JAL-3538 anti-aliasing enabled by default

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c3c9239..0d7d1b4 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -24,6 +24,8 @@ 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.BackupFilesPresetEntry;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -109,6 +111,14 @@ public class Preferences extends GPreferences
 
   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 USE_LEGACY_GAP = "USE_LEGACY_GAP";
+
+  public static final String GAP_COLOUR = "GAP_COLOUR";
+
+  public static final String HIDDEN_COLOUR = "HIDDEN_COLOUR";
+
   private static final int MIN_FONT_SIZE = 1;
 
   private static final int MAX_FONT_SIZE = 30;
@@ -155,13 +165,11 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new ArrayList<String>();
+    groupURLLinks = new ArrayList<>();
   }
 
   JInternalFrame frame;
 
-  DasSourceBrowser dasSource;
-
   private WsPreferences wsPrefs;
 
   private OptionsParam promptEachTimeOpt = new OptionsParam(
@@ -182,8 +190,6 @@ public class Preferences extends GPreferences
     super();
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    dasSource = new DasSourceBrowser();
-    dasTab.add(dasSource, BorderLayout.CENTER);
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
     int width = 500, height = 450;
@@ -247,7 +253,7 @@ public class Preferences extends GPreferences
     fontStyleCB.setSelectedItem(
             Cache.getDefault("FONT_STYLE", Font.PLAIN + ""));
 
-    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", false));
+    smoothFont.setSelected(Cache.getDefault("ANTI_ALIAS", true));
     scaleProteinToCdna
             .setSelected(Cache.getDefault(SCALE_PROTEIN_TO_CDNA, false));
 
@@ -309,6 +315,21 @@ public class Preferences extends GPreferences
             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);
@@ -380,7 +401,7 @@ public class Preferences extends GPreferences
     doReset.addActionListener(onReset);
 
     // filter to display only custom urls
-    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<TableModel, Object>()
+    final RowFilter<TableModel, Object> customUrlFilter = new RowFilter<>()
     {
       @Override
       public boolean include(
@@ -502,8 +523,10 @@ public class Preferences extends GPreferences
     autoIdWidth.setSelected(Cache.getDefault("FIGURE_AUTOIDWIDTH", false));
     userIdWidth.setEnabled(!autoIdWidth.isSelected());
     userIdWidthlabel.setEnabled(!autoIdWidth.isSelected());
-    Integer wi = Cache.getIntegerProperty("FIGURE_USERIDWIDTH");
+    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));
@@ -525,6 +548,12 @@ public class Preferences extends GPreferences
 
     annotations_actionPerformed(null); // update the display of the annotation
                                        // settings
+    
+    
+    /*
+     * Set Backups tab defaults
+     */
+    loadLastSavedBackupsOptions();
   }
 
   /**
@@ -631,6 +660,16 @@ public class Preferences extends GPreferences
             maxColour.getBackground());
 
     /*
+     * Save Overview settings
+     */
+    Cache.setColourProperty(GAP_COLOUR, gapColour.getBackground());
+    Cache.setColourProperty(HIDDEN_COLOUR, hiddenColour.getBackground());
+    Cache.applicationProperties.setProperty(USE_LEGACY_GAP,
+            Boolean.toString(useLegacyGap.isSelected()));
+    Cache.applicationProperties.setProperty(SHOW_OV_HIDDEN_AT_START,
+            Boolean.toString(showHiddenAtStart.isSelected()));
+
+    /*
      * Save Structure settings
      */
     Cache.applicationProperties.setProperty(ADD_TEMPFACT_ANN,
@@ -749,7 +788,7 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("FIGURE_AUTOIDWIDTH",
             Boolean.toString(autoIdWidth.isSelected()));
     userIdWidth_actionPerformed();
-    Cache.applicationProperties.setProperty("FIGURE_USERIDWIDTH",
+    Cache.applicationProperties.setProperty("FIGURE_FIXEDIDWIDTH",
             userIdWidth.getText());
 
     /*
@@ -762,8 +801,31 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
-    dasSource.saveProperties(Cache.applicationProperties);
     wsPrefs.updateAndRefreshWsMenuConfig(false);
+
+    /*
+     * Save Backups settings
+     */
+    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+            Boolean.toString(enableBackupFiles.isSelected()));
+    int preset = getComboIntStringKey(backupfilesPresetsCombo);
+    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+
+    if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+    {
+      BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
+      BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+              BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
+      Cache.applicationProperties
+              .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
+                      customBFPE.toString());
+    }
+
+    BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .get(preset);
+    Cache.applicationProperties.setProperty(
+            BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
+
     Cache.saveProperties();
     Desktop.instance.doConfigureStructurePrefs();
     try
@@ -1035,6 +1097,63 @@ public class Preferences extends GPreferences
   }
 
   @Override
+  public void gapColour_actionPerformed(JPanel gap)
+  {
+    if (!useLegacyGap.isSelected())
+    {
+      Color col = JColorChooser.showDialog(this,
+              MessageManager.getString("label.select_gap_colour"),
+              gapColour.getBackground());
+      if (col != null)
+      {
+        gap.setBackground(col);
+      }
+      gap.repaint();
+    }
+  }
+
+  @Override
+  public void hiddenColour_actionPerformed(JPanel hidden)
+  {
+    Color col = JColorChooser.showDialog(this,
+            MessageManager.getString("label.select_hidden_colour"),
+            hiddenColour.getBackground());
+    if (col != null)
+    {
+      hidden.setBackground(col);
+    }
+    hidden.repaint();
+  }
+
+  @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