X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FFeatureSettings.java;h=3f1d9c7f9975dd61c1bf680ba87f1a1c83f27d94;hb=refs%2Fheads%2Fbug%2FJAL-2776toggleGroupColour;hp=151ae9b594e58b9c4146cd6db32f5aeabb20c5b5;hpb=6efcc6b872e24abc34363d37577eac99a8756614;p=jalview.git

diff --git a/src/jalview/gui/FeatureSettings.java b/src/jalview/gui/FeatureSettings.java
index 151ae9b..3f1d9c7 100644
--- a/src/jalview/gui/FeatureSettings.java
+++ b/src/jalview/gui/FeatureSettings.java
@@ -491,7 +491,7 @@ public class FeatureSettings extends JPanel
   @Override
   synchronized public void discoverAllFeatureData()
   {
-    Set<String> allGroups = new HashSet<String>();
+    Set<String> allGroups = new HashSet<>();
     AlignmentI alignment = af.getViewport().getAlignment();
 
     for (int i = 0; i < alignment.getHeight(); i++)
@@ -541,13 +541,8 @@ public class FeatureSettings extends JPanel
       public void itemStateChanged(ItemEvent evt)
       {
         fr.setGroupVisibility(check.getText(), check.isSelected());
-        af.alignPanel.getSeqPanel().seqCanvas.repaint();
-        if (af.alignPanel.overviewPanel != null)
-        {
-          af.alignPanel.overviewPanel.updateOverviewImage();
-        }
-
         resetTable(new String[] { grp });
+        af.alignPanel.paintAlignment(true, true);
       }
     });
     groupPanel.add(check);
@@ -563,12 +558,12 @@ public class FeatureSettings extends JPanel
       return;
     }
     resettingTable = true;
-    typeWidth = new Hashtable<String, float[]>();
+    typeWidth = new Hashtable<>();
     // TODO: change avWidth calculation to 'per-sequence' average and use long
     // rather than float
 
-    Set<String> displayableTypes = new HashSet<String>();
-    Set<String> foundGroups = new HashSet<String>();
+    Set<String> displayableTypes = new HashSet<>();
+    Set<String> foundGroups = new HashSet<>();
 
     /*
      * determine which feature types may be visible depending on 
@@ -584,7 +579,7 @@ public class FeatureSettings extends JPanel
        * 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 || checkGroupState(group))
@@ -1064,7 +1059,7 @@ public class FeatureSettings extends JPanel
   {
     if (fr.setFeaturePriority(data, visibleNew))
     {
-      af.alignPanel.paintAlignment(true);
+      af.alignPanel.paintAlignment(true, true);
     }
   }
 
@@ -1243,11 +1238,10 @@ public class FeatureSettings extends JPanel
       @Override
       public void stateChanged(ChangeEvent evt)
       {
-        fr.setTransparency((100 - transparency.getValue()) / 100f);
         if (!inConstruction)
         {
           fr.setTransparency((100 - transparency.getValue()) / 100f);
-        af.alignPanel.paintAlignment(true);
+          af.alignPanel.paintAlignment(true,true);
         }
       }
     });