showOccupancy.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()));
+  }
+
+  @Override
+  public void newLink_actionPerformed(ActionEvent e)
+  {
+    GSequenceLink link = new GSequenceLink();
+    boolean valid = false;
+    while (!valid)
+    {
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
+              MessageManager.getString("label.new_sequence_url_link"),
+              JvOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JvOptionPane.OK_OPTION)
+      {
+        if (link.checkValid())
+        {
+          if (((UrlLinkTableModel) linkUrlTable.getModel())
+                  .isUniqueName(link.getName()))
+          {
+            ((UrlLinkTableModel) linkUrlTable.getModel())
+                    .insertRow(link.getName(), link.getURL());
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
+        }
+      }
+      else
+      {
+        break;
+      }
+    }
+  }
+
+  @Override
+  public void editLink_actionPerformed(ActionEvent e)
+  {
+    GSequenceLink link = new GSequenceLink();
+
+    int index = linkUrlTable.getSelectedRow();
+    if (index == -1)
+    {
+      // button no longer enabled if row is not selected
+      Cache.log.debug("Edit with no row selected in linkUrlTable");
+      return;
+    }
+
+    int nameCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getNameColumn();
+    int urlCol = ((UrlLinkTableModel) linkUrlTable.getModel())
+            .getUrlColumn();
+    String oldName = linkUrlTable.getValueAt(index, nameCol).toString();
+    link.setName(oldName);
+    link.setURL(linkUrlTable.getValueAt(index, urlCol).toString());
+
+    boolean valid = false;
+    while (!valid)
+    {
+      if (JvOptionPane.showInternalConfirmDialog(Desktop.getDesktopPane(), link,
+              MessageManager.getString("label.edit_sequence_url_link"),
+              JvOptionPane.OK_CANCEL_OPTION, -1,
+              null) == JvOptionPane.OK_OPTION)
+      {
+        if (link.checkValid())
+        {
+          if ((oldName.equals(link.getName()))
+                  || (((UrlLinkTableModel) linkUrlTable.getModel())
+                          .isUniqueName(link.getName())))
+          {
+            linkUrlTable.setValueAt(link.getName(), index, nameCol);
+            linkUrlTable.setValueAt(link.getURL(), index, urlCol);
+            valid = true;
+          }
+          else
+          {
+            link.notifyDuplicate();
+            continue;
+          }
+        }
+      }
+      else
+      {
+        break;
+      }
+    }
+  }
+
+  @Override
+  public void deleteLink_actionPerformed(ActionEvent e)
+  {
+    int index = linkUrlTable.getSelectedRow();
+    int modelIndex = -1;
+    if (index == -1)
+    {
+      // button no longer enabled if row is not selected
+      Cache.log.debug("Delete with no row selected in linkUrlTable");
+      return;
+    }
+    else
+    {
+      modelIndex = linkUrlTable.convertRowIndexToModel(index);
+    }
+
+    // make sure we use the model index to delete, and not the table index
+    ((UrlLinkTableModel) linkUrlTable.getModel()).removeRow(modelIndex);
+  }
+
+  @Override
+  public void defaultBrowser_mouseClicked(MouseEvent e)
+  {
+    // TODO: JAL-3048 not needed for j2s
+    if (!Platform.isJS()) // BH 2019
+    /**
+     * Java only
+     * 
+     * @j2sIgnore
+     */
+    {
+      JFileChooser chooser = new JFileChooser(".");
+      chooser.setDialogTitle(
+              MessageManager.getString("label.select_default_browser"));
+
+      int value = chooser.showOpenDialog(this);
+
+      if (value == JFileChooser.APPROVE_OPTION)
+      {
+        defaultBrowser.setText(chooser.getSelectedFile().getAbsolutePath());
+      }
+    }
+  }
+
+  /*
+   * (non-Javadoc)
+   * 
+   * @see
+   * jalview.jbgui.GPreferences#showunconserved_actionPerformed(java.awt.event
+   * .ActionEvent)
+   */
+  @Override
+  protected void showunconserved_actionPerformed(ActionEvent e)
+  {
+    // TODO Auto-generated method stub
+    super.showunconserved_actionPerformed(e);
+  }
+
+  /**
+   * not implemented -- returns empty list
+   * 
+   * @return
+   */
+  public static List<String> getGroupURLLinks()
+  {
+    return groupURLLinks;
+  }
+
+  @Override
+  public void minColour_actionPerformed(JPanel panel)
+  {
+    JalviewColourChooser.showColourChooser(this,
+            MessageManager.getString("label.select_colour_minimum_value"),
+            panel);
+  }
+
+  @Override
+  public void maxColour_actionPerformed(JPanel panel)
+  {
+    JalviewColourChooser.showColourChooser(this,
+            MessageManager.getString("label.select_colour_maximum_value"),
+            panel);
+  }
+
+  @Override
+  public void gapColour_actionPerformed(JPanel gap)
