Merge branch 'develop' into bug/JAL-2225mapMultipleChains

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

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index c3c9239..6635dbe 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -109,6 +109,14 @@ 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;
@@ -155,7 +163,7 @@ public class Preferences extends GPreferences
      * .properties file as '|' separated strings
      */
 
-    groupURLLinks = new ArrayList<String>();
+    groupURLLinks = new ArrayList<>();
   }
 
   JInternalFrame frame;
@@ -309,6 +317,21 @@ 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, true));
+
+    /*
      * Set Structure tab defaults.
      */
     final boolean structSelected = Cache.getDefault(STRUCT_FROM_PDB, false);
@@ -631,6 +654,16 @@ 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,
@@ -1035,6 +1068,63 @@ 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(true);
+    hiddenColour.setBackground(
+            jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
+  }
+
+  @Override
   protected void userIdWidth_actionPerformed()
   {
     try