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

[jalview.git] / src / jalview / appletgui / FeatureSettings.java

diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java
index 20d4d74..9a67499 100755 (executable)
--- a/src/jalview/appletgui/FeatureSettings.java
+++ b/src/jalview/appletgui/FeatureSettings.java
@@ -377,8 +377,8 @@ public class FeatureSettings extends Panel
   // Group selection states
   void resetTable(boolean groupsChanged)
   {
-    List<String> displayableTypes = new ArrayList<String>();
-    Set<String> foundGroups = new HashSet<String>();
+    List<String> displayableTypes = new ArrayList<>();
+    Set<String> foundGroups = new HashSet<>();
 
     AlignmentI alignment = av.getAlignment();
 
@@ -391,7 +391,7 @@ public class FeatureSettings extends Panel
        * and keep track of which groups are visible
        */
       Set<String> groups = seq.getFeatures().getFeatureGroups(true);
-      Set<String> visibleGroups = new HashSet<String>();
+      Set<String> visibleGroups = new HashSet<>();
       for (String group : groups)
       {
         // if (group == null || fr.checkGroupVisibility(group, true))
@@ -600,7 +600,7 @@ public class FeatureSettings extends Panel
 
     fr.setFeaturePriority(data);
 
-    ap.paintAlignment(updateOverview);
+    ap.paintAlignment(updateOverview, updateOverview);
   }
 
   MyCheckbox selectedCheck;
@@ -680,7 +680,7 @@ public class FeatureSettings extends Panel
   {
     featurePanel.removeAll();
     resetTable(false);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   @Override
@@ -732,7 +732,7 @@ public class FeatureSettings extends Panel
   public void adjustmentValueChanged(AdjustmentEvent evt)
   {
     fr.setTransparency((100 - transparency.getValue()) / 100f);
-    ap.paintAlignment(true);
+    ap.paintAlignment(true, true);
   }
 
   class MyCheckbox extends Checkbox