+  {
+    if (!useLegacyGap.isSelected())
+    {
+      JalviewColourChooser.showColourChooser(this,
+              MessageManager.getString("label.select_gap_colour"),
+              gap);
+    }
+  }
+
+  @Override
+  public void hiddenColour_actionPerformed(JPanel hidden)
+  {
+    JalviewColourChooser.showColourChooser(this,
+            MessageManager.getString("label.select_hidden_colour"),
+            hidden);
+  }
+
+  @Override
+  protected void useLegacyGaps_actionPerformed(ActionEvent e)
+  {
+    boolean enabled = useLegacyGap.isSelected();
+    if (enabled)
+    {
+      gapColour.setBackground(
+              jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_LEGACY_GAP);
+    }
+    else
+    {
+      gapColour.setBackground(
+              jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_GAP);
+    }
+    gapColour.setEnabled(!enabled);
+    gapLabel.setEnabled(!enabled);
+  }
+
+  @Override
+  protected void resetOvDefaults_actionPerformed(ActionEvent e)
+  {
+    useLegacyGap.setSelected(false);
+    useLegacyGaps_actionPerformed(null);
+    showHiddenAtStart.setSelected(false);
+    hiddenColour.setBackground(
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+  }
+
+  @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)
+    {
+      userIdWidth.setText("");
+      JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+              MessageManager
+                      .getString("warn.user_defined_width_requirements"),
+              MessageManager.getString("label.invalid_id_column_width"),
+              JvOptionPane.WARNING_MESSAGE);
+    }
+  }
+
+  @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.
+   */
+  protected boolean validateChimeraPath()
+  {
+    if (chimeraPath.getText().trim().length() > 0)
+    {
+      File f = new File(chimeraPath.getText());
+      if (!f.canExecute())
+      {
+        JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+                MessageManager.getString("label.invalid_chimera_path"),
+                MessageManager.getString("label.invalid_name"),
+                JvOptionPane.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 = JvOptionPane.showInternalOptionDialog(Desktop.getDesktopPane(),
+              JvSwingUtils.wrapTooltip(true,
+                      MessageManager.getString("label.chimera_missing")),
+              "", JvOptionPane.YES_NO_OPTION, JvOptionPane.WARNING_MESSAGE,
+              null, options, options[0]);
+      if (showHelp == JvOptionPane.NO_OPTION)
+      {
+        try
+        {
+          Help.showHelpWindow(HelpId.StructureViewer);
+        } catch (HelpSetException e)
+        {
+          e.printStackTrace();
+        }
+      }
+    }
+  }
+
+  public class OptionsParam
+  {
+    private String name;
+
+    private String code;
+
+    public OptionsParam(String name, String code)
+    {
+      this.name = name;
+      this.code = code;
+    }
+
+    public String getName()
+    {
+      return name;
+    }
+
+    public void setName(String name)
+    {
+      this.name = name;
+    }
+
+    public String getCode()
+    {
+      return code;
+    }
+
+    public void setCode(String code)
+    {
+      this.code = code;
+    }
+
+    @Override
+    public String toString()
+    {
+      return name;
+    }
+
+    @Override
+    public boolean equals(Object that)
+    {
+      if (!(that instanceof OptionsParam))
+      {
+        return false;
+      }
+      return this.code.equalsIgnoreCase(((OptionsParam) that).code);
+    }
+
+    @Override
+    public int hashCode()
+    {
+      return name.hashCode() + code.hashCode();
+    }
+  }
+
+  protected class UrlListSelectionHandler implements ListSelectionListener
+  {
+
+    @Override
+    public void valueChanged(ListSelectionEvent e)
+    {
+      ListSelectionModel lsm = (ListSelectionModel) e.getSource();
+
+      int index = lsm.getMinSelectionIndex();
+      if (index == -1)
+      {
+        // no selection, so disable delete/edit buttons
+        editLink.setEnabled(false);
+        deleteLink.setEnabled(false);
+        return;
+      }
+      int modelIndex = linkUrlTable.convertRowIndexToModel(index);
+
+      // enable/disable edit and delete link buttons
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowDeletable(modelIndex))
+      {
+        deleteLink.setEnabled(true);
+      }
+      else
+      {
+        deleteLink.setEnabled(false);
+      }
+
+      if (((UrlLinkTableModel) linkUrlTable.getModel())
+              .isRowEditable(modelIndex))
+      {
+        editLink.setEnabled(true);
+      }
+      else
+      {
+        editLink.setEnabled(false);
+      }
+    }
+  }
+}